| Back to Build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-07 15:40 -0400 (Sat, 07 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4711 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1744/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RMassBank 3.15.1 (landing page) RMassBank at Eawag
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
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To the developers/maintainers of the RMassBank package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RMassBank.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: RMassBank |
| Version: 3.15.1 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 RMassBank |
| StartedAt: 2024-09-06 19:09:40 -0400 (Fri, 06 Sep 2024) |
| EndedAt: 2024-09-06 19:16:11 -0400 (Fri, 06 Sep 2024) |
| EllapsedTime: 391.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### 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 [2024-09-06 19:10:47] Loaded compoundlist successfully INFO [2024-09-06 19:10:47] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-09-06 19:10:53] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-09-06 19:11:12] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-09-06 19:11:12] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-09-06 19:11:13] msmsWorkflow: Done. INFO [2024-09-06 19:12:13] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-09-06 19:12:19] msmsWorkflow: Done. INFO [2024-09-06 19:12:19] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-09-06 19:12:19] msmsWorkflow: Done. INFO [2024-09-06 19:12:19] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-09-06 19:12:37] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-09-06 19:12:38] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-09-06 19:14:13] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-09-06 19:14:14] msmsWorkflow: Done. INFO [2024-09-06 19:14:14] 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 [2024-09-06 19:15:21] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-09-06 19:15:25] msmsWorkflow: Done. INFO [2024-09-06 19:15:28] Loaded compoundlist successfully INFO [2024-09-06 19:15:28] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-09-06 19:15:33] msmsWorkflow: Done. INFO [2024-09-06 19:15:33] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-09-06 19:15:35] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-09-06 19:15:35] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-09-06 19:15:36] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-09-06 19:15:38] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-09-06 19:15:38] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-09-06 19:15:48] msmsWorkflow: Done. INFO [2024-09-06 19:15:48] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-09-06 19:15:55] msmsWorkflow: Done. INFO [2024-09-06 19:15:55] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-09-06 19:15:56] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-09-06 19:15:56] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-09-06 19:15:56] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-09-06 19:15:58] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-09-06 19:15:58] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-09-06 19:16:09] msmsWorkflow: Done. INFO [2024-09-06 19:16:09] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-09-06 19:16:10] msmsWorkflow: Done. --- finished re-building ‘RMassBankNonstandard.Rmd’ SUMMARY: processing the following file failed: ‘RMassBank.Rmd’ Error: Vignette re-building failed. Execution halted