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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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

Package 1121/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
linkSet 0.99.19  (landing page)
Gilbert Han
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/linkSet
git_branch: devel
git_last_commit: 66d472d
git_last_commit_date: 2025-07-23 09:19:11 -0400 (Wed, 23 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  YES
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped


BUILD results for linkSet on kjohnson3

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: 0.99.19
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data linkSet
StartedAt: 2025-08-08 16:47:09 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 16:48:18 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 68.8 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 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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE950Pe/Rinst142246a93ab68/linkSet/extdata/toyExample.pair.gz (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE950Pe/Rinst142246a93ab68/linkSet/extdata/toyExample.pair.gz.Z): No such file or directory
zcat: can't stat: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE950Pe/Rinst142246a93ab68/linkSet/extdata/toyExample.pair.gz (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpE950Pe/Rinst142246a93ab68/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
2025-08-08 16:47:34.014 R[84849:486614564] XType: Using static font registry.
--- finished re-building ‘linkSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted