############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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 [2024-08-14 19:16:54] Loaded compoundlist successfully INFO [2024-08-14 19:16:54] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-08-14 19:17:00] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 19:17:19] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-08-14 19:17:19] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 19:17:19] msmsWorkflow: Done. INFO [2024-08-14 19:18:20] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 19:18:25] msmsWorkflow: Done. INFO [2024-08-14 19:18:25] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 19:18:26] msmsWorkflow: Done. INFO [2024-08-14 19:18:26] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 19:18:44] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-08-14 19:18:44] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 19:20:21] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-08-14 19:20:22] msmsWorkflow: Done. INFO [2024-08-14 19:20:22] 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: Opening and ending tag mismatch: META line 2 and HEAD [76] --- failed re-building ‘RMassBank.Rmd’ --- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown INFO [2024-08-14 19:21:31] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 19:21:35] msmsWorkflow: Done. INFO [2024-08-14 19:21:38] Loaded compoundlist successfully INFO [2024-08-14 19:21:38] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-08-14 19:21:43] msmsWorkflow: Done. INFO [2024-08-14 19:21:43] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 19:21:45] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-08-14 19:21:45] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 19:21:45] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 19:21:47] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-08-14 19:21:47] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 19:21:57] msmsWorkflow: Done. INFO [2024-08-14 19:21:57] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-08-14 19:22:04] msmsWorkflow: Done. INFO [2024-08-14 19:22:04] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 19:22:05] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-08-14 19:22:05] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 19:22:05] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 19:22:07] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-08-14 19:22:07] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 19:22:18] msmsWorkflow: Done. INFO [2024-08-14 19:22:18] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-08-14 19:22:19] msmsWorkflow: Done. --- finished re-building ‘RMassBankNonstandard.Rmd’ SUMMARY: processing the following file failed: ‘RMassBank.Rmd’ Error: Vignette re-building failed. Execution halted