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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4902
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4692
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4638
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 linkSet on lconway

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

Version: 1.0.0

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

StartedAt: 2025-11-02 17:36:31 -0500 (Sun, 02 Nov 2025)

EndedAt: 2025-11-02 17:37:49 -0500 (Sun, 02 Nov 2025)

EllapsedTime: 77.7 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 linkSet
###
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* checking for file ‘linkSet/DESCRIPTION’ ... OK
* preparing ‘linkSet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘hic_workthrough.Rmd’ using rmarkdown
zcat: can't stat: /private/tmp/RtmptUn7nQ/Rinst3e976e0e1cc4/linkSet/extdata/toyExample.pair.gz (/private/tmp/RtmptUn7nQ/Rinst3e976e0e1cc4/linkSet/extdata/toyExample.pair.gz.Z): No such file or directory
zcat: can't stat: /private/tmp/RtmptUn7nQ/Rinst3e976e0e1cc4/linkSet/extdata/toyExample.pair.gz (/private/tmp/RtmptUn7nQ/Rinst3e976e0e1cc4/linkSet/extdata/toyExample.pair.gz.Z): No such file or directory

Quitting from hic_workthrough.Rmd:94-132 [setup-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readvalidPairs()`:
! File has fewer columns than expected minimum
---
Backtrace:
    ▆
 1. └─linkSet::readvalidPairs(hic_file, format = "pair")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'hic_workthrough.Rmd' failed with diagnostics:
File has fewer columns than expected minimum
--- failed re-building ‘hic_workthrough.Rmd’

--- re-building ‘linkSet.Rmd’ using rmarkdown
2025-11-02 17:37:41.824 R[20034:707812514] XType: com.apple.fonts is not accessible.
2025-11-02 17:37:41.824 R[20034:707812514] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘linkSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted