############################################################################## ############################################################################## ### ### 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 18:29:45] Loaded compoundlist successfully INFO [2024-08-14 18:29:45] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-08-14 18:29:47] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:29:53] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-08-14 18:29:53] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra 2024-08-14 18:29:53.400 R[62003:177551176] XType: Using static font registry. INFO [2024-08-14 18:29:53] msmsWorkflow: Done. INFO [2024-08-14 18:30:12] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 18:30:14] msmsWorkflow: Done. INFO [2024-08-14 18:30:14] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 18:30:14] msmsWorkflow: Done. INFO [2024-08-14 18:30:14] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:30:20] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-08-14 18:30:20] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:30:52] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-08-14 18:30:52] msmsWorkflow: Done. INFO [2024-08-14 18:30:52] 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 18:31:53] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 18:31:54] msmsWorkflow: Done. INFO [2024-08-14 18:31:55] Loaded compoundlist successfully INFO [2024-08-14 18:31:55] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-08-14 18:31:57] msmsWorkflow: Done. INFO [2024-08-14 18:31:57] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:31:58] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-08-14 18:31:58] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 18:31:58] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:31:59] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-08-14 18:31:59] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:32:02] msmsWorkflow: Done. INFO [2024-08-14 18:32:02] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-08-14 18:32:04] msmsWorkflow: Done. INFO [2024-08-14 18:32:04] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:32:05] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-08-14 18:32:05] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-08-14 18:32:05] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:32:06] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-08-14 18:32:06] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-08-14 18:32:09] msmsWorkflow: Done. INFO [2024-08-14 18:32:09] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-08-14 18:32:10] msmsWorkflow: Done. --- finished re-building ‘RMassBankNonstandard.Rmd’ SUMMARY: processing the following file failed: ‘RMassBank.Rmd’ Error: Vignette re-building failed. Execution halted