Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-04-09 11:55 -0400 (Wed, 09 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 beta (2025-04-02 r88102) -- "How About a Twenty-Six" 4737
palomino8Windows Server 2022 Datacenterx644.5.0 RC (2025-04-03 r88103 ucrt) -- "How About a Twenty-Six" 4524
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 519/2335HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dce 1.15.1  (landing page)
Kim Philipp Jablonski
Snapshot Date: 2025-04-08 13:00 -0400 (Tue, 08 Apr 2025)
git_url: https://git.bioconductor.org/packages/dce
git_branch: devel
git_last_commit: 0c098ac
git_last_commit_date: 2024-12-17 10:47:08 -0400 (Tue, 17 Dec 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped

BUILD results for dce on nebbiolo2

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: 1.15.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 dce
StartedAt: 2025-04-08 16:58:09 -0400 (Tue, 08 Apr 2025)
EndedAt: 2025-04-08 17:00:07 -0400 (Tue, 08 Apr 2025)
EllapsedTime: 118.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 dce
###
##############################################################################
##############################################################################


* 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
INFO [2025-04-08 16:59:41] 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 [2025-04-08 16:59:47] Processing pathbank
INFO [2025-04-08 17:00:03] Processing kegg
--- finished re-building ‘pathway_databases.Rmd’

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

Error: Vignette re-building failed.
Execution halted