Back to Workflows build report for BioC 3.21

This page was generated on 2025-04-22 16:30 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
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 14/30HostnameOS / ArchINSTALLBUILD
GeoMxWorkflows 1.14.0  (landing page)
Maddy Griswold
Snapshot Date: 2025-04-22 12:45 -0400 (Tue, 22 Apr 2025)
git_url: https://git.bioconductor.org/packages/GeoMxWorkflows
git_branch: RELEASE_3_21
git_last_commit: 0465814
git_last_commit_date: 2025-04-15 10:29:54 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  

BUILD results for GeoMxWorkflows on lconway

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: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GeoMxWorkflows
StartedAt: 2025-04-22 13:03:53 -0400 (Tue, 22 Apr 2025)
EndedAt: 2025-04-22 13:06:35 -0400 (Tue, 22 Apr 2025)
EllapsedTime: 162.9 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 GeoMxWorkflows
###
##############################################################################
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* checking for file ‘GeoMxWorkflows/DESCRIPTION’ ... OK
* preparing ‘GeoMxWorkflows’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GeomxTools_RNA-NGS_Analysis.Rmd’ using rmarkdown
2025-04-22 13:06:02.830 R[76821:731856145] XType: com.apple.fonts is not accessible.
2025-04-22 13:06:02.833 R[76821:731856145] XType: XTFontStaticRegistry is enabled.

Quitting from GeomxTools_RNA-NGS_Analysis.Rmd:900-926 [CVheatmap]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `multiassign()`:
! envir argument is not an environment
---
Backtrace:
    ▆
 1. ├─NanoStringNCTools::assayDataApply(...)
 2. └─NanoStringNCTools::assayDataApply(...)
 3.   └─NanoStringNCTools (local) .local(X, MARGIN, FUN, ...)
 4.     └─NanoStringNCTools:::.apply(...)
 5.       └─Biobase::multiassign(names(.kvs), .kvs, environment(FUN))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GeomxTools_RNA-NGS_Analysis.Rmd' failed with diagnostics:
envir argument is not an environment
--- 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