CRAN Package Check Results for Maintainer ‘Vadim I. Nazarov <support at immunomind.com>’

Last updated on 2026-03-27 02:51:52 CET.

Package	ERROR	NOTE	OK
immunarch		2	12
immundata	6	3	5

Package immunarch

Current CRAN status: NOTE: 2, OK: 12

Version: 0.10.3
Check: installed package size
Result: NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 2.4Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package immundata

Current CRAN status: ERROR: 6, NOTE: 3, OK: 5

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [654s/340s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699ba1a12e/annotations.parquet] > test-annotate-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699ba1a12e/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699ba1a12e] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699ba1a12e'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699ba1a12e'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 9.08 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c682fd0ff/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c682fd0ff/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c682fd0ff] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c682fd0ff'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c682fd0ff'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 10.98 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c47ef1074/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c47ef1074/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c47ef1074] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c47ef1074'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c47ef1074'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.73 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6995ce65620/annotations.parquet] > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6995ce65620/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6995ce65620] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6995ce65620'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6995ce65620'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 7.9 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997171f549/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c3151d044/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997171f549/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997171f549] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997171f549'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997171f549'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 7.33 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c3151d044/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c3151d044] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c3151d044'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c3151d044'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.82 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699214225a1/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699214225a1/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699214225a1] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699214225a1'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699214225a1'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 7.55 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7461a50e/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7461a50e/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7461a50e] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7461a50e'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7461a50e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.71 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6993c69561f/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6993c69561f/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6993c69561f] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6993c69561f'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6993c69561f'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 7.6 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7fc3f54a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7fc3f54a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7fc3f54a] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7fc3f54a'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7fc3f54a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.61 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997116896c/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997116896c/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997116896c] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997116896c'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997116896c'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 7.54 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6994656f83f/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c3dc8fff3/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c3dc8fff3/metadata.json] > test-annotate-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6994656f83f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c3dc8fff3] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c3dc8fff3'] > test-annotate-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6994656f83f] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6994656f83f'] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6994656f83f'] > test-annotate-receptors.R: > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c3dc8fff3'] > test-agg-strata.R: > test-annotate-receptors.R: -- Summary > test-agg-strata.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 7.49 secs > test-agg-strata.R: i Time elapsed: 9.46 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6999adeacb/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6999adeacb/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6999adeacb] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6999adeacb'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6999adeacb'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 9.82 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7881ae2/annotations.parquet] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7881ae2/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7881ae2] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7881ae2'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c7881ae2'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.75 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6994d298016/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6994d298016/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6994d298016] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6994d298016'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6994d298016'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 10.03 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c42b07e7/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c42b07e7/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c42b07e7] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c42b07e7'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c42b07e7'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 10.03 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69972570754/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69972570754/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69972570754] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69972570754'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69972570754'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 10.21 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c852df67/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c852df67/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c852df67] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c852df67'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c852df67'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 10.96 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6995320029/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6995320029/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6995320029] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6995320029'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6995320029'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 10.61 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c6e802af7/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c6e802af7/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c6e802af7] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c6e802af7'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c6e802af7'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.63 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6992b5ab4c5/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6992b5ab4c5/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6992b5ab4c5] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6992b5ab4c5'] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6992b5ab4c5'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 7.55 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c38c3c57b/annotations.parquet] > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6991994ccdb/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c38c3c57b/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c38c3c57b] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c38c3c57b'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c38c3c57b'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.77 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6991994ccdb/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6991994ccdb] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6991994ccdb'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6991994ccdb'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 7.53 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69911b196/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69911b196/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69911b196] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69911b196'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69911b196'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 7.61 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c147468d2/annotations.parquet] > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c147468d2/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c147468d2] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c147468d2'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c147468d2'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 10.03 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69963424822/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69963424822/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69963424822] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69963424822'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69963424822'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 7.56 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c5e6c63e4/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c5e6c63e4/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c5e6c63e4] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c5e6c63e4'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c5e6c63e4'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 9.78 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69932df71d1/annotations.parquet] > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69932df71d1/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69932df71d1] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69932df71d1'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69932df71d1'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 7.55 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c2c8b7e84/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c2c8b7e84/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c2c8b7e84] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c2c8b7e84'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c2c8b7e84'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 7.5 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69977e6bcde/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69977e6bcde/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69977e6bcde] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69977e6bcde'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69977e6bcde'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 9.6 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c1df8a09e/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c1df8a09e/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c1df8a09e] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c1df8a09e'] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c1df8a09e'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 7.55 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/legacy_v1_23e69c694aa80a/annotations.parquet] > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699120aaf66/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/legacy_v1_23e69c694aa80a/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/legacy_v1_23e69c694aa80a] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/legacy_v1_23e69c694aa80a'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/legacy_v1_23e69c694aa80a'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.36 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/legacy_v1_23e69c694aa80a'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699120aaf66/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699120aaf66] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699120aaf66'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699120aaf66'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 7.51 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699554a44d4.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69975673a83/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69975673a83/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69975673a83] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69975673a83'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69975673a83'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.48 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6992299c85a.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996dfed420/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996dfed420/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996dfed420] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996dfed420'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996dfed420'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.42 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.33 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699957d2b5.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699efe1804/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699efe1804/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699efe1804] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699efe1804'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699efe1804'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.94 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699705e86df.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.33 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699690cd5ca/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699690cd5ca/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699690cd5ca] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699690cd5ca'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699690cd5ca'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.63 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6996663502d.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996c734109/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996c734109/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996c734109] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996c734109'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996c734109'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.66 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.38 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997f7664aa.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6993345a91d/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6993345a91d/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6993345a91d] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6993345a91d'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6993345a91d'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.14 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69974152be4.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69976804383/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69976804383/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69976804383] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69976804383'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69976804383'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.98 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699296cac23.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69915e39f4/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69915e39f4/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69915e39f4] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69915e39f4'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69915e39f4'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.41 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6992f056cfa.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997da8a303/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997da8a303/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997da8a303] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997da8a303'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997da8a303'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.38 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69936a298fe.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6994626f070/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6994626f070/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6994626f070] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6994626f070'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6994626f070'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.53 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699b801d81.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 8.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69934c15f0f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69934c15f0f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69934c15f0f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69934c15f0f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69934c15f0f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.53 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69946df9683.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6992f02b8c7/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6992f02b8c7/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6992f02b8c7] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6992f02b8c7'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6992f02b8c7'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.94 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69978700db5.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.42 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997b89c6fe/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997b89c6fe/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997b89c6fe] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997b89c6fe'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997b89c6fe'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.83 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e6997ebc874b.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699aeae441/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699aeae441/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699aeae441] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699aeae441'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699aeae441'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.23 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69957a2e83f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997c48d18d/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997c48d18d/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997c48d18d] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997c48d18d'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997c48d18d'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.52 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69957a2e83f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.41 secs > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6991406ebc3/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6991406ebc3/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6991406ebc3] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6991406ebc3'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6991406ebc3'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.83 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.4 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699379c0004/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699379c0004/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699379c0004] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699379c0004'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699379c0004'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.47 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.38 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69950ad6bff/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69950ad6bff/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69950ad6bff] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69950ad6bff'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69950ad6bff'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 6.51 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c61289cef/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c61289cef/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c61289cef] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c61289cef'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c61289cef'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 7.42 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996f2db6de/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996f2db6de/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996f2db6de] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996f2db6de'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6996f2db6de'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 6.53 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-immundata.R: i Time elapsed: 3.32 secs > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB/annotations.parquet] > test-io-repertoires-files.R: > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB/metadata.json] > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.41 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699777803fc/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699777803fc/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699777803fc] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699777803fc'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e699777803fc'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 8.37 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c6fc4736e/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c6fc4736e/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c6fc4736e] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c6fc4736e'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c6fc4736e'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 7.52 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6991889888d/annotations.parquet > test-io-repertoires-files.R: ] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6991889888d/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6991889888d] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6991889888d'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6991889888d'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 8.32 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c1cfbabef/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c1cfbabef/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c1cfbabef] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c1cfbabef'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c1cfbabef'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 7.56 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 3.6 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69944f747a0/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69944f747a0/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69944f747a0] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69944f747a0'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69944f747a0'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 8.27 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 4.03 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 3.57 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6995e4f10ab/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6995e4f10ab/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6995e4f10ab] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6995e4f10ab'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6995e4f10ab'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 44.94 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c163c044f/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c163c044f/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c163c044f] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c163c044f'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c163c044f'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 41.26 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors Saving _problems/test-io-repertoires-processing-90.R Saving _problems/test-io-repertoires-processing-110.R > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c6dbc58b7/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c6dbc58b7/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c6dbc58b7] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c6dbc58b7'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c6dbc58b7'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 7.66 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c75bf9226.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c4bff4f49/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c4bff4f49/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c4bff4f49] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c4bff4f49'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c4bff4f49'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.41 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/RtmpYAaQDL/file23e69c5c2adb2d.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c690eb735/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c690eb735/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c690eb735] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c690eb735'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test_immundata_23e69c690eb735'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.44 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYAaQDL/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYAaQDL/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 4.32 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997d318109/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997d318109/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997d318109] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997d318109'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6997d318109'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 49.07 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e699506d0a01.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6993e5eccc0/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6993e5eccc0/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6993e5eccc0] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6993e5eccc0'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e6993e5eccc0'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.91 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/Rtmp8pzgyr/file23e69929f527ae.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69976cb4d73/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69976cb4d73/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69976cb4d73] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69976cb4d73'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp8pzgyr/test_immundata_23e69976cb4d73'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.5 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-processing.R:87:3'): read_repertoires() removes non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:87:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires-processing.R:106:3'): read_repertoires() correctly reads non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:106:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [325s/208s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file15645816b3d4ad/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e3654c2e5/annotations.parquet] > test-annotate-barcodes.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file15645816b3d4ad/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file15645816b3d4ad] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645816b3d4ad'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645816b3d4ad'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 5.08 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e3654c2e5/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e3654c2e5] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e3654c2e5'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e3654c2e5'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.46 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-agg-strata.R: v Joining plan is ready > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e2f17cffe/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e2f17cffe/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e2f17cffe] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e2f17cffe'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e2f17cffe'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.54 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file15645867e189b1/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file15645867e189b1/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file15645867e189b1] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645867e189b1'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645867e189b1'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.91 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e35e71bac/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e35e71bac/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e35e71bac] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e35e71bac'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e35e71bac'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.51 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file15645814c2bdd7/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file15645814c2bdd7/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file15645814c2bdd7] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645814c2bdd7'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645814c2bdd7'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.02 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file15645812a54ba9/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file15645812a54ba9/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file15645812a54ba9] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645812a54ba9'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645812a54ba9'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.68 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e43f137e0/annotations.parquet] > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e43f137e0/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e43f137e0] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e43f137e0'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e43f137e0'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.21 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file15645822c08f06/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file15645822c08f06/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file15645822c08f06] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645822c08f06'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645822c08f06'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.33 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e2c067046/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e2c067046/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e2c067046] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e2c067046'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e2c067046'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.76 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file1564582a763b37/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file1564582a763b37/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file1564582a763b37] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564582a763b37'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564582a763b37'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.62 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e12105736/annotations.parquet] > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file15645855eb2109/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e12105736/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e12105736] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e12105736'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e12105736'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.44 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file15645855eb2109/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file15645855eb2109] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645855eb2109'] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645855eb2109'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 4.55 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file1564587c2aab14/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file1564587c2aab14/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file1564587c2aab14] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564587c2aab14'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564587c2aab14'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.7 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e12d9ad56/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e12d9ad56/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e12d9ad56] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e12d9ad56'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e12d9ad56'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.46 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file1564586f205fdc/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file1564586f205fdc/metadata.json] > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file1564586f205fdc] > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564586f205fdc'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564586f205fdc'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.21 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Respons > test-compute-collect-immundata.R: e, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e74553bd/annotations.parquet] > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file15645811430b16/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file15645811430b16/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file15645811430b16] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645811430b16'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645811430b16'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.43 secs > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e74553bd/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e74553bd] > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e74553bd'] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e74553bd'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.68 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file1564586e3b3729/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e50fd2649/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file1564586e3b3729/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file1564586e3b3729] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564586e3b3729'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564586e3b3729'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 5.5 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e50fd2649/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e50fd2649] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e50fd2649'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e50fd2649'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.96 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file156458275bc8bf/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-barcodes.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file156458275bc8bf/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file156458275bc8bf] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file156458275bc8bf'] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file156458275bc8bf'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 3.81 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e73d04a82/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e73d04a82/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e73d04a82] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e73d04a82'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e73d04a82'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.27 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file1564587b6f9055/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file1564587b6f9055/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file1564587b6f9055] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564587b6f9055'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564587b6f9055'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 3.99 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file156458901d52a/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e6a0b81c3/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file156458901d52a/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file156458901d52a] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file156458901d52a'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file156458901d52a'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 3.92 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e6a0b81c3/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e6a0b81c3] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e6a0b81c3'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e6a0b81c3'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.17 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata-lev.R: v Renaming is finished > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata-lev.R: > test-agg-strata.R: v Metadata parsed successfully > test-filter-immundata-lev.R: -- Preprocessing the data > test-agg-strata.R: > test-filter-immundata-lev.R: 1. exclude_columns > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file156458cb56e1d/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file156458cb56e1d/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file156458cb56e1d] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file156458cb56e1d'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file156458cb56e1d'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.07 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e4802822c/annotations.parquet] > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e4802822c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e4802822c] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e4802822c'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e4802822c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.2 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file15645879d5e2b7/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file15645879d5e2b7/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file15645879d5e2b7] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645879d5e2b7'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645879d5e2b7'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.22 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e4bb1907/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e4bb1907/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e4bb1907] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e4bb1907'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e4bb1907'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.34 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Respons > test-filter-immundata.R: e, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FAL > test-filter-immundata.R: SE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file1564586dcb76f0/annotations.parquet] > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file1564586dcb76f0/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file1564586dcb76f0] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564586dcb76f0'] > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564586dcb76f0'] > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 4.26 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file15645826f8b921/annotations.parquet] > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e3a3abb45/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file15645826f8b921/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file15645826f8b921] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645826f8b921'] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645826f8b921'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 4.06 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e3a3abb45/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e3a3abb45] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e3a3abb45'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e3a3abb45'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 5.36 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-io-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: v All files have the same extension > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/legacy_v1_1564581e560f79/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/legacy_v1_1564581e560f79/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/legacy_v1_1564581e560f79] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/legacy_v1_1564581e560f79'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/legacy_v1_1564581e560f79'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.86 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/legacy_v1_1564581e560f79'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/file15643e544ccc71/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.63 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpUvFyjR/file15643e544ccc71/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/file15643e544ccc71] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e544ccc71'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/file15643e544ccc71'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 3.91 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /tmp/RtmpUvFyjR/file15643e548b368b.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e742fb813/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e742fb813/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e742fb813] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e742fb813'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e742fb813'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.39 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e66650a96/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e66650a96/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e66650a96] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e66650a96'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e66650a96'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.36 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.03 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpUvFyjR/file15643e38b17b31.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e7b7afc11/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e7b7afc11/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e7b7afc11] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e7b7afc11'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e7b7afc11'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.13 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.87 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Respons > test-io-immundata.R: e, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpUvFyjR/file15643e68a1f7a8.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e711f41ff/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e711f41ff/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e711f41ff] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e711f41ff'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e711f41ff'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.04 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpUvFyjR/file15643e527101de.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e43300087/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e43300087/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e43300087] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e43300087'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e43300087'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.27 secs > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpUvFyjR/file15643e160238a2.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.82 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e4a65ee9c/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e4a65ee9c/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e4a65ee9c] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e4a65ee9c'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e4a65ee9c'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.16 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpUvFyjR/file15643e1d5ff4c6.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.66 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e49b23579/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e49b23579/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e49b23579] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e49b23579'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e49b23579'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.45 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-64.R Saving _problems/test-io-repertoires-agg-70.R Saving _problems/test-io-repertoires-agg-88.R Saving _problems/test-io-repertoires-agg-96.R > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.75 secs > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpUvFyjR/file15643e5f6f81b3.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e5b7f0b3d/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e5b7f0b3d/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e5b7f0b3d] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e5b7f0b3d'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB/annotations.parquet] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e5b7f0b3d'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.31 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectB'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpUvFyjR/file15643e7b6bce85.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643eb9490ed/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643eb9490ed/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643eb9490ed] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643eb9490ed'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643eb9490ed'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.39 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpUvFyjR/file15643e371c65a7.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e49a8d737/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e49a8d737/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e49a8d737] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e49a8d737'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e49a8d737'] > test-io-immundata.R: i Time elapsed: 1.75 secs > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.31 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-repertoires-counts.R: 1. /tmp/RtmpUvFyjR/file15643e459cdcb.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e2e8016f2/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e2e8016f2/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e2e8016f2] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e2e8016f2'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e2e8016f2'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.03 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpUvFyjR/file15643e3b26c966.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e53b8e671/annotations.parquet] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.81 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e53b8e671/metadata.json] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e53b8e671] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e53b8e671'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e53b8e671'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.05 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpUvFyjR/file15643e77f0cb6.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e5373e886/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e5373e886/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e5373e886] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e5373e886'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e5373e886'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.54 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpUvFyjR/file15643e779ef83d.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e1f6f4926/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e1f6f4926/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e1f6f4926] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e1f6f4926'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e1f6f4926'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.27 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpUvFyjR/file15643e201d4ead.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e7efd058e/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e7efd058e/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e7efd058e] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e7efd058e'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e7efd058e'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.46 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpUvFyjR/file15643e201d4ead.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file1564583f604cc/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file1564583f604cc/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file1564583f604cc] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564583f604cc'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564583f604cc'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.2 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e70403c31/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e70403c31/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e70403c31] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e70403c31'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e70403c31'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.69 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.71 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e9b010ed/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e9b010ed/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e9b010ed] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e9b010ed'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e9b010ed'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.36 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.13 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e5e0720fb/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e5e0720fb/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e5e0720fb] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e5e0720fb'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e5e0720fb'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.79 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file1564587d02bf17/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file1564587d02bf17/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file1564587d02bf17] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564587d02bf17'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file1564587d02bf17'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.33 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e3d055b91/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e3d055b91/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e3d055b91] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e3d055b91'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e3d055b91'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.45 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Respons > test-io-repertoires-files.R: e, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FAL > test-io-repertoires-files.R: SE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/file15645821730617/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/file15645821730617/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/file15645821730617] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645821730617'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/file15645821730617'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.88 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/test-exclude/annotations.parquet] > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e48a9faf2/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.02 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e48a9faf2/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e48a9faf2] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e48a9faf2'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e48a9faf2'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.34 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Respons > test-io-repertoires-files.R: e, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FAL > test-io-repertoires-files.R: SE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.32 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/test-exclude-rename/annotations.parquet] > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e5617fa16/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.06 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e5617fa16/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e5617fa16] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e5617fa16'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e5617fa16'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.44 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immund > test-io-repertoires-processing.R: ata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e4818ac20/annotations.parquet] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e4818ac20/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e4818ac20] > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e4818ac20'] > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e4818ac20'] > test-io-repertoires-files.R: > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.04 secs > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e4028c3c9/annotations.parquet] > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/test_immundata_1564581eb22bfd/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/test_immundata_1564581eb22bfd/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/test_immundata_1564581eb22bfd] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test_immundata_1564581eb22bfd'] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e4028c3c9/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e4028c3c9] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e4028c3c9'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e4028c3c9'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 28.11 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test_immundata_1564581eb22bfd'] > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 29.22 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors Saving _problems/test-io-repertoires-processing-90.R Saving _problems/test-io-repertoires-processing-110.R > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/test_immundata_1564582f43b377/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/test_immundata_1564582f43b377/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/test_immundata_1564582f43b377] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test_immundata_1564582f43b377'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test_immundata_1564582f43b377'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 4.39 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/Rtmpqdu7gP/file156458410b1dab.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/test_immundata_1564585a68307e/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/test_immundata_1564585a68307e/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/test_immundata_1564585a68307e] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test_immundata_1564585a68307e'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test_immundata_1564585a68307e'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.38 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/Rtmpqdu7gP/file1564585e1ad840.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/test_immundata_1564584a308755/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/test_immundata_1564584a308755/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/test_immundata_1564584a308755] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test_immundata_1564584a308755'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test_immundata_1564584a308755'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.37 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/tmp/Rtmpqdu7gP/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/tmp/Rtmpqdu7gP/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/tmp/Rtmpqdu7gP/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/Rtmpqdu7gP/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 2.33 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e6d652d1b/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e6d652d1b/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e6d652d1b] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e6d652d1b'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e6d652d1b'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 28.03 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/RtmpUvFyjR/file15643e66625e82.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643eb280469/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643eb280469/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643eb280469] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643eb280469'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643eb280469'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.15 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/RtmpUvFyjR/file15643e1ebc2d76.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpUvFyjR/test_immundata_15643e3cbdeace/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpUvFyjR/test_immundata_15643e3cbdeace/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpUvFyjR/test_immundata_15643e3cbdeace] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e3cbdeace'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpUvFyjR/test_immundata_15643e3cbdeace'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.26 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 10 | WARN 0 | SKIP 0 | PASS 314 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ── <duckdb_error/rlang_error/error/condition> Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x54) [0x7f7120ca17b4]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f7120ca17e1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f7120ca4851]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1a9) [0x7f7120fb91d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(+0x90b74c) [0x7f712010b74c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x118) [0x7f71218a48f8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x86) [0x7f71218a6626]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x3f) [0x7f71218a6bef]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x86) [0x7f7120fa6726]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x3c) [0x7f71218b348c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x8a) [0x7f7120fa711a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x2a) [0x7f7120fa730a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x691) [0x7f71216990b1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x47a) [0x7f71216997fa]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xae) [0x7f712169ca7e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa3) [0x7f712169cef3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x8c) [0x7f712169d11c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x9b) [0x7f712169ddeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x18b) [0x7f71216a0d3b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x7d) [0x7f71216a102d]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x51) [0x7f71216a1a21]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x137) [0x7f71203cfd97]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2b1) [0x7f71203d04b1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x45) [0x7f71203d0b95]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa6add) [0x7f713d2a6add]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7f713d35b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7f713d3a6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a7247) [0x7f713d3a7247]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15f6a0) [0x7f713d35f6a0]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa9a47) [0x7f713d2a9a47]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7f713d35b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7f713d3a6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7f713d3a73d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7f713d3a763c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7f713d34c40f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7f713d35b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7f713d3a6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7f713d3a73d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7f713d3a763c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7f713d34c40f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15d16d) [0x7f713d35d16d]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7f713d35babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15e67f) [0x7f713d35e67f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15eb44) [0x7f713d35eb44]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7f713d35babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7f713d2cff1e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7f713d2cff1e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7f713d3587f4]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x158b05) [0x7f713d358b05]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x150a74) [0x7f713d350a74]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7f713d35babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7f713d3587f4]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER) Stack Trace: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x54) [0x7f7120ca17b4] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f7120ca17e1] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f7120ca4851] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1a9) [0x7f7120fb91d9] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(+0x90b74c) [0x7f712010b74c] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x118) [0x7f71218a48f8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x86) [0x7f71218a6626] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x3f) [0x7f71218a6bef] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x86) [0x7f7120fa6726] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x3c) [0x7f71218b348c] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x8a) [0x7f7120fa711a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x2a) [0x7f7120fa730a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x691) [0x7f71216990b1] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x47a) [0x7f71216997fa] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xae) [0x7f712169ca7e] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa3) [0x7f712169cef3] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x8c) [0x7f712169d11c] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x9b) [0x7f712169ddeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x18b) [0x7f71216a0d3b] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x7d) [0x7f71216a102d] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x51) [0x7f71216a1a21] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x137) [0x7f71203cfd97] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2b1) [0x7f71203d04b1] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x45) [0x7f71203d0b95] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa6add) [0x7f713d2a6add] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7f713d35b739] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7f713d3a6cc3] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a7247) [0x7f713d3a7247] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15f6a0) [0x7f713d35f6a0] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa9a47) [0x7f713d2a9a47] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7f713d35b739] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7f713d3a6cc3] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7f713d3a73d9] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7f713d3a763c] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7f713d34c40f] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7f713d35b739] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7f713d3a6cc3] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7f713d3a73d9] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7f713d3a763c] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7f713d34c40f] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15d16d) [0x7f713d35d16d] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7f713d35babc] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15e67f) [0x7f713d35e67f] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15eb44) [0x7f713d35eb44] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7f713d35babc] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7f713d2cff1e] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7f713d2cff1e] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7f713d3587f4] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x158b05) [0x7f713d358b05] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x150a74) [0x7f713d350a74] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7f713d35babc] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7] /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7f713d3587f4] This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic. For more information, see https://duckdb.org/docs/stable/dev/internal_errors i Context: GetQueryResult Backtrace: ▆ 1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3 2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations) 3. │ ├─dplyr::collect(out) 4. │ └─duckplyr:::collect.duckplyr_df(out) 5. │ └─base::nrow(x) 6. │ ├─base::dim(x) 7. │ └─base::dim.data.frame(x) 8. │ └─base::.row_names_info(x, 2L) 9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x54) [0x7f7120ca17b4]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f7120ca17e1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x11) [0x7f7120ca4851]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1a9) [0x7f7120fb91d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(+0x90b74c) [0x7f712010b74c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x118) [0x7f71218a48f8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x86) [0x7f71218a6626]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x3f) [0x7f71218a6bef]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x86) [0x7f7120fa6726]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x3c) [0x7f71218b348c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x4d) [0x7f71218b77bd]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b) [0x7f7120fa671b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x8a) [0x7f7120fa711a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x2a) [0x7f7120fa730a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x691) [0x7f71216990b1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x47a) [0x7f71216997fa]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xae) [0x7f712169ca7e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa3) [0x7f712169cef3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x8c) [0x7f712169d11c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x9b) [0x7f712169ddeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x18b) [0x7f71216a0d3b]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x7d) [0x7f71216a102d]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x51) [0x7f71216a1a21]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x137) [0x7f71203cfd97]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2b1) [0x7f71203d04b1]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x45) [0x7f71203d0b95]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa6add) [0x7f713d2a6add]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7f713d35b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7f713d3a6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a7247) [0x7f713d3a7247]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15f6a0) [0x7f713d35f6a0]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xa9a47) [0x7f713d2a9a47]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7f713d35b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7f713d3a6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7f713d3a73d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7f713d3a763c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7f713d34c40f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15b739) [0x7f713d35b739]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a6cc3) [0x7f713d3a6cc3]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a73d9) [0x7f713d3a73d9]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1a763c) [0x7f713d3a763c]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c40f) [0x7f713d34c40f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15d16d) [0x7f713d35d16d]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7f713d35babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15e67f) [0x7f713d35e67f]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15eb44) [0x7f713d35eb44]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7f713d35babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7f713d2cff1e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0xcff1e) [0x7f713d2cff1e]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x14c624) [0x7f713d34c624]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7f713d3587f4]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x158b05) [0x7f713d358b05]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x150a74) [0x7f713d350a74]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x157aeb) [0x7f713d357aeb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x14b) [0x7f713d357ecb]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x159edf) [0x7f713d359edf]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15acc8) [0x7f713d35acc8]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x28a) [0x7f713d35800a]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x15babc) [0x7f713d35babc]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(Rf_eval+0x537) [0x7f713d3582b7]\n/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libR.so(+0x1587f4) [0x7f713d3587f4]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors") 10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/RtmpUvFyjR/file15643e6ed475f4.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5 ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Error ('test-io-repertoires-processing.R:87:3'): read_repertoires() removes non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:87:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires-processing.R:106:3'): read_repertoires() correctly reads non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:106:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) [ FAIL 10 | WARN 0 | SKIP 0 | PASS 314 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [18m/24m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 8. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd39e63d9/annotations.parquet] > test-annotate-barcodes.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd39e63d9/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd39e63d9] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd39e63d9'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd39e63d9'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 26.5 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9726790c7/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9726790c7/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9726790c7] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9726790c7'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9726790c7'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 43.97 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc93b0405e7/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc93b0405e7/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc93b0405e7] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc93b0405e7'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc93b0405e7'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 41.38 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-annotate-external.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31722959e/annotations.parquet] > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31722959e/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31722959e] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31722959e'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31722959e'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 30.87 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3a0aca5a/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3a0aca5a/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3a0aca5a] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3a0aca5a'] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc94f72fb75/annotations.parquet] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3a0aca5a'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 27.29 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc94f72fb75/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc94f72fb75] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc94f72fb75'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc94f72fb75'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 36.15 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31c766567/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31c766567/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31c766567] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31c766567'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31c766567'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 33.25 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92294b533/annotations.parquet] > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34e24d8f5/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92294b533/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92294b533] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92294b533'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92294b533'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 47.59 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34e24d8f5/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34e24d8f5] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34e24d8f5'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34e24d8f5'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 26.37 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd320467bc9/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd320467bc9/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd320467bc9] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd320467bc9'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd320467bc9'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 34.62 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc91399c8a7/annotations.parquet] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc91399c8a7/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc91399c8a7] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc91399c8a7'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc91399c8a7'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 37.26 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3450610df/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3450610df/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3450610df] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3450610df'] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3450610df'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 34.55 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc94b8958ed/annotations.parquet] > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc94b8958ed/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc94b8958ed] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc94b8958ed'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc94b8958ed'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 45 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd336c96948/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd336c96948/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd336c96948] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd336c96948'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd336c96948'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 41.89 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc97c9afb9a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc97c9afb9a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc97c9afb9a] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc97c9afb9a'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc97c9afb9a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 36.61 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3431684aa/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3431684aa/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3431684aa] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3431684aa'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3431684aa'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 35.94 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9cd6255c/annotations.parquet] > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9cd6255c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9cd6255c] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9cd6255c'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9cd6255c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 37.22 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3185f710a/annotations.parquet] > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3185f710a/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3185f710a] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3185f710a'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3185f710a'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 50.53 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Respons > test-compute-collect-immundata.R: e, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92346027/annotations.parquet] > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd361fc5b0e/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92346027/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92346027] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92346027'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92346027'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 48.76 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd361fc5b0e/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd361fc5b0e] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd361fc5b0e'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd361fc5b0e'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 44.97 secs > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34d03927d/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-barcodes.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34d03927d/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34d03927d] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34d03927d'] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34d03927d'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 32.34 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9634e48ea/annotations.parquet] > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9634e48ea/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9634e48ea] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9634e48ea'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9634e48ea'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 46.48 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31cd9bcf3/annotations.parquet] > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31cd9bcf3/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31cd9bcf3] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31cd9bcf3'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31cd9bcf3'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 40.17 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc948d90b63/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc948d90b63/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc948d90b63] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc948d90b63'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc948d90b63'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 48.09 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34b2a8463/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34b2a8463/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34b2a8463] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34b2a8463'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd34b2a8463'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 30.75 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd377b908d/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc965e24781/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd377b908d/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd377b908d] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd377b908d'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd377b908d'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 30.59 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc965e24781/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc965e24781] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc965e24781'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc965e24781'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 42.73 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd328ccc003/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd328ccc003/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd328ccc003] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd328ccc003'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd328ccc003'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 30.15 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc965187ea7/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc965187ea7/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc965187ea7] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc965187ea7'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc965187ea7'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 39.85 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd36f591588/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd36f591588/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd36f591588] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd36f591588'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd36f591588'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 31.47 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc96f198ca3/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc96f198ca3/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc96f198ca3] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc96f198ca3'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc96f198ca3'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 42.02 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd373ed06f2/annotations.parquet] > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd373ed06f2/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd373ed06f2] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd373ed06f2'] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd373ed06f2'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 35.93 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/legacy_v1_28bfd34a9e0d40/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/legacy_v1_28bfd34a9e0d40/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/legacy_v1_28bfd34a9e0d40] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/legacy_v1_28bfd34a9e0d40'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/legacy_v1_28bfd34a9e0d40'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 12.29 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/legacy_v1_28bfd34a9e0d40'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc967e0ba67/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc967e0ba67/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc967e0ba67] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc967e0ba67'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc967e0ba67'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 31 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc910341883.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9136ff51c/annotations.parq > test-io-repertoires-agg-stepwise.R: uet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9136ff51c/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9136ff51c] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9136ff51c'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9136ff51c'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 1.53 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 12.84 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc96a7d3e6c/annotations.parq > test-io-repertoires-agg.R: uet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc96a7d3e6c/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc96a7d3e6c] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc96a7d3e6c'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc96a7d3e6c'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.51 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92f93478d.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc91e2807ec/annotations.parq > test-io-repertoires-agg.R: uet] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 13.33 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc91e2807ec/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc91e2807ec] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc91e2807ec'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc91e2807ec'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 6.77 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9322a190e.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc97c436293/annotations.parq > test-io-repertoires-agg.R: uet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc97c436293/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc97c436293] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc97c436293'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc97c436293'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 8.87 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc97713368.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 16.36 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Respons > test-io-immundata.R: e, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FAL > test-io-immundata.R: SE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc973e411eb/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc973e411eb/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc973e411eb] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc973e411eb'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc973e411eb'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 7.09 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92fd810c2.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9dce43a6/annotations.parqu > test-io-repertoires-agg.R: et] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9dce43a6/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9dce43a6] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9dce43a6'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9dce43a6'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 8.69 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc95f0e9ae5.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9560eb870/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9560eb870/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9560eb870] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9560eb870'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9560eb870'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 9.75 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-64.R Saving _problems/test-io-repertoires-agg-70.R Saving _problems/test-io-repertoires-agg-88.R Saving _problems/test-io-repertoires-agg-96.R > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9977452a.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9506ba731/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9506ba731/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9506ba731] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9506ba731'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9506ba731'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.39 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc95005ef20.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc938cc3df1/annotations.parq > test-io-repertoires-counts.R: uet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc938cc3df1/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc938cc3df1] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc938cc3df1'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc938cc3df1'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.6 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-repertoires-counts.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc957736274.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 34.53 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc949acd0f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc949acd0f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc949acd0f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc949acd0f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc949acd0f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 9.55 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc97dfd1e7c.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 11.76 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95ae0f909/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95ae0f909/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95ae0f909] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95ae0f909'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95ae0f909'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 8.39 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc968fa4e96.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc94e1d6922/annotations.parq > test-io-repertoires-counts.R: uet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc94e1d6922/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc94e1d6922] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc94e1d6922'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc94e1d6922'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 6.53 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc93a1df9e2.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 13.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9cb59f1c/annotations.parqu > test-io-repertoires-counts.R: et] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9cb59f1c/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9cb59f1c] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9cb59f1c'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9cb59f1c'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 7.07 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9250000d6.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc921e0faaa/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc921e0faaa/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc921e0faaa] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc921e0faaa'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc921e0faaa'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.24 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92d911f48.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 13.01 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc936919352/annotations.parquet] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc936919352/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc936919352] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc936919352'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc936919352'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 9.19 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92d911f48.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95fa116b3/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95fa116b3/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95fa116b3] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95fa116b3'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95fa116b3'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 6.26 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 12.44 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc926a2a686/annotations.parquet] > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc926a2a686/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc926a2a686] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc926a2a686'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc926a2a686'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 13.42 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31575f5f5/annotations.parquet] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc922ddc548/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31575f5f5/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31575f5f5] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31575f5f5'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd31575f5f5'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 33.61 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc922ddc548/metadata.json] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc922ddc548] > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc922ddc548'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc922ddc548'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 26.9 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 14.45 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9711d6ffa/annotations.parq > test-io-repertoires-files.R: uet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9711d6ffa/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9711d6ffa] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9711d6ffa'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9711d6ffa'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 25.63 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 15.95 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc924b8e80f/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc924b8e80f/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc924b8e80f] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc924b8e80f'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc924b8e80f'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 30.84 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Respons > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3500e404a/annotations.parquet] > test-io-repertoires-files.R: e, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FAL > test-io-repertoires-files.R: SE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3500e404a/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3500e404a] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3500e404a'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd3500e404a'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 32.25 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-files.R: v Joining plan is ready > test-io-immundata.R: v Postprocessing plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc92b179f3c/annotations.parquet] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd340ab52e5/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd340ab52e5/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd340ab52e5] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd340ab52e5'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd340ab52e5'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 26.84 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc92b179f3c/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc92b179f3c] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc92b179f3c'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc92b179f3c'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 33.93 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 16.66 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-rename/annotations.parquet] > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc91afbc617/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 15.23 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc91afbc617/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc91afbc617] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc91afbc617'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc91afbc617'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 33.47 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 14.41 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 16.8 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_ > test-io-repertoires-processing.R: 1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0 > test-io-repertoires-processing.R: _1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sam > test-io-repertoires-processing.R: ple_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 15.62 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9683def34/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9683def34/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9683def34] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9683def34'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9683def34'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 3.21 mins > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd34d1bda05/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd34d1bda05/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd34d1bda05] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd34d1bda05'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd34d1bda05'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 3.31 mins > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd335b0d967/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd335b0d967/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd335b0d967] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd335b0d967'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd335b0d967'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 30.16 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd37b63cd35.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd321c5d6d/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd321c5d6d/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd321c5d6d] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd321c5d6d'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd321c5d6d'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 2.05 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/file28bfd36e22536f.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd3a27b93d/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd3a27b93d/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd3a27b93d] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd3a27b93d'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test_immundata_28bfd3a27b93d'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 1.26 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp2lhyYP/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 18.48 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95d6929dc/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95d6929dc/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95d6929dc] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95d6929dc'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95d6929dc'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 2.99 mins > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc91b864aa.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9535a9de0/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9535a9de0/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9535a9de0] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9535a9de0'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc9535a9de0'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 4.88 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc9a924410.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95b94c5d2/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95b94c5d2/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95b94c5d2] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95b94c5d2'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/test_immundata_28bfc95b94c5d2'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 5.01 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ── <duckdb_error/rlang_error/error/condition> Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)+0x34) [0x7f8830675a44]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&)+0xa6) [0x7f8830a237c6]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x298) [0x7f8830a05e78]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x1c7) [0x7f8831569a77]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&)+0x6fb) [0x7f883156973b]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x2a) [0x7f883156873a]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7c0) [0x7f8830a05950]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::__1::allocator<unsigned long> >&)+0x2e) [0x7f8831568c9e]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x75) [0x7f8830a1a4c5]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x2b) [0x7f8830a1a3db]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x655) [0x7f883129e775]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x40b) [0x7f883129f44b]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0x7b) [0x7f88312a36cb]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x113) [0x7f88312a5813]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xaac) [0x7f88312a30ec]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x96) [0x7f88312a4046]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x277) [0x7f88312a8217]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x8c) [0x7f88312a885c]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x80) [0x7f88312cd7f0]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x1bd) [0x7f882fb4057d]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x303) [0x7f882fb40073]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x44) [0x7f882fb3ec24]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x35277) [0x55946ee63277]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x55946eef7556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x55946ef5a642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12bf65) [0x55946ef59f65]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe7c52) [0x55946ef15c52]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x39663) [0x55946ee67663]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x55946eef7556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x55946ef5a642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x55946ef5a069]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x55946ef5ab9e]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x55946eefdb06]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x55946eef7556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x55946ef5a642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x55946ef5a069]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x55946ef5ab9e]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x55946eefdb06]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5978) [0x55946ef13978]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x55946ef12abb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe6de8) [0x55946ef14de8]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe71c8) [0x55946ef151c8]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x55946ef12abb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x55946ee83db0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x55946ee83db0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x55946eef6e84]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x55946ef0abe0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x55946eefb2b9]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x55946ef12abb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x55946eef6e84]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x55946ef0abe0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x55946eefb2b9]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER) Stack Trace: /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)+0x34) [0x7f8830675a44] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&)+0xa6) [0x7f8830a237c6] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x298) [0x7f8830a05e78] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x1c7) [0x7f8831569a77] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&)+0x6fb) [0x7f883156973b] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x2a) [0x7f883156873a] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7c0) [0x7f8830a05950] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::__1::allocator<unsigned long> >&)+0x2e) [0x7f8831568c9e] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x75) [0x7f8830a1a4c5] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x2b) [0x7f8830a1a3db] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x655) [0x7f883129e775] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x40b) [0x7f883129f44b] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0x7b) [0x7f88312a36cb] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x113) [0x7f88312a5813] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xaac) [0x7f88312a30ec] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x96) [0x7f88312a4046] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x277) [0x7f88312a8217] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x8c) [0x7f88312a885c] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x80) [0x7f88312cd7f0] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x1bd) [0x7f882fb4057d] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x303) [0x7f882fb40073] /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x44) [0x7f882fb3ec24] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x35277) [0x55946ee63277] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x55946eef7556] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x55946ef5a642] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12bf65) [0x55946ef59f65] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe7c52) [0x55946ef15c52] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x39663) [0x55946ee67663] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x55946eef7556] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x55946ef5a642] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x55946ef5a069] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x55946ef5ab9e] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x55946eefdb06] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x55946eef7556] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x55946ef5a642] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x55946ef5a069] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x55946ef5ab9e] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x55946eefdb06] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5978) [0x55946ef13978] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x55946ef12abb] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe6de8) [0x55946ef14de8] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe71c8) [0x55946ef151c8] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x55946ef12abb] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x55946ee83db0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x55946ee83db0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x55946eef6e84] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x55946ef0abe0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x55946eefb2b9] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x55946ef12abb] /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x55946eef6e84] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x55946ef0abe0] /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x55946eefb2b9] This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic. For more information, see https://duckdb.org/docs/stable/dev/internal_errors i Context: GetQueryResult Backtrace: ▆ 1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3 2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations) 3. │ ├─dplyr::collect(out) 4. │ └─duckplyr:::collect.duckplyr_df(out) 5. │ └─base::nrow(x) 6. │ ├─base::dim(x) 7. │ └─base::dim.data.frame(x) 8. │ └─base::.row_names_info(x, 2L) 9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)+0x34) [0x7f8830675a44]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long&, unsigned long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&&)+0xa6) [0x7f8830a237c6]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x298) [0x7f8830a05e78]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)+0x1c7) [0x7f8831569a77]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&)+0x6fb) [0x7f883156973b]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x2a) [0x7f883156873a]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7c0) [0x7f8830a05950]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::__1::allocator<unsigned long> >&)+0x2e) [0x7f8831568c9e]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x54) [0x7f88315686d4]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x7b5) [0x7f8830a05945]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x75) [0x7f8830a1a4c5]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>)+0x2b) [0x7f8830a1a3db]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x655) [0x7f883129e775]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x40b) [0x7f883129f44b]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0x7b) [0x7f88312a36cb]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0x113) [0x7f88312a5813]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xaac) [0x7f88312a30ec]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0x96) [0x7f88312a4046]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x277) [0x7f88312a8217]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x8c) [0x7f88312a885c]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x80) [0x7f88312cd7f0]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x1bd) [0x7f882fb4057d]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x303) [0x7f882fb40073]\n/data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x44) [0x7f882fb3ec24]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x35277) [0x55946ee63277]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x55946eef7556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x55946ef5a642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12bf65) [0x55946ef59f65]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe7c52) [0x55946ef15c52]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x39663) [0x55946ee67663]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x55946eef7556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x55946ef5a642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x55946ef5a069]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x55946ef5ab9e]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x55946eefdb06]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9556) [0x55946eef7556]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c642) [0x55946ef5a642]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12c069) [0x55946ef5a069]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x12cb9e) [0x55946ef5ab9e]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb06) [0x55946eefdb06]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5978) [0x55946ef13978]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x55946ef12abb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe6de8) [0x55946ef14de8]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe71c8) [0x55946ef151c8]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x55946ef12abb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x55946ee83db0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0x55db0) [0x55946ee83db0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8a4) [0x55946eefd8a4]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x55946eef6e84]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x55946ef0abe0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x55946eefb2b9]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c2c) [0x55946eef6c2c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55946eef63b5]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0449) [0x55946ef0e449]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf94c) [0x55946ef0d94c]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55946eef6806]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4abb) [0x55946ef12abb]\n/data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55946eef65e0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8e84) [0x55946eef6e84]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcbe0) [0x55946ef0abe0]\n/data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2b9) [0x55946eefb2b9]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors") 10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmp2IONjK/working_dir/Rtmp3t4GbJ/file28bfc92bd69300.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5 ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [13m/15m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 7. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926d9acbd3/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926d9acbd3/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926d9acbd3] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926d9acbd3'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926d9acbd3'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 17.69 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79051bd943e/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79051bd943e/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79051bd943e] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79051bd943e'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79051bd943e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 25.87 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792363e61d3/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792363e61d3/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792363e61d3] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792363e61d3'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792363e61d3'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 14.51 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907dfbbe0f/annotations.parquet] > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907dfbbe0f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907dfbbe0f] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907dfbbe0f'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907dfbbe0f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 30.03 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792463f8a28/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792463f8a28/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792463f8a28] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792463f8a28'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792463f8a28'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 16.77 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79237f55209/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79237f55209/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79237f55209] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79237f55209'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79237f55209'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 13.55 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902cb48d71/annotations.parquet] > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902cb48d71/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902cb48d71] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902cb48d71'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902cb48d71'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 25.19 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235eefab5/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235eefab5/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235eefab5] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235eefab5'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235eefab5'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 14.11 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79268757dd4/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904aac5f0e/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79268757dd4/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79268757dd4] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79268757dd4'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79268757dd4'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 16.01 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904aac5f0e/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904aac5f0e] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904aac5f0e'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904aac5f0e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 23.54 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-agg-strata.R: Rows: 2 Columns: 4 > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79277fdda51/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79277fdda51/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79277fdda51] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79277fdda51'] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79277fdda51'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 14.54 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907234acfe/annotations.parquet] > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79212852720/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907234acfe/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907234acfe] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907234acfe'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907234acfe'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 28.34 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79212852720/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79212852720] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79212852720'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79212852720'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 16.97 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924c4f5663/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924c4f5663/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924c4f5663] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924c4f5663'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924c4f5663'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 16.35 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907ca88ea1/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907ca88ea1/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907ca88ea1] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907ca88ea1'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907ca88ea1'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 25.07 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927d096fc3/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927d096fc3/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927d096fc3] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927d096fc3'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927d096fc3'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 18.33 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926640ef44/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926640ef44/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926640ef44] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926640ef44'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926640ef44'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 19.32 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902899a603/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902899a603/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902899a603] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902899a603'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7902899a603'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 21.03 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922974e07b/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922974e07b/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922974e07b] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922974e07b'] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922974e07b'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 12.71 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924d9d00f4/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924d9d00f4/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924d9d00f4] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924d9d00f4'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924d9d00f4'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 21.45 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790689f60fb/annotations.parquet] > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790689f60fb/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790689f60fb] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790689f60fb'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790689f60fb'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 22.02 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79256fdde69/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79256fdde69/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79256fdde69] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79256fdde69'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79256fdde69'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 17.86 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903a74680a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903a74680a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903a74680a] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903a74680a'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903a74680a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 25.86 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922898512e/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922898512e/metadata.json] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922898512e] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922898512e'] > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7922898512e'] > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: i Time elapsed: 14.68 secs > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79236c2bafd/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79236c2bafd/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79236c2bafd] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79236c2bafd'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79236c2bafd'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 15.84 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790532f86c5/annotations.parquet] > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926e086477/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790532f86c5/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790532f86c5] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790532f86c5'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790532f86c5'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 28.53 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926e086477/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926e086477] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926e086477'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7926e086477'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 10.26 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FAL > test-filter-immundata.R: SE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Respons > test-agg-strata.R: e, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-filter-immundata.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata.R: 2. filter_nonproductive > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927e329b63/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927e329b63/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927e329b63] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927e329b63'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7927e329b63'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 17.89 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79242a04fa1/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79046718a3c/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79242a04fa1/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79242a04fa1] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79242a04fa1'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79242a04fa1'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 12.96 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79046718a3c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79046718a3c] > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79046718a3c'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79046718a3c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 32.83 secs > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FAL > test-agg-strata.R: SE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235be0531/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235be0531/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235be0531] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235be0531'] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d79235be0531'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 15.73 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.35 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/legacy_v1_27d7927bee8f5c'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.4 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-agg-strata.R: 1. prefix_barcodes > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 7.93 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790a667ad3/annotations.parquet] > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790a667ad3/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790a667ad3] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790a667ad3'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790a667ad3'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 33.42 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 8.67 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-agg-strata.R: 2. filter_nonproductive > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79048da6beb/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 18.89 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79048da6beb/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79048da6beb] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79048da6beb'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79048da6beb'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 22.09 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79016200e56.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7903532b234/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7903532b234/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7903532b234] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7903532b234'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7903532b234'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 1.94 secs > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors Saving _problems/test-io-repertoires-agg-stepwise-125.R > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv > test-io-immundata.R: i Time elapsed: 9.56 secs > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 2/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790664c0555/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790664c0555/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790664c0555] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790664c0555'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790664c0555'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.05 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907846cb0e.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 9.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905b6c363e/annotations.parquet] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/treated/v001 > test-io-immundata.R: /annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905b6c363e/metadata.json] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905b6c363e] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905b6c363e'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905b6c363e'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 5.76 secs > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/annotations.parquet] > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79019eaec78.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.74 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 2/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790570e6e64/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790570e6e64/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790570e6e64] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790570e6e64'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790570e6e64'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 9.28 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7904b5e1971.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 6.86 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901913eefa/annotations.parquet] > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901913eefa/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901913eefa] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901913eefa'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901913eefa'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 7.15 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7906f49ea23.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ca52421/annotations.parq > test-io-repertoires-agg.R: uet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bafd3c6/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ca52421/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ca52421] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ca52421'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ca52421'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 9.48 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79074551a6e.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bafd3c6/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bafd3c6] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bafd3c6'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bafd3c6'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 18.8 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904e1b9dc7/annotations.parquet] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 7.92 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/snapshots/baseline/v00 > test-io-immundata.R: 1/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904e1b9dc7/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904e1b9dc7] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904e1b9dc7'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904e1b9dc7'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 13.06 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-47.R Saving _problems/test-io-repertoires-agg-64.R Saving _problems/test-io-repertoires-agg-70.R Saving _problems/test-io-repertoires-agg-88.R Saving _problems/test-io-repertoires-agg-96.R > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7907da37725.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.46 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790444b60b6/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790444b60b6/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790444b60b6] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790444b60b6'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790444b60b6'] > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.71 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903294b521.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ec722f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ec722f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ec722f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ec722f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906ec722f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.19 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79066e64c6f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924fa94d3/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901cf40a2f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901cf40a2f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901cf40a2f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901cf40a2f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7901cf40a2f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 11.13 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924fa94d3/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924fa94d3] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924fa94d3'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924fa94d3'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 14.85 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7901a50e3a8.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: v Renaming is finished > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904cf22ab1/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904cf22ab1/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904cf22ab1] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904cf22ab1'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7904cf22ab1'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 8.49 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7906482be5.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792785862c4/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792785862c4/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792785862c4] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792785862c4'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d792785862c4'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 14.34 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7921f1c9deb/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906c53502f/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7921f1c9deb/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7921f1c9deb] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7921f1c9deb'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7921f1c9deb'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 8.77 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906c53502f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906c53502f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906c53502f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906c53502f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 14.45 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7903e35e67e.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924b6992cc/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790207c37cf/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924b6992cc/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924b6992cc] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924b6992cc'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924b6992cc'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 13.75 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790207c37cf/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790207c37cf] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790207c37cf'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790207c37cf'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 12.42 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79052b879fe.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790349b89c0/annotations.parq > test-io-repertoires-counts.R: uet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790349b89c0/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790349b89c0] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790349b89c0'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790349b89c0'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.96 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79020b2eca8.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79266e07a20/annotations.parq > test-io-repertoires-files.R: uet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79076bfb7b4/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79076bfb7b4/metadata.json] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79266e07a20/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79076bfb7b4] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79076bfb7b4'] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79266e07a20] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79266e07a20'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79076bfb7b4'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79266e07a20'] > test-io-repertoires-counts.R: i Time elapsed: 9.08 secs > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-files.R: i Time elapsed: 12.62 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-counts.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d79020b2eca8.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790c2c08bc/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790c2c08bc/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790c2c08bc] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790c2c08bc'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d790c2c08bc'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: i Time elapsed: 10.97 secs > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792df7b924/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792df7b924/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792df7b924] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792df7b924'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792df7b924'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 17.24 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 10.41 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79255118757/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79255118757/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79255118757] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79255118757'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79255118757'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 15.82 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 14.13 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 10.61 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7927635141f/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7927635141f/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7927635141f] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7927635141f'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7927635141f'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 17.29 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_ > test-io-repertoires-processing.R: 1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 17.81 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FAL > test-io-repertoires-processing.R: SE` to quiet this message. > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/imm > test-io-repertoires-processing.R: undata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/immundata-sam > test-io-repertoires-processing.R: ple_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 14.9 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoi > test-io-repertoires-processing.R: re_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FAL > test-io-repertoires-processing.R: SE` to quiet this message. > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FAL > test-io-repertoires-processing.R: SE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792782cba21/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792782cba21/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792782cba21] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792782cba21'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d792782cba21'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.74 mins > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79071eb7c22/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79071eb7c22/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79071eb7c22] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79071eb7c22'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79071eb7c22'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.61 mins > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79074e4b8b9/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79074e4b8b9/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79074e4b8b9] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79074e4b8b9'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d79074e4b8b9'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 21.93 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7906e9369c6.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905df630a5/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905df630a5/metadata.json] > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905df630a5] > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79262e5e50b/annotations.parq > test-io-repertoires-schema-paired.R: uet] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905df630a5'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7905df630a5'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 1.34 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d790707ccc2.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906b2315fe/annotations.parq > test-io-repertoires-schema-single.R: uet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906b2315fe/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906b2315fe] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906b2315fe'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test_immundata_27d7906b2315fe'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 1.96 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79262e5e50b/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79262e5e50b] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79262e5e50b'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79262e5e50b'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 2.24 mins > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-table.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/test-no-barcodes'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-paired.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7925bab20eb.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-table.R: i Time elapsed: 14.7 secs > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79215fff633/annotations.parquet] > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79215fff633/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79215fff633] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79215fff633'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d79215fff633'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 9.66 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/file27d7924674c7b4.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924ace5889/annotations.parquet] > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924ace5889/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924ace5889] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924ace5889'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpm1qGsP/working_dir/RtmppWBsg6/test_immundata_27d7924ace5889'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 7.21 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ── <duckdb_error/rlang_error/error/condition> Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x66) [0x7f8cffc20186]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x23) [0x7f8cffc201e3]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x15) [0x7f8cffc236c5]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1ba) [0x7f8cfff7631a]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(+0x34914f) [0x7f8cfef4914f]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x136) [0x7f8d008ef736]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x95) [0x7f8d008f18a5]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x51) [0x7f8d008f1e71]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x96) [0x7f8cfff628d6]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x4c) [0x7f8d008ff43c]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x9d) [0x7f8cfff632fd]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x39) [0x7f8cfff634f9]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x695) [0x7f8d006bb065]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x4ea) [0x7f8d006bb87a]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xaf) [0x7f8d006befcf]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xbf) [0x7f8d006bf43f]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa8) [0x7f8d006bf6c8]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0xb4) [0x7f8d006c0464]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x1bd) [0x7f8d006c399d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x92) [0x7f8d006c3d02]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x62) [0x7f8d006c4782]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x148) [0x7f8cff2dfe68]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2df) [0x7f8cff2e05ff]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x6f) [0x7f8cff2e0f6f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x43b61a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544d22]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e283d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x43e43a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4df445]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1c0f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1f18]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e60bc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4f12d1]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER) Stack Trace: /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x66) [0x7f8cffc20186] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x23) [0x7f8cffc201e3] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x15) [0x7f8cffc236c5] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1ba) [0x7f8cfff7631a] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(+0x34914f) [0x7f8cfef4914f] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x136) [0x7f8d008ef736] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x95) [0x7f8d008f18a5] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x51) [0x7f8d008f1e71] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x96) [0x7f8cfff628d6] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x4c) [0x7f8d008ff43c] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x9d) [0x7f8cfff632fd] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x39) [0x7f8cfff634f9] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x695) [0x7f8d006bb065] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x4ea) [0x7f8d006bb87a] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xaf) [0x7f8d006befcf] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xbf) [0x7f8d006bf43f] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa8) [0x7f8d006bf6c8] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0xb4) [0x7f8d006c0464] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x1bd) [0x7f8d006c399d] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x92) [0x7f8d006c3d02] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x62) [0x7f8d006c4782] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x148) [0x7f8cff2dfe68] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2df) [0x7f8cff2e05ff] /data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x6f) [0x7f8cff2e0f6f] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x43b61a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544d22] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e283d] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x43e43a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4df445] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1c0f] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1f18] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e60bc] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4f12d1] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5] /data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924] /data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15] This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic. For more information, see https://duckdb.org/docs/stable/dev/internal_errors i Context: GetQueryResult Backtrace: ▆ 1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3 2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations) 3. │ ├─dplyr::collect(out) 4. │ └─duckplyr:::collect.duckplyr_df(out) 5. │ └─base::nrow(x) 6. │ ├─base::dim(x) 7. │ └─base::dim.data.frame(x) 8. │ └─base::.row_names_info(x, 2L) 9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::ToJSON(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x66) [0x7f8cffc20186]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Exception::Exception(duckdb::ExceptionType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x23) [0x7f8cffc201e3]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x15) [0x7f8cffc236c5]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::InternalException::InternalException<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long&, unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x1ba) [0x7f8cfff7631a]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(+0x34914f) [0x7f8cfef4914f]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)+0x136) [0x7f8d008ef736]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::function<void (duckdb::unique_ptr<duckdb::Expression, std::default_delete<duckdb::Expression>, true>*)> const&)+0x95) [0x7f8d008f18a5]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&)+0x51) [0x7f8d008f1e71]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x96) [0x7f8cfff628d6]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long, true, std::allocator<unsigned long> >&)+0x4c) [0x7f8d008ff43c]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&)+0x5d) [0x7f8d00903b6d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&)+0x8b) [0x7f8cfff628cb]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x9d) [0x7f8cfff632fd]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::default_delete<duckdb::LogicalOperator>, true>)+0x39) [0x7f8cfff634f9]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters)+0x695) [0x7f8d006bb065]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode)+0x4ea) [0x7f8d006bb87a]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&)+0xaf) [0x7f8d006befcf]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xbf) [0x7f8d006bf43f]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&)+0xa8) [0x7f8d006bf6c8]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool)+0xb4) [0x7f8d006c0464]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters)+0x1bd) [0x7f8d006c399d]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&)+0x92) [0x7f8d006c3d02]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::Relation::Execute()+0x62) [0x7f8d006c4782]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::Materialize()+0x148) [0x7f8cff2dfe68]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(duckdb::AltrepRelationWrapper::GetQueryResult()+0x2df) [0x7f8cff2e05ff]\n/data/gannet/ripley/R/test-dev/duckdb/libs/duckdb.so(RelToAltrep::RownamesLength(SEXPREC*)+0x6f) [0x7f8cff2e0f6f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x43b61a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544d22]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e283d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x43e43a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x543dce]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544755]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x544e63]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x545122]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edbdc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4df445]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1c0f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e1f18]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x46976f]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4edd3a]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e60bc]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4f12d1]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4e043b]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x17b) [0x4d955b]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d830e]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d906d]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x261) [0x4d9641]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4db7f5]\n/data/gannet/ripley/R/R-devel/bin/exec/R(Rf_eval+0x544) [0x4d9924]\n/data/gannet/ripley/R/R-devel/bin/exec/R() [0x4d9e15]\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors") 10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5 ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors agg schema: sample_id input annotation shape: 5x13 input repertoire shape: <not captured> annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: <none> missing repertoire columns: <none> annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 0 input repertoires dump: <NULL> annotations dump: cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 /tmp/Rtmpm1qGsP/working_dir/RtmpAC73ei/file27d7905ebf783d.tsv cell5 5 1 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 Sample2 2 NA 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3 2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3 3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5 ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [451s/239s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5712a66cf81/annotations.parquet] > test-annotate-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5712a66cf81/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5712a66cf81] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5712a66cf81'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5712a66cf81'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 7.29 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7245de74/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7245de74/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7245de74] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7245de74'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7245de74'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 8.64 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e508ee606/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e508ee606/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e508ee606] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e508ee606'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e508ee606'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.23 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714cb2e5ab/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714cb2e5ab/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714cb2e5ab] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714cb2e5ab'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714cb2e5ab'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.9 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e58cc8347/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e58cc8347/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e58cc8347] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e58cc8347'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e58cc8347'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.16 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57133eda45f/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57133eda45f/metadata.json] > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57133eda45f] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57133eda45f'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57133eda45f'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.57 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa0498f/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa0498f/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa0498f] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa0498f'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa0498f'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.69 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e51b1fad4/annotations.parquet] > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e51b1fad4/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e51b1fad4] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e51b1fad4'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e51b1fad4'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.5 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571514dbd21/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571514dbd21/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571514dbd21] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571514dbd21'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571514dbd21'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.7 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5f07fbe8/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5f07fbe8/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5f07fbe8] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5f07fbe8'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5f07fbe8'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.4 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714876edc6/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714876edc6/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714876edc6] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714876edc6'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714876edc6'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.72 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e77e9e1cd/annotations.parquet] > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716ea16b2a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e77e9e1cd/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e77e9e1cd] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e77e9e1cd'] > test-annotate-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716ea16b2a/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716ea16b2a] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e77e9e1cd'] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716ea16b2a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.13 secs > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716ea16b2a'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: i Time elapsed: 4.75 secs > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57165843522/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57165843522/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57165843522] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57165843522'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57165843522'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 5.99 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FAL > test-compute-collect-immundata.R: SE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e83e6e8/annotations.parquet] > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e83e6e8/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e83e6e8] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e83e6e8'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e83e6e8'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.09 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57171aae9af/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57171aae9af/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57171aae9af] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57171aae9af'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57171aae9af'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.15 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Respons > test-compute-collect-immundata.R: e, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7812c511/annotations.parquet] > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7812c511/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7812c511] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7812c511'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7812c511'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.55 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f5c6296/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f5c6296/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f5c6296] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f5c6296'] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f5c6296'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: i Time elapsed: 6.11 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e26ee64ef/annotations.parquet] > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e26ee64ef/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e26ee64ef] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e26ee64ef'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e26ee64ef'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.5 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711b0fbfe8/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711b0fbfe8/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711b0fbfe8] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711b0fbfe8'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711b0fbfe8'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 7.14 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e6ecb15c8/annotations.parquet] > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571703d7ebc/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e6ecb15c8/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e6ecb15c8] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e6ecb15c8'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e6ecb15c8'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.12 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571703d7ebc/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571703d7ebc] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571703d7ebc'] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571703d7ebc'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 4.78 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57161cbd50b/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57161cbd50b/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57161cbd50b] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57161cbd50b'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57161cbd50b'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 4.77 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e1087349b/annotations.parquet] > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e1087349b/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e1087349b] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e1087349b'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e1087349b'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.16 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa3d70e/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa3d70e/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa3d70e] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa3d70e'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5716aa3d70e'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 4.72 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7d62dd0c/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7d62dd0c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7d62dd0c] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7d62dd0c'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7d62dd0c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.26 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711e6fc74b/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711e6fc74b/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711e6fc74b] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711e6fc74b'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5711e6fc74b'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.8 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57119b57338/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e62c770d5/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57119b57338/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57119b57338] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57119b57338'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57119b57338'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.68 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e62c770d5/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e62c770d5] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e62c770d5'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e62c770d5'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.52 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571285fe46a/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571285fe46a/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571285fe46a] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571285fe46a'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e571285fe46a'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 4.72 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4f311567/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4f311567/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4f311567] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4f311567'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4f311567'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 6.13 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714f7c4b2f/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714f7c4b2f/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714f7c4b2f] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714f7c4b2f'] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5714f7c4b2f'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 4.67 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e447ceb82/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e447ceb82/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e447ceb82] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e447ceb82'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/file27e56e447ceb82'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 4.69 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd/annotations.parquet] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e16e7be.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/legacy_v1_27e57170560ebd'] > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e359a0cd0/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e359a0cd0/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e359a0cd0] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e359a0cd0'] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e359a0cd0'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.41 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e395f3628.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e26f60e3e/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e26f60e3e/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e26f60e3e] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e26f60e3e'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e26f60e3e'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.39 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e7c5a30b8.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6dcc4633/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6dcc4633/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6dcc4633] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6dcc4633'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6dcc4633'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.99 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.21 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e3a1213cb.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6da6e07/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6da6e07/metadata.json] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6da6e07] > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6da6e07'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e6da6e07'] > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.18 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e220aa1b5.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e435451bb/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e435451bb/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e435451bb] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e435451bb'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e435451bb'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.79 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e741a6bca.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e402c82e2/annotations.parquet] > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e402c82e2/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e402c82e2] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e402c82e2'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e402c82e2'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.78 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e50154974.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-immundata.R: i Time elapsed: 5.12 secs > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-agg.R: 1. exclude_columns > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56edb726b1/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56edb726b1/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56edb726b1] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56edb726b1'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56edb726b1'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.89 secs > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.21 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e548ad262.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5f66cad7/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5f66cad7/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5f66cad7] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5f66cad7'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5f66cad7'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.48 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e2b40fcc2.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e11424709/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e11424709/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e11424709] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e11424709'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e11424709'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.43 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e3a93c26a.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.18 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e63dcc282/annotations.parquet] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e63dcc282/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e63dcc282] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e63dcc282'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e63dcc282'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.86 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56ebc0fe45.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e331b7826/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e331b7826/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e331b7826] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e331b7826'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e331b7826'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.38 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e5fece4f4.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.17 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32ddf55f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32ddf55f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32ddf55f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32ddf55f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32ddf55f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.46 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e11604388.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.15 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e643fc9b/annotations.parquet] > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e643fc9b/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e643fc9b] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e643fc9b'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e643fc9b'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.22 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e143786ca.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e66842747/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e66842747/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e66842747] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e66842747'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e66842747'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.27 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e2434ce9.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e355eb090/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e355eb090/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e355eb090] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e355eb090'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e355eb090'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.96 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e2434ce9.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57126114b77/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e42b23417/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57126114b77/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57126114b77] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57126114b77'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57126114b77'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.72 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e42b23417/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e42b23417] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e42b23417'] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e42b23417'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.69 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.16 secs > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e3d95b89f/annotations.parquet] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e3d95b89f/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e3d95b89f] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e3d95b89f'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e3d95b89f'] > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-immundata.R: v All files have the same extension > test-io-repertoires-files.R: i Time elapsed: 2.23 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: v Renaming is finished > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.14 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e13bd8c16/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e13bd8c16/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e13bd8c16] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e13bd8c16'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e13bd8c16'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.03 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57130bcd6b7/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57130bcd6b7/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57130bcd6b7] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57130bcd6b7'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e57130bcd6b7'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.8 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e1cf933b/annotations.parquet] > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e1cf933b/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e1cf933b] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e1cf933b'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e1cf933b'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.03 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f7636fa/annotations.parquet] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f7636fa/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f7636fa] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f7636fa'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/file27e5713f7636fa'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.72 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b7f81d2/annotations.parquet > test-io-repertoires-files.R: ] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b7f81d2/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b7f81d2] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b7f81d2'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b7f81d2'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.17 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude/annotations.parquet] > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.29 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-rename/metadata.json] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-rename'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.64 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b5258c3/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b5258c3/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b5258c3] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b5258c3'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e5b5258c3'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.12 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude-rename/annotations.parquet] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.32 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e14bd5690/annotations.parquet] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e14bd5690/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e14bd5690] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e14bd5690'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e14bd5690'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.59 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57137a436c2/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57137a436c2/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57137a436c2] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57137a436c2'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57137a436c2'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 25.46 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors Saving _problems/test-io-repertoires-processing-90.R Saving _problems/test-io-repertoires-processing-110.R > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56eb5b311b/annotations.parquet] > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e571323f179b/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e571323f179b/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e571323f179b] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e571323f179b'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e571323f179b'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 5.51 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56eb5b311b/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56eb5b311b] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56eb5b311b'] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56eb5b311b'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 31.46 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/RtmpQtwpxz/file27e57121ff23cb.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57151a8cfb7/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57151a8cfb7/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57151a8cfb7] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57151a8cfb7'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57151a8cfb7'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.37 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/RtmpQtwpxz/file27e571553cf8a0.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57156001248/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57156001248/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57156001248] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57156001248'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test_immundata_27e57156001248'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.39 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpQtwpxz/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpQtwpxz/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 2.61 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e49c2496e/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e49c2496e/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e49c2496e] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e49c2496e'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e49c2496e'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 32.14 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e4edff99f.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e392c0147/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e392c0147/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e392c0147] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e392c0147'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e392c0147'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.48 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/RtmpWisKwM/file27e56e226e5641.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32498da2/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32498da2/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32498da2] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32498da2'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpWisKwM/test_immundata_27e56e32498da2'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.57 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-processing.R:87:3'): read_repertoires() removes non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:87:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires-processing.R:106:3'): read_repertoires() correctly reads non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:106:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] Error: ! Test failures. Execution halted Flavor: r-patched-linux-x86_64

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [453s/239s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5808ac3ffa/annotations.parquet] > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5808ac3ffa/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5808ac3ffa] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5808ac3ffa'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5808ac3ffa'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 6.18 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5752938196d/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5752938196d/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5752938196d] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5752938196d'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5752938196d'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 7.35 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575438c55e9/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575438c55e9/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575438c55e9] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575438c55e9'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575438c55e9'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.99 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5806471cb2a/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5806471cb2a/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5806471cb2a] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5806471cb2a'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5806471cb2a'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.86 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5754a5e7d73/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5754a5e7d73/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5754a5e7d73] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5754a5e7d73'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5754a5e7d73'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.09 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580651c78b7/annotations.parquet] > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580651c78b7/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580651c78b7] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580651c78b7'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580651c78b7'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.66 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804e4c2d5a/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575716b2eff/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804e4c2d5a/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804e4c2d5a] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804e4c2d5a'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804e4c2d5a'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.71 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575716b2eff/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575716b2eff] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575716b2eff'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575716b2eff'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.09 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580100fd94c/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580100fd94c/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580100fd94c] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580100fd94c'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580100fd94c'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.76 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575640fc05a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575640fc05a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575640fc05a] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575640fc05a'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575640fc05a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.1 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580386155b9/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580386155b9/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580386155b9] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580386155b9'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580386155b9'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.76 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5753613cf5a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5753613cf5a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5753613cf5a] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5753613cf5a'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5753613cf5a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.04 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58042e53a2a/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58042e53a2a/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58042e53a2a] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58042e53a2a'] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58042e53a2a'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 4.77 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5752817804b/annotations.parquet] > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5805d4abb55/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5752817804b/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5752817804b] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5752817804b'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5752817804b'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.23 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5805d4abb55/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5805d4abb55] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5805d4abb55'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5805d4abb55'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.12 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804b1e88f7/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804b1e88f7/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804b1e88f7] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804b1e88f7'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804b1e88f7'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.49 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5751aa6fda8/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5751aa6fda8/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5751aa6fda8] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5751aa6fda8'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5751aa6fda8'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.45 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580225a214/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580225a214/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580225a214] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580225a214'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580225a214'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.11 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756e867f18/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756e867f18/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756e867f18] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756e867f18'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756e867f18'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.08 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58015d6ee1/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58015d6ee1/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58015d6ee1] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58015d6ee1'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58015d6ee1'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.75 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-agg-strata.R: > test-filter-barcodes.R: 1. exclude_columns > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5754586f1fb/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5754586f1fb/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5754586f1fb] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5754586f1fb'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5754586f1fb'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.27 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5803041a54e/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5803041a54e/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5803041a54e] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5803041a54e'] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5803041a54e'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 5.11 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756f4c5165/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756f4c5165/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756f4c5165] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756f4c5165'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756f4c5165'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.15 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580393826a9/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-filter-immundata-exact.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580393826a9/metadata.json] > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-exact.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580393826a9] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580393826a9'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580393826a9'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 4.87 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580411b8350/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580411b8350/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580411b8350] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580411b8350'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580411b8350'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 4.72 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57538829fc2/annotations.parquet] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57538829fc2/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57538829fc2] > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57538829fc2'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57538829fc2'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.31 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580477531d9/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580477531d9/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580477531d9] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580477531d9'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580477531d9'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.78 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5755cc07532/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5755cc07532/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5755cc07532] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5755cc07532'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5755cc07532'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.94 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804f317274/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804f317274/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804f317274] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804f317274'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5804f317274'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.78 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756de2d10e/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756de2d10e/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756de2d10e] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756de2d10e'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5756de2d10e'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 4.81 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580941d997/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580941d997/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580941d997] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580941d997'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580941d997'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 6.18 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57520d27d4f/annotations.parquet] > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57520d27d4f/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57520d27d4f] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57520d27d4f'] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57520d27d4f'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 4.77 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/legacy_v1_1bd57582b8987/annotations.parquet] > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580271188eb/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/legacy_v1_1bd57582b8987/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/legacy_v1_1bd57582b8987] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/legacy_v1_1bd57582b8987'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/legacy_v1_1bd57582b8987'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.29 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/legacy_v1_1bd57582b8987'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580271188eb/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580271188eb] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580271188eb'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580271188eb'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 4.72 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580bd40b28.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5804b3479a5/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5804b3479a5/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5804b3479a5] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5804b3479a5'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5804b3479a5'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.42 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58070889c3c.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.2 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580127a646c/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580127a646c/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580127a646c] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580127a646c'] > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580127a646c'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.43 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5806f119c55.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5802d989708/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.28 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5802d989708/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5802d989708] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5802d989708'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5802d989708'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: i Time elapsed: 1.59 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5803059f735.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58072865971/annotations.parquet > test-io-repertoires-agg.R: ] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58072865971/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58072865971] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58072865971'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58072865971'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.54 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.46 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58033d8e900.tsv > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803653c4a2/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803653c4a2/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803653c4a2] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803653c4a2'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803653c4a2'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.64 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5803c473d93.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58078c429cc/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58078c429cc/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58078c429cc] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58078c429cc'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58078c429cc'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.87 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58032e3ba53.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.43 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580756a0f31/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580756a0f31/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580756a0f31] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580756a0f31'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580756a0f31'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.72 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5807c2b8590.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803d079f1/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803d079f1/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803d079f1] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803d079f1'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803d079f1'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.43 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5801a5f02bd.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58020b377b7/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58020b377b7/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58020b377b7] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58020b377b7'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58020b377b7'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.3 secs > test-io-repertoires-counts.R: i Time elapsed: 0.44 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5807e5616a8.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580443dc525/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580443dc525/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580443dc525] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580443dc525'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580443dc525'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.49 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5807e7a84b.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.27 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB'] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5801f098c84/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5801f098c84/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5801f098c84] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5801f098c84'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5801f098c84'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.22 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5803b3ff641.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: i Time elapsed: 2.26 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5801ad75b43/annotations.parquet] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5801ad75b43/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5801ad75b43] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5801ad75b43'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5801ad75b43'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.58 secs > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5807ee2438e.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580139e595c/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.29 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580139e595c/metadata.json] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580139e595c] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580139e595c'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd580139e595c'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.23 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5807186e736.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803e0b88f0/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803e0b88f0/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803e0b88f0] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803e0b88f0'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803e0b88f0'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.26 secs > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58038f7a5f4.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58067645896/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58067645896/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58067645896] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58067645896'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58067645896'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.68 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd58038f7a5f4.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58064d80f13/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58064d80f13/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58064d80f13] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58064d80f13'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58064d80f13'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.79 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57510538199/annotations.parquet] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57510538199/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57510538199] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57510538199'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57510538199'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.73 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58019d7a441/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58019d7a441/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58019d7a441] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58019d7a441'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58019d7a441'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.31 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.21 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.23 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5805777111c/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5805777111c/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5805777111c] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5805777111c'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5805777111c'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.13 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5753cacfb5a/annotations.parquet] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58079a27c56/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5753cacfb5a/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5753cacfb5a] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5753cacfb5a'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5753cacfb5a'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.88 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58079a27c56/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58079a27c56] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58079a27c56'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58079a27c56'] > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.25 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5755b56cab8/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5755b56cab8/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5755b56cab8] > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5755b56cab8'] > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58046204e5e/annotations.parquet] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/file1bd5755b56cab8'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.86 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58046204e5e/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58046204e5e] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58046204e5e'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58046204e5e'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.38 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.38 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.63 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5805d1e3ecf/annotations.parquet] > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5805d1e3ecf/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5805d1e3ecf] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5805d1e3ecf'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5805d1e3ecf'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.25 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.3 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803f3c3290/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803f3c3290/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803f3c3290] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803f3c3290'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5803f3c3290'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.32 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5756769a433/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5756769a433/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5756769a433] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5756769a433'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5756769a433'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 25.64 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors Saving _problems/test-io-repertoires-processing-90.R Saving _problems/test-io-repertoires-processing-110.R > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5802d6f08c/annotations.parquet] > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5754bfd95b0/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5802d6f08c/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5802d6f08c] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5802d6f08c'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5802d6f08c'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 31.99 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5754bfd95b0/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5754bfd95b0] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5754bfd95b0'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5754bfd95b0'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 5.51 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/Rtmp640wyJ/file1bd575b3c580f.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5757c27de64/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5757c27de64/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5757c27de64] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5757c27de64'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd5757c27de64'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.38 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/Rtmp640wyJ/file1bd57546ca6b54.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd57573d793bd/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd57573d793bd/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd57573d793bd] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd57573d793bd'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test_immundata_1bd57573d793bd'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.42 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmp640wyJ/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmp640wyJ/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 2.7 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5807b9cb14/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5807b9cb14/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5807b9cb14] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5807b9cb14'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd5807b9cb14'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 33.38 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd5807fe56866.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58015d7c477/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58015d7c477/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58015d7c477] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58015d7c477'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58015d7c477'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.53 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/RtmpLOOKx8/file1bd580551f7852.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58020beca6c/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58020beca6c/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58020beca6c] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58020beca6c'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpLOOKx8/test_immundata_1bd58020beca6c'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.62 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-processing.R:87:3'): read_repertoires() removes non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:87:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires-processing.R:106:3'): read_repertoires() correctly reads non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:106:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] Error: ! Test failures. Execution halted Flavor: r-release-linux-x86_64

Version: 0.0.6
Check: Rd cross-references
Result: NOTE Unknown package ‘anndataR’ in Rd xrefs Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64