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This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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 1784/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 3.14.1  (landing page)
RMassBank at Eawag
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/RMassBank
git_branch: RELEASE_3_19
git_last_commit: 83643e2
git_last_commit_date: 2024-10-11 11:52:45 -0400 (Fri, 11 Oct 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  ERROR    ERROR  skippedskipped

BUILD results for RMassBank on nebbiolo1

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.

raw results


Summary

Package: RMassBank
Version: 3.14.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank
StartedAt: 2024-10-16 20:28:49 -0400 (Wed, 16 Oct 2024)
EndedAt: 2024-10-16 20:35:16 -0400 (Wed, 16 Oct 2024)
EllapsedTime: 387.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank
###
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* 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 [2024-10-16 20:29:54] Loaded compoundlist successfully
INFO [2024-10-16 20:29:54] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================================================| 100%INFO [2024-10-16 20:29:59] msmsWorkflow: Step 2. First analysis pre recalibration

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INFO [2024-10-16 20:30:18] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-10-16 20:30:18] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-10-16 20:30:19] msmsWorkflow: Done.
INFO [2024-10-16 20:31:20] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-10-16 20:31:26] msmsWorkflow: Done.
INFO [2024-10-16 20:31:26] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-10-16 20:31:26] msmsWorkflow: Done.
INFO [2024-10-16 20:31:27] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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INFO [2024-10-16 20:31:45] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-10-16 20:31:45] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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INFO [2024-10-16 20:33:22] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2024-10-16 20:33:23] msmsWorkflow: Done.
INFO [2024-10-16 20:33:23] mbWorkflow: Step 1. Gather info from several databases
INFO [2024-10-16 20:33:26] 2819: smiles
INFO [2024-10-16 20:33:26] mbWorkflow: Step 2. Export infolist (if required)
INFO [2024-10-16 20:33:26] The file ./Narcotics_infolist.csv was generated with new compound information. Please check and edit the table, and add it to your infolist folder.
INFO [2024-10-16 20:33:26] mbWorkflow: Step 1. Gather info from several databases
INFO [2024-10-16 20:33:26] mbWorkflow: Step 2. Export infolist (if required)
INFO [2024-10-16 20:33:26] No new data added.
INFO [2024-10-16 20:33:26] mbWorkflow: Step 3. Data reformatting
INFO [2024-10-16 20:33:26] mbWorkflow: Step 4. Spectra compilation
INFO [2024-10-16 20:33:26] Compiling: 1-(3-Chlorophenyl)piperazine

Quitting from lines 471-472 [unnamed-chunk-25] (RMassBank.Rmd)
Error: processing vignette 'RMassBank.Rmd' failed with diagnostics:
is.environment(.envir) is not TRUE
--- failed re-building ‘RMassBank.Rmd’

--- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown
INFO [2024-10-16 20:34:29] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-10-16 20:34:33] msmsWorkflow: Done.
INFO [2024-10-16 20:34:36] Loaded compoundlist successfully
INFO [2024-10-16 20:34:36] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================                                |  50%
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  |================================================================| 100%INFO [2024-10-16 20:34:41] msmsWorkflow: Done.
INFO [2024-10-16 20:34:41] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================================================| 100%
INFO [2024-10-16 20:34:43] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-10-16 20:34:43] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-10-16 20:34:43] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-10-16 20:34:45] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-10-16 20:34:45] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-10-16 20:34:55] msmsWorkflow: Done.
INFO [2024-10-16 20:34:55] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================                                |  50%
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  |================================================================| 100%INFO [2024-10-16 20:35:01] msmsWorkflow: Done.
INFO [2024-10-16 20:35:01] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-10-16 20:35:03] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-10-16 20:35:03] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-10-16 20:35:03] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-10-16 20:35:05] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-10-16 20:35:05] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-10-16 20:35:14] msmsWorkflow: Done.
INFO [2024-10-16 20:35:15] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2024-10-16 20:35:15] msmsWorkflow: Done.
--- finished re-building ‘RMassBankNonstandard.Rmd’

SUMMARY: processing the following file failed:
  ‘RMassBank.Rmd’

Error: Vignette re-building failed.
Execution halted