Multiple platform build/check report for BioC 3.20 - BUILD results for PCAtools on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4756
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4514
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4441
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4406
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 merida1

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: 2.18.0

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

StartedAt: 2025-03-17 21:51:22 -0400 (Mon, 17 Mar 2025)

EndedAt: 2025-03-17 21:54:16 -0400 (Mon, 17 Mar 2025)

EllapsedTime: 173.9 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 PCAtools
###
##############################################################################
##############################################################################


* 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

Quitting from PCAtools.Rmd:161-212 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! vector memory limit of 64.0 Gb reached, see mem.maxVSize()
---
Backtrace:
     ▆
  1. ├─GEOquery::getGEO("GSE2990", GSEMatrix = TRUE, getGPL = FALSE)
  2. │ └─GEOquery:::getAndParseGSEMatrices(...)
  3. │   └─GEOquery:::parseGSEMatrix(...)
  4. │     └─... %>% tidyr::spread(k, v)
  5. ├─tidyr::spread(., k, v)
  6. ├─base::unique(.)
  7. ├─dplyr::mutate(., v = paste0(trimws(v), collapse = ";"))
  8. ├─dplyr::group_by(., accession, k)
  9. ├─dplyr::filter(., !is.na(v))
 10. ├─dplyr::select(., -characteristics)
 11. ├─dplyr::mutate(., k = paste(k, characteristics, sep = ":"))
 12. ├─tidyr::separate(...)
 13. └─tidyr:::separate.data.frame(...)
 14.   └─tidyr:::str_separate(...)
 15.     └─tidyr:::str_split_fixed(...)
 16.       └─tidyr:::simplifyPieces(pieces, n, fill == "left")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'PCAtools.Rmd' failed with diagnostics:
vector memory limit of 64.0 Gb reached, see mem.maxVSize()
--- failed re-building ‘PCAtools.Rmd’

SUMMARY: processing the following file failed:
  ‘PCAtools.Rmd’

Error: Vignette re-building failed.
Execution halted