############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/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 22:41:07] Loaded compoundlist successfully INFO [2024-10-16 22:41:08] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-10-16 22:41:21] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 22:42:23] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-10-16 22:42:24] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 22:42:26] msmsWorkflow: Done. INFO [2024-10-16 22:45:51] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 22:46:07] msmsWorkflow: Done. INFO [2024-10-16 22:46:07] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 22:46:07] msmsWorkflow: Done. INFO [2024-10-16 22:46:09] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 22:47:11] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-10-16 22:47:12] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 22:52:29] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-10-16 22:52:32] msmsWorkflow: Done. INFO [2024-10-16 22:52:33] mbWorkflow: Step 1. Gather info from several databases INFO [2024-10-16 22:52:41] 2819: smiles INFO [2024-10-16 22:52:41] mbWorkflow: Step 2. Export infolist (if required) INFO [2024-10-16 22:52:41] 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 22:52:41] mbWorkflow: Step 1. Gather info from several databases INFO [2024-10-16 22:52:41] mbWorkflow: Step 2. Export infolist (if required) INFO [2024-10-16 22:52:41] No new data added. INFO [2024-10-16 22:52:41] mbWorkflow: Step 3. Data reformatting INFO [2024-10-16 22:52:41] mbWorkflow: Step 4. Spectra compilation INFO [2024-10-16 22:52:41] 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 22:56:32] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 22:56:44] msmsWorkflow: Done. INFO [2024-10-16 22:56:56] Loaded compoundlist successfully INFO [2024-10-16 22:56:56] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-10-16 22:57:13] msmsWorkflow: Done. INFO [2024-10-16 22:57:14] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 22:57:21] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-10-16 22:57:21] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 22:57:24] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 22:57:32] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-10-16 22:57:32] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 22:58:12] msmsWorkflow: Done. INFO [2024-10-16 22:58:14] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-10-16 22:58:33] msmsWorkflow: Done. INFO [2024-10-16 22:58:33] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 22:58:37] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-10-16 22:58:37] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-10-16 22:58:39] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 22:58:45] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-10-16 22:58:45] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-10-16 22:59:23] msmsWorkflow: Done. INFO [2024-10-16 22:59:24] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-10-16 22:59:25] msmsWorkflow: Done. --- finished re-building ‘RMassBankNonstandard.Rmd’ SUMMARY: processing the following file failed: ‘RMassBank.Rmd’ Error: Vignette re-building failed. Execution halted