############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/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 [2024-10-16 20:29:54] Loaded compoundlist successfully INFO [2024-10-16 20:29:54] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-10-16 20:29:59] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 20:30:18] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-10-16 20:30:18] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 20:30:19] msmsWorkflow: Done. INFO [2024-10-16 20:31:20] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 20:31:26] msmsWorkflow: Done. INFO [2024-10-16 20:31:26] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 20:31:26] msmsWorkflow: Done. INFO [2024-10-16 20:31:27] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 20:31:45] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-10-16 20:31:45] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 20:33:22] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-10-16 20:33:23] msmsWorkflow: Done. INFO [2024-10-16 20:33:23] mbWorkflow: Step 1. Gather info from several databases INFO [2024-10-16 20:33:26] 2819: smiles INFO [2024-10-16 20:33:26] mbWorkflow: Step 2. Export infolist (if required) INFO [2024-10-16 20:33:26] The file ./Narcotics_infolist.csv was generated with new compound information. Please check and edit the table, and add it to your infolist folder. INFO [2024-10-16 20:33:26] mbWorkflow: Step 1. Gather info from several databases INFO [2024-10-16 20:33:26] mbWorkflow: Step 2. Export infolist (if required) INFO [2024-10-16 20:33:26] No new data added. INFO [2024-10-16 20:33:26] mbWorkflow: Step 3. Data reformatting INFO [2024-10-16 20:33:26] mbWorkflow: Step 4. Spectra compilation INFO [2024-10-16 20:33:26] Compiling: 1-(3-Chlorophenyl)piperazine Quitting from lines 471-472 [unnamed-chunk-25] (RMassBank.Rmd) Error: processing vignette 'RMassBank.Rmd' failed with diagnostics: is.environment(.envir) is not TRUE --- failed re-building ‘RMassBank.Rmd’ --- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown INFO [2024-10-16 20:34:29] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 20:34:33] msmsWorkflow: Done. INFO [2024-10-16 20:34:36] Loaded compoundlist successfully INFO [2024-10-16 20:34:36] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-10-16 20:34:41] msmsWorkflow: Done. INFO [2024-10-16 20:34:41] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 20:34:43] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-10-16 20:34:43] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 20:34:43] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 20:34:45] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-10-16 20:34:45] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 20:34:55] msmsWorkflow: Done. INFO [2024-10-16 20:34:55] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-10-16 20:35:01] msmsWorkflow: Done. INFO [2024-10-16 20:35:01] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 20:35:03] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-10-16 20:35:03] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 20:35:03] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 20:35:05] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-10-16 20:35:05] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 20:35:14] msmsWorkflow: Done. INFO [2024-10-16 20:35:15] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-10-16 20:35:15] msmsWorkflow: Done. --- finished re-building ‘RMassBankNonstandard.Rmd’ SUMMARY: processing the following file failed: ‘RMassBank.Rmd’ Error: Vignette re-building failed. Execution halted