| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-02-27 02:34:42 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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 | ||||
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To the developers/maintainers of the RMassBank package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1685/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RMassBank 3.9.0 (landing page) RMassBank at Eawag
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: RMassBank |
| Version: 3.9.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank |
| StartedAt: 2023-02-23 23:59:03 -0000 (Thu, 23 Feb 2023) |
| EndedAt: 2023-02-24 00:07:41 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 518.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/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 [2023-02-23 23:59:53] Loaded compoundlist successfully INFO [2023-02-23 23:59:53] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2023-02-23 23:59:59] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2023-02-24 00:00:30] msmsWorkflow: Step 3. Aggregate all spectra INFO [2023-02-24 00:00:30] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2023-02-24 00:00:31] msmsWorkflow: Done. INFO [2023-02-24 00:01:53] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2023-02-24 00:02:01] msmsWorkflow: Done. INFO [2023-02-24 00:02:01] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2023-02-24 00:02:02] msmsWorkflow: Done. INFO [2023-02-24 00:02:02] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2023-02-24 00:02:30] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2023-02-24 00:02:31] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2023-02-24 00:04:27] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2023-02-24 00:04:29] msmsWorkflow: Done. INFO [2023-02-24 00:04:29] mbWorkflow: Step 1. Gather info from several databases Quitting from lines 433-434 (RMassBank.Rmd) Error: processing vignette 'RMassBank.Rmd' failed with diagnostics: Opening and ending tag mismatch: link line 13 and head [76] --- failed re-building ‘RMassBank.Rmd’ --- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown INFO [2023-02-24 00:06:00] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2023-02-24 00:06:05] msmsWorkflow: Done. INFO [2023-02-24 00:06:09] Loaded compoundlist successfully INFO [2023-02-24 00:06:09] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2023-02-24 00:06:15] msmsWorkflow: Done. INFO [2023-02-24 00:06:15] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2023-02-24 00:06:17] msmsWorkflow: Step 3. Aggregate all spectra INFO [2023-02-24 00:06:17] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2023-02-24 00:06:18] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2023-02-24 00:06:21] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2023-02-24 00:06:21] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2023-02-24 00:06:33] msmsWorkflow: Done. INFO [2023-02-24 00:06:34] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2023-02-24 00:06:41] msmsWorkflow: Done. INFO [2023-02-24 00:06:41] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2023-02-24 00:06:43] msmsWorkflow: Step 3. Aggregate all spectra INFO [2023-02-24 00:06:43] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2023-02-24 00:06:43] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2023-02-24 00:06:46] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2023-02-24 00:06:46] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2023-02-24 00:06:58] msmsWorkflow: Done. INFO [2023-02-24 00:06:59] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2023-02-24 00:06:59] msmsWorkflow: Done. --- finished re-building ‘RMassBankNonstandard.Rmd’ --- re-building ‘RMassBankXCMS.Rmd’ using rmarkdown INFO [2023-02-24 00:07:01] Loaded compoundlist successfully | | | 0% | |================================ | 50%INFO [2023-02-24 00:07:23] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================================================| 100% INFO [2023-02-24 00:07:24] msmsWorkflow: Step 3. Aggregate all spectra INFO [2023-02-24 00:07:24] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2023-02-24 00:07:24] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================================================| 100% INFO [2023-02-24 00:07:27] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2023-02-24 00:07:27] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================================================| 100% INFO [2023-02-24 00:07:29] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2023-02-24 00:07:29] msmsWorkflow: Done. INFO [2023-02-24 00:07:30] mbWorkflow: Step 1. Gather info from several databases INFO [2023-02-24 00:07:30] mbWorkflow: Step 2. Export infolist (if required) INFO [2023-02-24 00:07:30] No new data added. INFO [2023-02-24 00:07:30] mbWorkflow: Step 3. Data reformatting INFO [2023-02-24 00:07:30] mbWorkflow: Step 4. Spectra compilation INFO [2023-02-24 00:07:30] Compiling: Glucolesquerellin INFO [2023-02-24 00:07:30] mbWorkflow: [Legacy Step 5. Flattening records] ignored INFO [2023-02-24 00:07:30] mbWorkflow: Step 6. Generate molfiles INFO [2023-02-24 00:07:32] mbWorkflow: Step 7. Generate subdirs and export INFO [2023-02-24 00:07:32] mbWorkflow: Step 8. Create list.tsv INFO [2023-02-24 00:07:32] msmsWorkflow: Step 1. Acquire all MSMS spectra from files INFO [2023-02-24 00:07:33] Peaks read INFO [2023-02-24 00:07:33] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% INFO [2023-02-24 00:07:33] msmsWorkflow: Step 3. Aggregate all spectra INFO [2023-02-24 00:07:33] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2023-02-24 00:07:34] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% INFO [2023-02-24 00:07:37] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2023-02-24 00:07:37] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================================================| 100% INFO [2023-02-24 00:07:39] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2023-02-24 00:07:39] msmsWorkflow: Done. --- finished re-building ‘RMassBankXCMS.Rmd’ SUMMARY: processing the following file failed: ‘RMassBank.Rmd’ Error: Vignette re-building failed. Execution halted