Multiple platform build/check report for BioC 3.20 - BUILD results for GenomicAlignments on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4688
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4284
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4455
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4404
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 palomino8

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: 1.41.0

Command: chmod a+r GenomicAlignments -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GenomicAlignments

StartedAt: 2024-07-23 18:22:03 -0400 (Tue, 23 Jul 2024)

EndedAt: 2024-07-23 18:24:16 -0400 (Tue, 23 Jul 2024)

EllapsedTime: 133.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   chmod a+r GenomicAlignments -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe 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
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
--- 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

texify: major issue: So far, you have not checked for updates as a MiKTeX user.
--- 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