Last updated on 2025-03-09 05:52:23 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 10.65 | 137.09 | 147.74 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 7.69 | 96.12 | 103.81 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 246.10 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 254.47 | OK | |||
| r-devel-macos-arm64 | 1.1.0 | 70.00 | ERROR | |||
| r-devel-macos-x86_64 | 1.1.0 | 119.00 | ERROR | |||
| r-devel-windows-x86_64 | 1.1.0 | 13.00 | 155.00 | 168.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 11.05 | 126.10 | 137.15 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 10.90 | 128.15 | 139.05 | OK | |
| r-release-macos-arm64 | 1.1.0 | 78.00 | ERROR | |||
| r-release-macos-x86_64 | 1.1.0 | 105.00 | NOTE | |||
| r-release-windows-x86_64 | 1.1.0 | 13.00 | 150.00 | 163.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.1.0 | ERROR | ||||
| r-oldrel-macos-x86_64 | 1.1.0 | 151.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.1.0 | 17.00 | 197.00 | 214.00 | NOTE |
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-devel-macos-arm64, r-devel-macos-x86_64, r-release-macos-arm64
Version: 1.1.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘org.Mm.eg.db’
Flavors: r-release-macos-arm64, r-oldrel-macos-x86_64
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-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
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'
Quitting from lines 60-67 [read] (GEO_App.Rmd)
Error: processing vignette 'GEO_App.Rmd' failed with diagnostics:
cannot open URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE178620&format=file&file=GSE178620%5Fraw%5Fabundances%2Ecsv%2Egz'
--- failed re-building 'GEO_App.Rmd'
--- re-building 'IntegratingMultiomics.Rmd' using rmarkdown
--- finished re-building 'IntegratingMultiomics.Rmd'
--- re-building 'bulkAnalyseR.Rmd' using rmarkdown
--- finished re-building 'bulkAnalyseR.Rmd'
SUMMARY: processing the following file failed:
'GEO_App.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.1.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘GENIE3’
Package suggested but not available for checking: ‘org.Mm.eg.db’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-arm64