| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-04 11:32 -0500 (Tue, 04 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" | 4788 |
| 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 1543/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PCAtools 2.23.0 (landing page) Kevin Blighe
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the PCAtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PCAtools.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: PCAtools |
| Version: 2.23.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PCAtools |
| StartedAt: 2025-11-03 19:06:15 -0500 (Mon, 03 Nov 2025) |
| EndedAt: 2025-11-03 19:08:37 -0500 (Mon, 03 Nov 2025) |
| EllapsedTime: 142.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PCAtools
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* checking for file ‘PCAtools/DESCRIPTION’ ... OK
* preparing ‘PCAtools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘PCAtools.Rmd’ using rmarkdown
Warning: ggrepel: 18 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 22 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Quitting from PCAtools.Rmd:406-426 [ex9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'ggalt'
---
Backtrace:
▆
1. ├─PCAtools::biplot(...)
2. └─base::loadNamespace(x)
3. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4. └─base (local) withOneRestart(expr, restarts[[1L]])
5. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'PCAtools.Rmd' failed with diagnostics:
there is no package called 'ggalt'
--- failed re-building ‘PCAtools.Rmd’
SUMMARY: processing the following file failed:
‘PCAtools.Rmd’
Error: Vignette re-building failed.
Execution halted