Last updated on 2025-09-27 02:53:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 42.02 | 316.72 | 358.74 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 27.08 | 230.36 | 257.44 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 634.35 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 553.12 | NOTE | |||
| r-devel-windows-x86_64 | 1.0.1 | 40.00 | 305.00 | 345.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.1 | 35.70 | 331.29 | 366.99 | NOTE | |
| r-release-linux-x86_64 | 1.0.1 | 35.12 | 330.89 | 366.01 | NOTE | |
| r-release-macos-arm64 | 1.0.1 | 141.00 | NOTE | |||
| r-release-macos-x86_64 | 1.0.1 | 316.00 | NOTE | |||
| r-release-windows-x86_64 | 1.0.1 | 37.00 | 299.00 | 336.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.0.1 | 146.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.1 | 245.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.1 | 51.00 | 395.00 | 446.00 | OK |
Version: 1.0.1
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘GaussianMixtureCalls.R’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘karyotapR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCytobands
> ### Title: Add chromosome cytobands and chromosome arms to
> ### 'TapestriExperiment'
> ### Aliases: getCytobands
>
> ### ** Examples
>
> tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
ℹ Moving gRNA probe to `altExp` slot "grnaCounts".
ℹ Moving barcode probe to `altExp` slot "barcodeCounts".
ℹ Moving chrY probe(s) probe_231, probe_232, probe_233, probe_234, probe_235, probe_236, probe_237, probe_238, probe_239, and probe_240 to `altExp` slot "chrYCounts".
> tap.object <- getCytobands(tap.object, genome = "hg19")
ℹ Adding cytobands from hg19.
Loading required namespace: GenomeInfoDb
Failed with error: ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) :
unable to load required package ‘GenomeInfoDb’
Calls: getCytobands ... vapply -> FUN -> is -> getClassDef -> .requirePackage
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calcSmoothCopyNumber 4.464 0.111 5.742
assayHeatmap 4.216 0.135 5.602
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/16s]
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(karyotapR)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("karyotapR")
Failed with error: 'there is no package called 'GenomeInfoDb''
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-normalization.R:16:5'): NA in normalization input triggers message ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
▆
1. ├─base::suppressMessages(newDummyTapestriExperiment()) at test-normalization.R:16:5
2. │ └─base::withCallingHandlers(...)
3. └─karyotapR:::newDummyTapestriExperiment()
4. └─karyotapR::getCytobands(tapestri.object)
5. └─karyotapR:::.GetCytobands.df(amplicon.df, return.genomic.ranges = TRUE)
6. ├─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges)
7. └─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges)
8. └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...)
9. └─GenomicRanges:::findOverlaps_GNCList(...)
10. ├─base::merge(seqinfo(query), seqinfo(subject))
11. └─Seqinfo::merge(seqinfo(query), seqinfo(subject))
12. └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
13. └─base::vapply(args, function(arg) is(arg, class(x)), logical(1))
14. └─Seqinfo (local) FUN(X[[i]], ...)
15. └─methods::is(arg, class(x))
16. └─methods::getClassDef(class1)
17. └─methods:::.requirePackage(package)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘karyotapR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCytobands
> ### Title: Add chromosome cytobands and chromosome arms to
> ### 'TapestriExperiment'
> ### Aliases: getCytobands
>
> ### ** Examples
>
> tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
ℹ Moving gRNA probe to `altExp` slot "grnaCounts".
ℹ Moving barcode probe to `altExp` slot "barcodeCounts".
ℹ Moving chrY probe(s) probe_231, probe_232, probe_233, probe_234, probe_235, probe_236, probe_237, probe_238, probe_239, and probe_240 to `altExp` slot "chrYCounts".
> tap.object <- getCytobands(tap.object, genome = "hg19")
ℹ Adding cytobands from hg19.
Loading required namespace: GenomeInfoDb
Failed with error: ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) :
unable to load required package ‘GenomeInfoDb’
Calls: getCytobands ... vapply -> FUN -> is -> getClassDef -> .requirePackage
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/12s]
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(karyotapR)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("karyotapR")
Failed with error: 'there is no package called 'GenomeInfoDb''
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-normalization.R:16:5'): NA in normalization input triggers message ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
▆
1. ├─base::suppressMessages(newDummyTapestriExperiment()) at test-normalization.R:16:5
2. │ └─base::withCallingHandlers(...)
3. └─karyotapR:::newDummyTapestriExperiment()
4. └─karyotapR::getCytobands(tapestri.object)
5. └─karyotapR:::.GetCytobands.df(amplicon.df, return.genomic.ranges = TRUE)
6. ├─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges)
7. └─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges)
8. └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...)
9. └─GenomicRanges:::findOverlaps_GNCList(...)
10. ├─base::merge(seqinfo(query), seqinfo(subject))
11. └─Seqinfo::merge(seqinfo(query), seqinfo(subject))
12. └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
13. └─base::vapply(args, function(arg) is(arg, class(x)), logical(1))
14. └─Seqinfo (local) FUN(X[[i]], ...)
15. └─methods::is(arg, class(x))
16. └─methods::getClassDef(class1)
17. └─methods:::.requirePackage(package)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc