Back to Multiple platform build/check report for BioC 3.23:   simplified   long
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

This page was generated on 2026-03-14 11:34 -0400 (Sat, 14 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" 4837
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" 4050
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 1147/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
linkSet 1.1.0  (landing page)
Gilbert Han
Snapshot Date: 2026-03-13 13:40 -0400 (Fri, 13 Mar 2026)
git_url: https://git.bioconductor.org/packages/linkSet
git_branch: devel
git_last_commit: bdadbdd
git_last_commit_date: 2025-10-29 11:37:12 -0400 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  NO, package depends on 'Organism.dplyr' which is not available
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
See other builds for linkSet in R Universe.

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: 1.1.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data linkSet
StartedAt: 2026-03-13 16:19:37 -0400 (Fri, 13 Mar 2026)
EndedAt: 2026-03-13 16:20:06 -0400 (Fri, 13 Mar 2026)
EllapsedTime: 29.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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


* checking for file ‘linkSet/DESCRIPTION’ ... OK
* preparing ‘linkSet’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘hic_workthrough.Rmd’ using rmarkdown
zcat: can't stat: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpY7GtAa/Rinst75d7e310d22/linkSet/extdata/toyExample.pair.gz (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpY7GtAa/Rinst75d7e310d22/linkSet/extdata/toyExample.pair.gz.Z): No such file or directory
zcat: can't stat: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpY7GtAa/Rinst75d7e310d22/linkSet/extdata/toyExample.pair.gz (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpY7GtAa/Rinst75d7e310d22/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 `data.table::fread()`:
! External command failed with exit code 1. This can happen when the disk is full in the temporary directory ('/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4UHLuy'). See ?fread for the tmpdir argument.
---
Backtrace:
    ▆
 1. └─linkSet::readvalidPairs(hic_file, format = "pair")
 2.   └─data.table::fread(...)
 3.     └─data.table:::stopf(...)
 4.       └─data.table:::raise_condition(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'hic_workthrough.Rmd' failed with diagnostics:
External command failed with exit code 1. This can happen when the disk is full in the temporary directory ('/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4UHLuy'). See ?fread for the tmpdir argument.
--- failed re-building ‘hic_workthrough.Rmd’

--- re-building ‘linkSet.Rmd’ using rmarkdown
2026-03-13 16:20:01.954 R[31521:148059096] 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