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This page was generated on 2024-09-12 11:41 -0400 (Thu, 12 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4713
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4450
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4483
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4430
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4428
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 1744/2258HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 3.15.1  (landing page)
RMassBank at Eawag
Snapshot Date: 2024-09-11 14:00 -0400 (Wed, 11 Sep 2024)
git_url: https://git.bioconductor.org/packages/RMassBank
git_branch: devel
git_last_commit: 8af9a1d
git_last_commit_date: 2024-05-02 11:25:23 -0400 (Thu, 02 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped

BUILD results for RMassBank on nebbiolo2

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: 3.15.1
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 RMassBank
StartedAt: 2024-09-11 19:07:10 -0400 (Wed, 11 Sep 2024)
EndedAt: 2024-09-11 19:13:39 -0400 (Wed, 11 Sep 2024)
EllapsedTime: 388.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### 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 [2024-09-11 19:08:15] Loaded compoundlist successfully
INFO [2024-09-11 19:08:15] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================================================| 100%INFO [2024-09-11 19:08:20] msmsWorkflow: Step 2. First analysis pre recalibration

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INFO [2024-09-11 19:08:38] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-09-11 19:08:39] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-09-11 19:08:39] msmsWorkflow: Done.
INFO [2024-09-11 19:09:40] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-09-11 19:09:45] msmsWorkflow: Done.
INFO [2024-09-11 19:09:46] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-09-11 19:09:46] msmsWorkflow: Done.
INFO [2024-09-11 19:09:46] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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INFO [2024-09-11 19:10:05] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-09-11 19:10:05] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================================================| 100%
INFO [2024-09-11 19:11:40] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2024-09-11 19:11:41] msmsWorkflow: Done.
INFO [2024-09-11 19:11:41] 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 [2024-09-11 19:12:49] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-09-11 19:12:53] msmsWorkflow: Done.
INFO [2024-09-11 19:12:56] Loaded compoundlist successfully
INFO [2024-09-11 19:12:56] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================                                |  50%
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  |================================================================| 100%INFO [2024-09-11 19:13:01] msmsWorkflow: Done.
INFO [2024-09-11 19:13:01] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================================================| 100%
INFO [2024-09-11 19:13:03] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-09-11 19:13:03] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-09-11 19:13:03] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-09-11 19:13:05] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-09-11 19:13:05] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-09-11 19:13:15] msmsWorkflow: Done.
INFO [2024-09-11 19:13:16] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================                                |  50%
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  |================================================================| 100%INFO [2024-09-11 19:13:22] msmsWorkflow: Done.
INFO [2024-09-11 19:13:22] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-09-11 19:13:23] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-09-11 19:13:23] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-09-11 19:13:24] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-09-11 19:13:26] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-09-11 19:13:26] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-09-11 19:13:36] msmsWorkflow: Done.
INFO [2024-09-11 19:13:36] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2024-09-11 19:13:37] msmsWorkflow: Done.
--- finished re-building ‘RMassBankNonstandard.Rmd’

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

Error: Vignette re-building failed.
Execution halted