Gilbert Han
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-14 11:36 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 1127/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| linkSet 1.1.0 (landing page) Gilbert Han
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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. |
| Package: linkSet |
| Version: 1.1.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data linkSet |
| StartedAt: 2025-11-13 16:50:53 -0500 (Thu, 13 Nov 2025) |
| EndedAt: 2025-11-13 16:51:21 -0500 (Thu, 13 Nov 2025) |
| EllapsedTime: 28.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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 (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/RtmpMVlfDY/Rinstf2a9614f4526/linkSet/extdata/toyExample.pair.gz (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpMVlfDY/Rinstf2a9614f4526/linkSet/extdata/toyExample.pair.gz.Z): No such file or directory
zcat: can't stat: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpMVlfDY/Rinstf2a9614f4526/linkSet/extdata/toyExample.pair.gz (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpMVlfDY/Rinstf2a9614f4526/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
2025-11-13 16:51:18.492 R[64304:14218025] 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