##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Spectra
###
##############################################################################
##############################################################################


* 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 18:38:46.417 R[26366:152331601] XType: com.apple.fonts is not accessible.
2025-08-29 18:38:46.417 R[26366:152331601] XType: XTFontStaticRegistry is enabled.

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