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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 Spectra
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* checking for file ‘Spectra/DESCRIPTION’ ... OK
* preparing ‘Spectra’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MsBackend.Rmd’ using rmarkdown
--- finished re-building ‘MsBackend.Rmd’
--- re-building ‘Spectra-large-scale.Rmd’ using rmarkdown
--- finished re-building ‘Spectra-large-scale.Rmd’
--- re-building ‘Spectra.Rmd’ using rmarkdown
2025-08-29 17:45:14.191 R[57085:122964104] XType: Using static font registry.
Quitting from Spectra.Rmd:1151-1154 [export]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in .local(object, file, ...): Error checking parameter 'header': 'x' is missing one or more required columns: seqNum, acquisitionNum, msLevel, polarity, peaksCount, totIonCurrent, retentionTime, basePeakMZ, basePeakIntensity, collisionEnergy, electronBeamEnergy, ionisationEnergy, lowMZ, highMZ, precursorScanNum, precursorMZ, precursorCharge, precursorIntensity, mergedScan, mergedResultScanNum, mergedResultStartScanNum, mergedResultEndScanNum, injectionTime, filterString, centroided, ionMobilityDriftTime, isolationWindowTargetMZ, isolationWindowLowerOffset, isolationWindowUpperOffset, scanWindowLowerLimit, scanWindowUpperLimit
---
Backtrace:
▆
1. ├─Spectra::export(sps, MsBackendMzR(), file = fl)
2. └─Spectra::export(sps, MsBackendMzR(), file = fl)
3. └─Spectra (local) .local(object, ...)
4. ├─Spectra::export(backend, object, ...)
5. └─Spectra::export(backend, object, ...)
6. └─Spectra (local) .local(object, ...)
7. ├─BiocParallel::bpmapply(...)
8. └─BiocParallel::bpmapply(...)
9. ├─BiocParallel::bplapply(...)
10. └─BiocParallel::bplapply(...)
11. └─BiocParallel:::.bpinit(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Spectra.Rmd' failed with diagnostics:
BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in .local(object, file, ...): Error checking parameter 'header': 'x' is missing one or more required columns: seqNum, acquisitionNum, msLevel, polarity, peaksCount, totIonCurrent, retentionTime, basePeakMZ, basePeakIntensity, collisionEnergy, electronBeamEnergy, ionisationEnergy, lowMZ, highMZ, precursorScanNum, precursorMZ, precursorCharge, precursorIntensity, mergedScan, mergedResultScanNum, mergedResultStartScanNum, mergedResultEndScanNum, injectionTime, filterString, centroided, ionMobilityDriftTime, isolationWindowTargetMZ, isolationWindowLowerOffset, isolationWindowUpperOffset, scanWindowLowerLimit, scanWindowUpperLimit
--- failed re-building ‘Spectra.Rmd’
SUMMARY: processing the following file failed:
‘Spectra.Rmd’
Error: Vignette re-building failed.
Execution halted