Travis Blimkie
| Snapshot Date: 2026-03-09 13:40 -0400 (Mon, 09 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/pathlinkR |
| git_branch: devel |
| git_last_commit: bac4a67 |
| git_last_commit_date: 2025-12-31 14:19:45 -0400 (Wed, 31 Dec 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-10 11:33 -0400 (Tue, 10 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4522 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 2847 |
| 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 1558/2360 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pathlinkR 1.7.21 (landing page) Travis Blimkie
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for pathlinkR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the pathlinkR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathlinkR.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: pathlinkR |
| Version: 1.7.21 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pathlinkR |
| StartedAt: 2026-03-09 15:39:14 -0400 (Mon, 09 Mar 2026) |
| EndedAt: 2026-03-09 15:39:24 -0400 (Mon, 09 Mar 2026) |
| EllapsedTime: 10.1 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 pathlinkR
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* checking for file ‘pathlinkR/DESCRIPTION’ ... OK
* preparing ‘pathlinkR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘pathlinkR.Rmd’ using rmarkdown
Failed with error: 'there is no package called 'DESeq2''
Quitting from pathlinkR.Rmd:67-77 [datasets_and_preliminary_volcano_plot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'DESeq2'
---
Backtrace:
▆
1. ├─knitr::kable(head(exampleDESeqResults[[1]]))
2. ├─utils::head(exampleDESeqResults[[1]])
3. └─methods:::.extendsForS3(`<chr>`)
4. └─methods::extends(Class, maybe = FALSE)
5. └─methods::getClassDef(class1)
6. └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'pathlinkR.Rmd' failed with diagnostics:
unable to load required package 'DESeq2'
--- failed re-building ‘pathlinkR.Rmd’
SUMMARY: processing the following file failed:
‘pathlinkR.Rmd’
Error: Vignette re-building failed.
Execution halted