Multiple platform build/check report for BioC 3.21 - BUILD results for zenith on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4742
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 zenith on lconway

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

Version: 1.9.0

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

StartedAt: 2025-03-18 18:59:22 -0400 (Tue, 18 Mar 2025)

EndedAt: 2025-03-18 19:00:34 -0400 (Tue, 18 Mar 2025)

EllapsedTime: 72.0 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 zenith
###
##############################################################################
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* checking for file ‘zenith/DESCRIPTION’ ... OK
* preparing ‘zenith’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
Loading required namespace: zenith
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘loading_genesets.Rmd’ using rmarkdown
--- finished re-building ‘loading_genesets.Rmd’

--- re-building ‘zenith.Rmd’ using rmarkdown

Quitting from zenith.Rmd:34-73 [standard]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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("H", 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 'zenith.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 ‘zenith.Rmd’

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

Error: Vignette re-building failed.
Execution halted