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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4805
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4539
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BUILD results for MSstatsPTM on kjohnson3

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

Version: 2.13.0

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

StartedAt: 2026-01-20 17:04:44 -0500 (Tue, 20 Jan 2026)

EndedAt: 2026-01-20 17:04:58 -0500 (Tue, 20 Jan 2026)

EllapsedTime: 14.2 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 MSstatsPTM
###
##############################################################################
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* checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK
* preparing ‘MSstatsPTM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘MSstatsPTM_LabelFree_Workflow.Rmd’ using rmarkdown

Quitting from MSstatsPTM_LabelFree_Workflow.Rmd:79-116 [maxq]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
---
Backtrace:
    ▆
 1. └─MSstatsPTM::MaxQtoMSstatsPTMFormat(...)
 2.   └─MSstatsPTM:::MaxQtoMSstatsTMTFormatHelper(...)
 3.     └─MSstatsPTM:::.cleanRawMaxQuantPTM(...)
 4.       └─MSstatsConvert:::.filterFewMeasurements(...)
 5.         ├─...[]
 6.         └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MSstatsPTM_LabelFree_Workflow.Rmd' failed with diagnostics:
attempt access index 8/8 in VECTOR_ELT
--- failed re-building ‘MSstatsPTM_LabelFree_Workflow.Rmd’

--- re-building ‘MSstatsPTM_TMT_Workflow.Rmd’ using rmarkdown

Quitting from MSstatsPTM_TMT_Workflow.Rmd:62-67 [summarize]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
     ▆
  1. └─MSstatsPTM::dataSummarizationPTM_TMT(...)
  2.   └─MSstatsTMT::proteinSummarization(...)
  3.     └─MSstatsTMT:::MSstatsSummarizeTMT(...)
  4.       └─MSstatsTMT:::.summarizeTMT(...)
  5.         └─MSstatsTMT:::.summarizeMSstats(...)
  6.           └─MSstats::dataProcess(...)
  7.             └─MSstats::MSstatsSelectFeatures(...)
  8.               └─MSstats:::.selectTopFeatures(input, top_n)
  9.                 ├─mean_by_feature[, `:=`(feature_rank, rank(-MeanAbundance)), by = "PROTEIN"]
 10.                 └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MSstatsPTM_TMT_Workflow.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘MSstatsPTM_TMT_Workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘MSstatsPTM_LabelFree_Workflow.Rmd’ ‘MSstatsPTM_TMT_Workflow.Rmd’

Error: Vignette re-building failed.
Execution halted