Multiple platform build/check report for BioC 3.21 - BUILD results for dce on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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 dce on kjohnson3

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

Version: 1.16.0

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

StartedAt: 2025-04-21 16:06:00 -0400 (Mon, 21 Apr 2025)

EndedAt: 2025-04-21 16:07:01 -0400 (Mon, 21 Apr 2025)

EllapsedTime: 60.6 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 dce
###
##############################################################################
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* checking for file ‘dce/DESCRIPTION’ ... OK
* preparing ‘dce’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘dce.Rmd’ using rmarkdown
2025-04-21 16:06:27.866 R[38831:999745152] XType: Using static font registry.
INFO [2025-04-21 16:06:47] Processing kegg

Quitting from dce.Rmd:241-243 [unnamed-chunk-16]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dce()`:
! Not all nodes have expression vector in WT data
---
Backtrace:
    ▆
 1. ├─dce::dce(brca_pathway, t(brca_wt), t(brca_mt))
 2. └─dce::dce(brca_pathway, t(brca_wt), t(brca_mt))
 3.   ├─dce::dce(...)
 4.   └─dce::dce(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'dce.Rmd' failed with diagnostics:
Not all nodes have expression vector in WT data
--- failed re-building ‘dce.Rmd’

--- re-building ‘pathway_databases.Rmd’ using rmarkdown
INFO [2025-04-21 16:06:50] Processing pathbank
INFO [2025-04-21 16:06:58] Processing kegg
--- finished re-building ‘pathway_databases.Rmd’

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

Error: Vignette re-building failed.
Execution halted