Multiple platform build/check report for BioC 3.22 - BUILD results for VariantAnnotation on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4514
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4361
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	1031
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4491
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4496
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 VariantAnnotation on lconway

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

Version: 1.55.0

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

StartedAt: 2025-06-19 20:27:09 -0400 (Thu, 19 Jun 2025)

EndedAt: 2025-06-19 20:29:07 -0400 (Thu, 19 Jun 2025)

EllapsedTime: 118.9 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 VariantAnnotation
###
##############################################################################
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* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* preparing ‘VariantAnnotation’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘VariantAnnotation.Rmd’ using rmarkdown
2025-06-19 20:28:28.881 R[73781:1932338] XType: com.apple.fonts is not accessible.
2025-06-19 20:28:28.882 R[73781:1932338] XType: XTFontStaticRegistry is enabled.

Quitting from VariantAnnotation.Rmd:182-189 [examine_ggplot2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'ggplot2'
---
Backtrace:
    ▆
 1. └─base::library(ggplot2)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'VariantAnnotation.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘VariantAnnotation.Rmd’

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

Quitting from ensemblVEP.Rmd:66-69 [doj1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'rjsoncons'
---
Backtrace:
    ▆
 1. └─base::library(rjsoncons)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘filterVcf.Rmd’ using rmarkdown
--- finished re-building ‘filterVcf.Rmd’

SUMMARY: processing the following files failed:
  ‘VariantAnnotation.Rmd’ ‘ensemblVEP.Rmd’

Error: Vignette re-building failed.
Execution halted