Multiple platform build/check report for BioC 3.21 - BUILD results for epiregulon.extra on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4459
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*

BUILD results for epiregulon.extra on lconway

To the developers/maintainers of the epiregulon.extra package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epiregulon.extra.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: epiregulon.extra

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data epiregulon.extra

StartedAt: 2025-03-16 16:47:56 -0400 (Sun, 16 Mar 2025)

EndedAt: 2025-03-16 16:49:48 -0400 (Sun, 16 Mar 2025)

EllapsedTime: 112.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data epiregulon.extra
###
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* checking for file ‘epiregulon.extra/DESCRIPTION’ ... OK
* preparing ‘epiregulon.extra’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Data_visualization.Rmd’ using rmarkdown
2025-03-16 16:49:32.741 R[27831:415619877] XType: com.apple.fonts is not accessible.
2025-03-16 16:49:32.743 R[27831:415619877] XType: XTFontStaticRegistry is enabled.

Quitting from Data_visualization.Rmd:205-242 [enrichment]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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. └─EnrichmentBrowser::getGenesets(...)
 2.   └─EnrichmentBrowser:::.getMSigDb(...)
 3.     ├─base::unique(msigdbr::msigdbr_collections()$gs_cat)
 4.     └─msigdbr::msigdbr_collections()
 5.       └─msigdbr:::msigdbr_check_data()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Data_visualization.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 ‘Data_visualization.Rmd’

SUMMARY: processing the following file failed:
  ‘Data_visualization.Rmd’

Error: Vignette re-building failed.
Execution halted