Build/check report for BioC 3.22 experimental data - BUILD results for RforProteomics on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4815
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 RforProteomics on nebbiolo2

To the developers/maintainers of the RforProteomics 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: RforProteomics

Version: 1.47.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics

StartedAt: 2025-08-07 11:36:41 -0400 (Thu, 07 Aug 2025)

EndedAt: 2025-08-07 11:41:01 -0400 (Thu, 07 Aug 2025)

EllapsedTime: 259.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics
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* checking for file ‘RforProteomics/DESCRIPTION’ ... OK
* preparing ‘RforProteomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RProtVis.Rmd’ using rmarkdown
--- finished re-building ‘RProtVis.Rmd’

--- re-building ‘RforProteomics.Rmd’ using rmarkdown
starting worker pid=4000643 on localhost:11531 at 11:38:40.893
starting worker pid=4000642 on localhost:11531 at 11:38:40.913
Loading required package: mzID
Loading required package: mzID
loaded mzID and set parent environment
loaded mzID and set parent environment
reading 55merge_omssa.mzid...
reading 55merge_tandem.mzid...
55merge_omssa.mzid DONE!
55merge_tandem.mzid DONE!

Quitting from RforProteomics.Rmd:553-555 [mzp]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `data.frame()`:
! arguments imply differing number of rows: 23, 21
---
Backtrace:
     ▆
  1. ├─MSnbase::plotMzDelta(rawms, reporters = TMT6, verbose = FALSE)
  2. └─MSnbase::plotMzDelta(rawms, reporters = TMT6, verbose = FALSE)
  3.   └─MSnbase (local) .local(object, ...)
  4.     └─MSnbase:::plotMzDelta_MSnExp(...)
  5.       └─BiocGenerics::cbind(PSMatch::getAminoAcids(), x_offset, y_offset)
  6.         ├─BiocGenerics (local) standardGeneric("cbind")
  7.         │ ├─BiocGenerics::eval(mc, env)
  8.         │ └─base::eval(mc, env)
  9.         │   └─base::eval(mc, env)
 10.         └─base::cbind(...)
 11.           └─base::cbind(deparse.level, ...)
 12.             └─base::data.frame(..., check.names = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RforProteomics.Rmd' failed with diagnostics:
arguments imply differing number of rows: 23, 21
--- failed re-building ‘RforProteomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted