Multiple platform build/check report for BioC 3.23 - BUILD results for MSstatsBig 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"	4808
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4542
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BUILD results for MSstatsBig on kjohnson3

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

Version: 1.9.1

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

StartedAt: 2026-01-21 17:05:12 -0500 (Wed, 21 Jan 2026)

EndedAt: 2026-01-21 17:05:20 -0500 (Wed, 21 Jan 2026)

EllapsedTime: 7.1 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 MSstatsBig
###
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* checking for file ‘MSstatsBig/DESCRIPTION’ ... OK
* preparing ‘MSstatsBig’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘MSstatsBig_Workflow.Rmd’ using rmarkdown
Warning in in_dir(input_dir(), expr) :
  You changed the working directory to /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpPo4WD2 (probably via setwd()). It will be restored to /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpv2kVxx/Rbuild88e9610bf367/MSstatsBig/vignettes. See the Note section in ?knitr::knit

Quitting from MSstatsBig_Workflow.Rmd:87-106 [msstats_workflow]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 13/13 in VECTOR_ELT
---
Backtrace:
    ▆
 1. └─MSstats::dataProcess(converted_data, use_log_file = FALSE)
 2.   └─MSstats::MSstatsPrepareForDataProcess(raw, logTrans, fix_missing)
 3.     ├─MSstats:::.checkDataValidity(input, fix_missing = fix_missing)
 4.     └─MSstats:::.checkDataValidity(input, fix_missing = fix_missing)
 5.       └─MSstats (local) .local(input, ...)
 6.         └─MSstatsConvert::MSstatsBalancedDesign(...)
 7.           └─MSstatsConvert:::.filterFewMeasurements(...)
 8.             ├─...[]
 9.             └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MSstatsBig_Workflow.Rmd' failed with diagnostics:
attempt access index 13/13 in VECTOR_ELT
--- failed re-building ‘MSstatsBig_Workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted