############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/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 [2024-05-09 03:05:43] Loaded compoundlist successfully INFO [2024-05-09 03:05:43] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-05-09 03:05:52] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-05-09 03:06:23] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-05-09 03:06:23] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-05-09 03:06:24] msmsWorkflow: Done. INFO [2024-05-09 03:08:06] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-05-09 03:08:15] msmsWorkflow: Done. INFO [2024-05-09 03:08:15] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-05-09 03:08:16] msmsWorkflow: Done. INFO [2024-05-09 03:08:17] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-05-09 03:08:47] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-05-09 03:08:47] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-05-09 03:11:23] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-05-09 03:11:25] msmsWorkflow: Done. INFO [2024-05-09 03:11:25] mbWorkflow: Step 1. Gather info from several databases Quitting from lines at lines 433-434 [unnamed-chunk-22] (RMassBank.Rmd) Error: processing vignette 'RMassBank.Rmd' failed with diagnostics: not all data was parsed (0 chars were parsed out of a total of 573 chars) --- failed re-building ‘RMassBank.Rmd’ --- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown INFO [2024-05-09 03:13:45] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-05-09 03:13:52] msmsWorkflow: Done. INFO [2024-05-09 03:13:57] Loaded compoundlist successfully INFO [2024-05-09 03:13:58] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-05-09 03:14:06] msmsWorkflow: Done. INFO [2024-05-09 03:14:06] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-05-09 03:14:09] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-05-09 03:14:09] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-05-09 03:14:10] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-05-09 03:14:13] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-05-09 03:14:13] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-05-09 03:14:30] msmsWorkflow: Done. INFO [2024-05-09 03:14:31] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-05-09 03:14:42] msmsWorkflow: Done. INFO [2024-05-09 03:14:42] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-05-09 03:14:44] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-05-09 03:14:44] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-05-09 03:14:45] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-05-09 03:14:48] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-05-09 03:14:48] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-05-09 03:15:04] msmsWorkflow: Done. INFO [2024-05-09 03:15:05] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-05-09 03:15:06] msmsWorkflow: Done. --- finished re-building ‘RMassBankNonstandard.Rmd’ SUMMARY: processing the following file failed: ‘RMassBank.Rmd’ Error: Vignette re-building failed. Execution halted