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This page was generated on 2025-04-02 19:31 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2235/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
variancePartition 1.36.3  (landing page)
Gabriel E. Hoffman
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: RELEASE_3_20
git_last_commit: 6da3d03
git_last_commit_date: 2025-01-02 12:46:18 -0400 (Thu, 02 Jan 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for variancePartition on palomino8

To the developers/maintainers of the variancePartition package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/variancePartition.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: variancePartition
Version: 1.36.3
Command: chmod a+r variancePartition -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data variancePartition
StartedAt: 2025-03-31 22:31:39 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 22:45:36 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 836.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r variancePartition -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data variancePartition
###
##############################################################################
##############################################################################


* checking for file 'variancePartition/DESCRIPTION' ... OK
* preparing 'variancePartition':
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
Loading required namespace: variancePartition
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building 'FAQ.Rmd' using rmarkdown
--- finished re-building 'FAQ.Rmd'

--- re-building 'additional_visualization.Rmd' using rmarkdown
--- finished re-building 'additional_visualization.Rmd'

--- re-building 'dream.Rmd' using rmarkdown
--- finished re-building 'dream.Rmd'

--- re-building 'errors.Rmd' using rmarkdown
--- finished re-building 'errors.Rmd'

--- re-building 'mvtests.Rmd' using rmarkdown

Quitting from mvtests.Rmd:117-127 [zenith]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `msigdbr_check_data()`:
! Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
---
Backtrace:
    ▆
 1. └─zenith::get_MSigDB("C1", to = "ENSEMBL")
 2.   └─base::lapply(...)
 3.     └─zenith (local) FUN(X[[i]], ...)
 4.       └─EnrichmentBrowser::getGenesets(...)
 5.         └─EnrichmentBrowser:::.getMSigDb(...)
 6.           ├─base::unique(msigdbr::msigdbr_collections()$gs_cat)
 7.           └─msigdbr::msigdbr_collections()
 8.             └─msigdbr:::msigdbr_check_data()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'mvtests.Rmd' failed with diagnostics:
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
--- failed re-building 'mvtests.Rmd'

--- re-building 'rnd_effects.Rmd' using rmarkdown
--- finished re-building 'rnd_effects.Rmd'

--- re-building 'variancePartition.Rmd' using rmarkdown
--- finished re-building 'variancePartition.Rmd'

SUMMARY: processing the following file failed:
  'mvtests.Rmd'

Error: Vignette re-building failed.
Execution halted