############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r RMassBank -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RMassBank ### ############################################################################## ############################################################################## * 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 [2025-03-21 21:28:41] Loaded compoundlist successfully INFO [2025-03-21 21:28:41] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2025-03-21 21:28:49] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-21 21:29:24] msmsWorkflow: Step 3. Aggregate all spectra INFO [2025-03-21 21:29:25] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-21 21:29:26] msmsWorkflow: Done. INFO [2025-03-21 21:30:58] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-21 21:31:05] msmsWorkflow: Done. INFO [2025-03-21 21:31:05] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-21 21:31:05] msmsWorkflow: Done. INFO [2025-03-21 21:31:06] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-21 21:31:38] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2025-03-21 21:31:39] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-21 21:33:58] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2025-03-21 21:33:59] msmsWorkflow: Done. INFO [2025-03-21 21:34:00] mbWorkflow: Step 1. Gather info from several databases Quitting from RMassBank.Rmd:432-434 [unnamed-chunk-22] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `strsplit(inchikey, "=", fixed = TRUE)[[1]][[2]]`: ! subscript out of bounds --- Backtrace: ▆ 1. └─RMassBank::mbWorkflow(mb, infolist_path = "./Narcotics_infolist.csv") 2. ├─BiocGenerics::lapply(...) 3. └─base::lapply(...) 4. └─RMassBank (local) FUN(X[[i]], ...) 5. └─RMassBank::gatherData(id) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'RMassBank.Rmd' failed with diagnostics: subscript out of bounds --- failed re-building 'RMassBank.Rmd' --- re-building 'RMassBankNonstandard.Rmd' using rmarkdown INFO [2025-03-21 21:35:36] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-21 21:35:41] msmsWorkflow: Done. INFO [2025-03-21 21:35:45] Loaded compoundlist successfully INFO [2025-03-21 21:35:46] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2025-03-21 21:35:52] msmsWorkflow: Done. INFO [2025-03-21 21:35:52] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-21 21:35:55] msmsWorkflow: Step 3. Aggregate all spectra INFO [2025-03-21 21:35:55] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-21 21:35:55] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-21 21:35:58] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2025-03-21 21:35:58] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-21 21:36:14] msmsWorkflow: Done. INFO [2025-03-21 21:36:15] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2025-03-21 21:36:23] msmsWorkflow: Done. INFO [2025-03-21 21:36:23] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-21 21:36:25] msmsWorkflow: Step 3. Aggregate all spectra INFO [2025-03-21 21:36:25] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-21 21:36:25] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-21 21:36:29] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2025-03-21 21:36:29] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-21 21:36:46] msmsWorkflow: Done. INFO [2025-03-21 21:36:47] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2025-03-21 21:36:48] msmsWorkflow: Done. --- finished re-building 'RMassBankNonstandard.Rmd' SUMMARY: processing the following file failed: 'RMassBank.Rmd' Error: Vignette re-building failed. Execution halted