Multiple platform build/check report for BioC 3.22 - BUILD results for PCAtools on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4726
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4545
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4529
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4554
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*

BUILD results for PCAtools on lconway

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.

raw results

Summary

Package: PCAtools

Version: 2.21.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data PCAtools

StartedAt: 2025-09-15 17:58:06 -0400 (Mon, 15 Sep 2025)

EndedAt: 2025-09-15 18:01:35 -0400 (Mon, 15 Sep 2025)

EllapsedTime: 209.4 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 PCAtools
###
##############################################################################
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* checking for file ‘PCAtools/DESCRIPTION’ ... OK
* preparing ‘PCAtools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘PCAtools.Rmd’ using rmarkdown
2025-09-15 17:59:43.715 R[76947:290318622] XType: com.apple.fonts is not accessible.
2025-09-15 17:59:43.715 R[76947:290318622] XType: XTFontStaticRegistry is enabled.
Warning: ggrepel: 16 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 21 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