Back to Workflows build report for BioC 3.22

This page was generated on 2025-04-25 16:30 -0400 (Fri, 25 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4722
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4494
lconwaymacOS 12.7.1 Montereyx86_644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4520
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 27/29HostnameOS / ArchINSTALLBUILD
spicyWorkflow 1.9.0  (landing page)
SOMS Maintainer
Snapshot Date: 2025-04-25 12:45 -0400 (Fri, 25 Apr 2025)
git_url: https://git.bioconductor.org/packages/spicyWorkflow
git_branch: devel
git_last_commit: 517dc71
git_last_commit_date: 2025-04-15 10:30:35 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  

BUILD results for spicyWorkflow on lconway

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: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data spicyWorkflow
StartedAt: 2025-04-25 13:09:27 -0400 (Fri, 25 Apr 2025)
EndedAt: 2025-04-25 13:30:59 -0400 (Fri, 25 Apr 2025)
EllapsedTime: 1291.4 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 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
2025-04-25 13:19:36.776 R[47079:760470705] XType: com.apple.fonts is not accessible.
2025-04-25 13:19:36.776 R[47079:760470705] XType: XTFontStaticRegistry is enabled.

Quitting from spicyWorkflow.Rmd:582-593 [unnamed-chunk-27]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `FUN()`:
! object 'r' not found
---
Backtrace:
    ▆
 1. └─spicyR::spicy(...)
 2.   └─spicyR::getPairwise(...)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'spicyWorkflow.Rmd' failed with diagnostics:
object 'r' not found
--- failed re-building ‘spicyWorkflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted