Back to Workflows build report for BioC 3.21

This page was generated on 2025-09-19 16:30 -0400 (Fri, 19 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
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 28/30HostnameOS / ArchINSTALLBUILD
spicyWorkflow 1.8.0  (landing page)
SOMS Maintainer
Snapshot Date: 2025-09-19 12:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/spicyWorkflow
git_branch: RELEASE_3_21
git_last_commit: 2acaa1c
git_last_commit_date: 2025-04-15 10:30:35 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  

BUILD results for spicyWorkflow on merida1

To the developers/maintainers of the spicyWorkflow 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: spicyWorkflow
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data spicyWorkflow
StartedAt: 2025-09-19 13:38:39 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 15:10:24 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 5505.8 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 spicyWorkflow
###
##############################################################################
##############################################################################


* checking for file ‘spicyWorkflow/DESCRIPTION’ ... OK
* preparing ‘spicyWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘spicyWorkflow.Rmd’ using rmarkdown
2025-09-19 14:16:37.518 R[91856:411687036] XType: com.apple.fonts is not accessible.
2025-09-19 14:16:37.519 R[91856:411687036] XType: XTFontStaticRegistry is enabled.

Quitting from spicyWorkflow.Rmd:693-703 [unnamed-chunk-36]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 21 rows, data has 155876
---
Backtrace:
    ▆
 1. └─Statial::getDistances(...)
 2.   ├─base::`$<-`(`*tmp*`, "cellID", value = `<chr>`)
 3.   └─base::`$<-.data.frame`(`*tmp*`, "cellID", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'spicyWorkflow.Rmd' failed with diagnostics:
replacement has 21 rows, data has 155876
--- failed re-building ‘spicyWorkflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted