Multiple platform build/check report for BioC 3.23 - BUILD results for msPurity on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4958
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4705
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 msPurity on kjohnson3

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

Version: 1.37.3

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

StartedAt: 2026-04-23 17:13:23 -0400 (Thu, 23 Apr 2026)

EndedAt: 2026-04-23 17:16:16 -0400 (Thu, 23 Apr 2026)

EllapsedTime: 172.8 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data msPurity
###
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* checking for file ‘msPurity/DESCRIPTION’ ... OK
* preparing ‘msPurity’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd’ using rmarkdown
Sizes of mz and intensity arrays don't match.

Quitting from msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd:124-127 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `object@backend$getPeakList()`:
! dims [product 4516] do not match the length of object [2258]
---
Backtrace:
     ▆
  1. └─msPurity::createDatabase(...)
  2.   └─msPurity:::export2sqlite(...)
  3.     └─msPurity:::getScanPeaks(pa)
  4.       └─plyr::ddply(filedf, ~fileid, scanPeaksFromfiledf)
  5.         └─plyr::ldply(...)
  6.           └─plyr::llply(...)
  7.             ├─plyr:::loop_apply(n, do.ply)
  8.             └─plyr (local) `<fn>`(3L)
  9.               └─msPurity (local) .fun(piece, ...)
 10.                 ├─mzR::peaks(mr)
 11.                 └─mzR::peaks(mr)
 12.                   └─mzR (local) .local(object, ...)
 13.                     └─mzR:::.peaks(object, scans)
 14.                       └─object@backend$getPeakList(scans)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd' failed with diagnostics:
dims [product 4516] do not match the length of object [2258]
--- failed re-building ‘msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd’

--- re-building ‘msPurity-spectral-database-vignette.Rmd’ using rmarkdown
--- finished re-building ‘msPurity-spectral-database-vignette.Rmd’

--- re-building ‘msPurity-vignette.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
--- finished re-building ‘msPurity-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted