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### Running command:
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###   chmod a+r RMassBank -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RMassBank
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* checking for file 'RMassBank/DESCRIPTION' ... OK
* preparing 'RMassBank':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'RMassBank.Rmd' using rmarkdown
INFO [2025-02-12 21:22:43] Loaded compoundlist successfully
INFO [2025-02-12 21:22:43] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================================================| 100%INFO [2025-02-12 21:22:51] msmsWorkflow: Step 2. First analysis pre recalibration

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INFO [2025-02-12 21:23:26] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-02-12 21:23:26] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-02-12 21:23:27] msmsWorkflow: Done.
INFO [2025-02-12 21:24:59] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-02-12 21:25:06] msmsWorkflow: Done.
INFO [2025-02-12 21:25:06] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-02-12 21:25:06] msmsWorkflow: Done.
INFO [2025-02-12 21:25:07] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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INFO [2025-02-12 21:25:36] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-02-12 21:25:36] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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INFO [2025-02-12 21:27:57] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2025-02-12 21:27:58] msmsWorkflow: Done.
INFO [2025-02-12 21:27:59] mbWorkflow: Step 1. Gather info from several databases

Quitting from lines 433-434 [unnamed-chunk-22] (RMassBank.Rmd)
Error: processing vignette 'RMassBank.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'RMassBank.Rmd'

--- re-building 'RMassBankNonstandard.Rmd' using rmarkdown
INFO [2025-02-12 21:29:27] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-02-12 21:29:31] msmsWorkflow: Done.
INFO [2025-02-12 21:29:41] Loaded compoundlist successfully
INFO [2025-02-12 21:29:41] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================================================| 100%INFO [2025-02-12 21:29:48] msmsWorkflow: Done.
INFO [2025-02-12 21:29:49] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================================================| 100%
INFO [2025-02-12 21:29:51] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-02-12 21:29:51] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-02-12 21:29:52] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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  |================================================================| 100%
INFO [2025-02-12 21:29:54] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-02-12 21:29:54] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================================================| 100%
INFO [2025-02-12 21:30:10] msmsWorkflow: Done.
INFO [2025-02-12 21:30:10] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================================================| 100%INFO [2025-02-12 21:30:19] msmsWorkflow: Done.
INFO [2025-02-12 21:30:19] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================================================| 100%
INFO [2025-02-12 21:30:21] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-02-12 21:30:21] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-02-12 21:30:21] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2025-02-12 21:30:24] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-02-12 21:30:24] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================================================| 100%
INFO [2025-02-12 21:30:38] msmsWorkflow: Done.
INFO [2025-02-12 21:30:38] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2025-02-12 21:30:39] msmsWorkflow: Done.
--- finished re-building 'RMassBankNonstandard.Rmd'

SUMMARY: processing the following file failed:
  'RMassBank.Rmd'

Error: Vignette re-building failed.
Execution halted