Last updated on 2025-04-30 01:50:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 10.68 | 141.55 | 152.23 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 8.36 | 96.77 | 105.13 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 244.31 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 229.99 | OK | |||
| r-devel-windows-x86_64 | 1.1.0 | 15.00 | 165.00 | 180.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 12.88 | 133.49 | 146.37 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 11.11 | 135.09 | 146.20 | OK | |
| r-release-macos-arm64 | 1.1.0 | 96.00 | ERROR | |||
| r-release-macos-x86_64 | 1.1.0 | 198.00 | ERROR | |||
| r-release-windows-x86_64 | 1.1.0 | 13.00 | 160.00 | 173.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 78.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.1.0 | 105.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.1.0 | 17.00 | 212.00 | 229.00 | NOTE |
Version: 1.1.0
Check: examples
Result: NOTE
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DEanalysis 6.160 0.358 8.203
jaccard_heatmap 5.151 0.101 6.088
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘GEO_App.Rmd’ using rmarkdown
trying URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE178620&format=file&file=GSE178620%5Fraw%5Fabundances%2Ecsv%2Egz'
Content type 'application/octet-stream' length 1892945 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bulkAnalyseR.Rcheck/vign_test/bulkAnalyseR/vignettes/GEO_App_files/figure-html/preprocess-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31284 bytes
Input file size = 31398 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27518
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27518
Output IDAT size = 27518 bytes (3766 bytes decrease)
Output file size = 27596 bytes (3802 bytes = 12.11% decrease)
[WARNING] Div at GEO_App.knit.md line 10 column 1 unclosed at GEO_App.knit.md line 200 column 1, closing implicitly.
--- finished re-building ‘GEO_App.Rmd’
--- re-building ‘IntegratingMultiomics.Rmd’ using rmarkdown
Quitting from IntegratingMultiomics.Rmd:155-168 [li data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://raw.githubusercontent.com/Core-Bioinformatics/bulkAnalyseR/master/exampledata/Li2021_miRNA_mRNA/expression_matrix_mRNA_preprocessed.csv'
---
Backtrace:
▆
1. ├─... %>% as.matrix
2. ├─base::as.matrix(.)
3. └─utils::read.csv(...)
4. └─utils::read.table(...)
5. ├─base::open(file, "rt")
6. └─base::open.connection(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'IntegratingMultiomics.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/Core-Bioinformatics/bulkAnalyseR/master/exampledata/Li2021_miRNA_mRNA/expression_matrix_mRNA_preprocessed.csv'
--- failed re-building ‘IntegratingMultiomics.Rmd’
--- re-building ‘bulkAnalyseR.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bulkAnalyseR.Rcheck/vign_test/bulkAnalyseR/vignettes/bulkAnalyseR_files/figure-html/preprocess-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 56447 bytes
Input file size = 56597 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48532
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48532
Output IDAT size = 48532 bytes (7915 bytes decrease)
Output file size = 48610 bytes (7987 bytes = 14.11% decrease)
[WARNING] Div at bulkAnalyseR.knit.md line 10 column 1 unclosed at bulkAnalyseR.knit.md line 603 column 1, closing implicitly.
--- finished re-building ‘bulkAnalyseR.Rmd’
SUMMARY: processing the following file failed:
‘IntegratingMultiomics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘bulkAnalyseR-Ex.R’ failed
The error most likely occurred in:
> ### Name: DEanalysis
> ### Title: Perform differential expression (DE) analysis on an expression
> ### matrix
> ### Aliases: DEanalysis DEanalysis_edger DEanalysis_deseq2
>
> ### ** Examples
>
> expression.matrix.preproc <- as.matrix(read.csv(
+ system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"),
+ row.names = 1
+ ))[1:100, 1:4]
>
> anno <- AnnotationDbi::select(
+ getExportedValue('org.Mm.eg.db', 'org.Mm.eg.db'),
+ keys = rownames(expression.matrix.preproc),
+ keytype = 'ENSEMBL',
+ columns = 'SYMBOL'
+ ) %>%
+ dplyr::distinct(ENSEMBL, .keep_all = TRUE) %>%
+ dplyr::mutate(NAME = ifelse(is.na(SYMBOL), ENSEMBL, SYMBOL))
Error in (function (cond) :
error in evaluating the argument 'x' in selecting a method for function 'select': there is no package called ‘org.Mm.eg.db’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64
Version: 1.1.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘org.Mm.eg.db’
Flavor: r-oldrel-macos-arm64
Version: 1.1.0
Check: installed package size
Result: NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 2.3Mb
extdata 3.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64