Back to Workflows build report for BioC 3.23

This page was generated on 2025-12-16 16:30 -0500 (Tue, 16 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4875
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4623
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 13/28HostnameOS / ArchINSTALLBUILD
GeoMxWorkflows 1.17.0  (landing page)
Maddy Griswold
Snapshot Date: 2025-12-16 12:45 -0500 (Tue, 16 Dec 2025)
git_url: https://git.bioconductor.org/packages/GeoMxWorkflows
git_branch: devel
git_last_commit: c01ff41
git_last_commit_date: 2025-10-29 09:47:36 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK  

BUILD results for GeoMxWorkflows on nebbiolo1

To the developers/maintainers of the GeoMxWorkflows package:
- 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: GeoMxWorkflows
Version: 1.17.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GeoMxWorkflows
StartedAt: 2025-12-16 13:05:02 -0500 (Tue, 16 Dec 2025)
EndedAt: 2025-12-16 13:08:07 -0500 (Tue, 16 Dec 2025)
EllapsedTime: 185.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GeoMxWorkflows
###
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* checking for file ‘GeoMxWorkflows/DESCRIPTION’ ... OK
* preparing ‘GeoMxWorkflows’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘GeomxTools_RNA-NGS_Analysis.Rmd’ using rmarkdown

Quitting from GeomxTools_RNA-NGS_Analysis.Rmd:969-1009 [deNativeComplex]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.check_ncores()`:
! 72 simultaneous processes spawned
---
Backtrace:
    ▆
 1. └─GeomxTools::mixedModelDE(...)
 2.   └─parallel::makeCluster(getOption("cl.cores", nCores))
 3.     └─parallel::makePSOCKcluster(names = spec, ...)
 4.       └─parallel:::.check_ncores(length(names))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GeomxTools_RNA-NGS_Analysis.Rmd' failed with diagnostics:
72 simultaneous processes spawned
--- failed re-building ‘GeomxTools_RNA-NGS_Analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘GeomxTools_RNA-NGS_Analysis.Rmd’

Error: Vignette re-building failed.
Execution halted