Multiple platform build/check report for BioC 3.20 - BUILD results for beadarray 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"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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 beadarray on merida1

To the developers/maintainers of the beadarray package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/beadarray.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: beadarray

Version: 2.56.0

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

StartedAt: 2025-03-31 17:04:13 -0400 (Mon, 31 Mar 2025)

EndedAt: 2025-03-31 17:09:41 -0400 (Mon, 31 Mar 2025)

EllapsedTime: 328.5 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 beadarray
###
##############################################################################
##############################################################################


* checking for file ‘beadarray/DESCRIPTION’ ... OK
* preparing ‘beadarray’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ImageProcessing.Rmd’ using rmarkdown
--- finished re-building ‘ImageProcessing.Rmd’

--- re-building ‘beadarray.Rmd’ using rmarkdown
--- finished re-building ‘beadarray.Rmd’

--- re-building ‘beadlevel.Rmd’ using rmarkdown
--- finished re-building ‘beadlevel.Rmd’

--- re-building ‘beadsummary.Rmd’ using rmarkdown
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33126/matrix/GSE33126_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3658664 bytes (3.5 MB)
==================================================
downloaded 3.5 MB


Quitting from beadsummary.Rmd:426-434 [unnamed-chunk-32]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! vector memory limit of 64.0 Gb reached, see mem.maxVSize()
---
Backtrace:
     ▆
  1. ├─GEOquery::getGEO(filename = filenm)
  2. │ └─GEOquery::parseGEO(...)
  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 'beadsummary.Rmd' failed with diagnostics:
vector memory limit of 64.0 Gb reached, see mem.maxVSize()
--- failed re-building ‘beadsummary.Rmd’

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

Error: Vignette re-building failed.
Execution halted