############################################################################## ############################################################################## ### ### 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 [2024-08-14 17:58:52] Loaded compoundlist successfully INFO [2024-08-14 17:58:52] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-08-14 17:58:58] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 17:59:21] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-08-14 17:59:21] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra 2024-08-14 17:59:22.281 R[56382:39581734] XType: com.apple.fonts is not accessible. 2024-08-14 17:59:22.281 R[56382:39581734] XType: XTFontStaticRegistry is enabled. INFO [2024-08-14 17:59:22] msmsWorkflow: Done. INFO [2024-08-14 18:00:39] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 18:00:46] msmsWorkflow: Done. INFO [2024-08-14 18:00:46] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 18:00:46] msmsWorkflow: Done. INFO [2024-08-14 18:00:47] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:01:09] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-08-14 18:01:10] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:03:04] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-08-14 18:03:05] msmsWorkflow: Done. INFO [2024-08-14 18:03:06] 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 18:04:31] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 18:04:39] msmsWorkflow: Done. INFO [2024-08-14 18:04:48] Loaded compoundlist successfully INFO [2024-08-14 18:04:48] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-08-14 18:05:00] msmsWorkflow: Done. INFO [2024-08-14 18:05:00] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:05:02] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-08-14 18:05:02] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 18:05:03] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:05:06] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-08-14 18:05:06] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:05:20] msmsWorkflow: Done. INFO [2024-08-14 18:05:21] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-08-14 18:05:30] msmsWorkflow: Done. INFO [2024-08-14 18:05:30] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:05:31] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-08-14 18:05:31] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 18:05:32] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:05:35] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-08-14 18:05:35] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:05:48] msmsWorkflow: Done. INFO [2024-08-14 18:05:48] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-08-14 18:05:49] msmsWorkflow: Done. --- finished re-building ‘RMassBankNonstandard.Rmd’ SUMMARY: processing the following file failed: ‘RMassBank.Rmd’ Error: Vignette re-building failed. Execution halted