Multiple platform build/check report for BioC 3.22 - BUILD results for GenomicDataCommons on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4734
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4496
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4534
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4476
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4410
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: 1.33.0

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

StartedAt: 2025-04-29 16:24:52 -0400 (Tue, 29 Apr 2025)

EndedAt: 2025-04-29 16:25:35 -0400 (Tue, 29 Apr 2025)

EllapsedTime: 42.4 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 GenomicDataCommons
###
##############################################################################
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* checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK
* preparing ‘GenomicDataCommons’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘overview.Rmd’ using rmarkdown
2025-04-29 16:25:08.378 R[46470:1052845927] XType: Using static font registry.
--- 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