Build/check report for BioC 3.23 experimental data - BUILD results for RforProteomics on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4813
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 nebbiolo1

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: 1.49.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics

StartedAt: 2026-04-07 11:37:04 -0400 (Tue, 07 Apr 2026)

EndedAt: 2026-04-07 11:42:55 -0400 (Tue, 07 Apr 2026)

EllapsedTime: 350.8 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘RProtVis.Rmd’ using rmarkdown

Quitting from RProtVis.Rmd:642-650 [msnbviz]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'nrow': unused argument (modifications = 57.02146)
---
Backtrace:
     ▆
  1. ├─base::plot(...)
  2. ├─MSnbase::plot(...)
  3. │ └─MSnbase:::plotSpectrumVsSpectrum(list(x, y), ...)
  4. │   └─MSnbase:::.plotSpectrumVsSpectrum(spectra, common = common, ...)
  5. │     └─MSnbase:::.plotSingleSpectrum(...)
  6. │       ├─base::nrow(fragments)
  7. │       └─MSnbase:::calculateFragments_Spectrum2(...)
  8. │         ├─ProtGenerics::calculateFragments(sequence, ...)
  9. │         └─PSMatch::calculateFragments(sequence, ...)
 10. └─base::.handleSimpleError(...)
 11.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'nrow': unused argument (modifications = 57.02146)
--- failed re-building ‘RProtVis.Rmd’

--- re-building ‘RforProteomics.Rmd’ using rmarkdown
starting worker pid=2077958 on localhost:11611 at 11:38:53.722
starting worker pid=2077957 on localhost:11611 at 11:38:53.727
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!
trying URL 'http://www.uniprot.org/uniprot/P00924.fasta'
Content type 'text/plain;format=fasta' length 562 bytes
==================================================
downloaded 562 bytes

--- finished re-building ‘RforProteomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted