Multiple platform build/check report for BioC 3.23 - BUILD results for GenomicDataCommons on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"	4453
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-02-28 r89501) -- "Unsuffered Consequences"	3376
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 GenomicDataCommons on kjohnson3

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

Version: 1.35.1

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

StartedAt: 2026-03-06 16:00:52 -0500 (Fri, 06 Mar 2026)

EndedAt: 2026-03-06 16:01:31 -0500 (Fri, 06 Mar 2026)

EllapsedTime: 39.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicDataCommons
###
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* checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK
* preparing ‘GenomicDataCommons’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘overview.Rmd’ using rmarkdown
2026-03-06 16:01:06.254 R[51660:111962307] XType: Using static font registry.
The magick package is required to crop "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmphNwiWN/Rbuildc2041919a452/GenomicDataCommons/vignettes/overview_files/figure-html/casesPerProject-1.png" but not available.
The magick package is required to crop "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmphNwiWN/Rbuildc2041919a452/GenomicDataCommons/vignettes/overview_files/figure-html/filesVCFCount-1.png" but not available.
--- finished re-building ‘overview.Rmd’

--- re-building ‘questions-and-answers.Rmd’ using rmarkdown
--- finished re-building ‘questions-and-answers.Rmd’

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

Quitting from somatic_mutations.Rmd:120-123 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'maftools'
---
Backtrace:
    ▆
 1. └─base::library(maftools)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'somatic_mutations.Rmd' failed with diagnostics:
there is no package called 'maftools'
--- failed re-building ‘somatic_mutations.Rmd’

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

Error: Vignette re-building failed.
Execution halted