Multiple platform build/check report for BioC 3.21 - BUILD results for GenomicAlignments on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4609
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4393
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	3839
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	3835
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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 GenomicAlignments on kjohnson3

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

Version: 1.43.0

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

StartedAt: 2025-01-23 16:00:01 -0500 (Thu, 23 Jan 2025)

EndedAt: 2025-01-23 16:00:38 -0500 (Thu, 23 Jan 2025)

EllapsedTime: 36.4 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 GenomicAlignments
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* checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK
* preparing ‘GenomicAlignments’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘WorkingWithAlignedNucleotides.Rmd’ using rmarkdown
--- finished re-building ‘WorkingWithAlignedNucleotides.Rmd’

--- re-building ‘GenomicAlignmentsIntroduction.Rnw’ using Sweave
--- finished re-building ‘GenomicAlignmentsIntroduction.Rnw’

--- re-building ‘OverlapEncodings.Rnw’ using Sweave
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: ‘rtracklayer’

The following object is masked from ‘package:BiocIO’:

    FileForFormat

--- finished re-building ‘OverlapEncodings.Rnw’

--- re-building ‘summarizeOverlaps.Rnw’ using Sweave

Error: processing vignette 'summarizeOverlaps.Rnw' failed with diagnostics:
 chunk 3 (label = firstExample) 
Error in library(DESeq2) : there is no package called ‘DESeq2’

--- failed re-building ‘summarizeOverlaps.Rnw’

SUMMARY: processing the following file failed:
  ‘summarizeOverlaps.Rnw’

Error: Vignette re-building failed.
Execution halted