############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R 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 [2025-03-22 02:01:52] Loaded compoundlist successfully INFO [2025-03-22 02:01:52] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2025-03-22 02:02:00] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-22 02:02:30] msmsWorkflow: Step 3. Aggregate all spectra INFO [2025-03-22 02:02:30] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-22 02:02:31] msmsWorkflow: Done. INFO [2025-03-22 02:04:14] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-22 02:04:22] msmsWorkflow: Done. INFO [2025-03-22 02:04:22] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-22 02:04:23] msmsWorkflow: Done. INFO [2025-03-22 02:04:24] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-22 02:04:53] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2025-03-22 02:04:53] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-22 02:07:37] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2025-03-22 02:07:39] msmsWorkflow: Done. INFO [2025-03-22 02:07:39] 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 [2025-03-22 02:09:39] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-22 02:09:45] msmsWorkflow: Done. INFO [2025-03-22 02:09:49] Loaded compoundlist successfully INFO [2025-03-22 02:09:50] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2025-03-22 02:09:57] msmsWorkflow: Done. INFO [2025-03-22 02:09:57] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-22 02:10:00] msmsWorkflow: Step 3. Aggregate all spectra INFO [2025-03-22 02:10:00] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-22 02:10:01] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-22 02:10:04] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2025-03-22 02:10:04] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-22 02:10:21] msmsWorkflow: Done. INFO [2025-03-22 02:10:22] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2025-03-22 02:10:31] msmsWorkflow: Done. INFO [2025-03-22 02:10:31] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-22 02:10:33] msmsWorkflow: Step 3. Aggregate all spectra INFO [2025-03-22 02:10:33] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2025-03-22 02:10:34] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-22 02:10:37] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2025-03-22 02:10:37] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2025-03-22 02:10:53] msmsWorkflow: Done. INFO [2025-03-22 02:10:54] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2025-03-22 02:10:54] msmsWorkflow: Done. --- finished re-building ‘RMassBankNonstandard.Rmd’ SUMMARY: processing the following file failed: ‘RMassBank.Rmd’ Error: Vignette re-building failed. Execution halted