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This page was generated on 2024-03-28 11:41:14 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1762/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 3.13.0  (landing page)
RMassBank at Eawag
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/RMassBank
git_branch: devel
git_last_commit: a5f1bff
git_last_commit_date: 2023-10-24 09:50:49 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

BUILD results for RMassBank on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: RMassBank
Version: 3.13.0
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank
StartedAt: 2024-03-28 01:07:43 -0000 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 01:18:29 -0000 (Thu, 28 Mar 2024)
EllapsedTime: 645.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/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 [2024-03-28 01:09:10] Loaded compoundlist successfully
INFO [2024-03-28 01:09:10] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================================================| 100%INFO [2024-03-28 01:09:18] msmsWorkflow: Step 2. First analysis pre recalibration

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INFO [2024-03-28 01:09:48] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-03-28 01:09:48] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-28 01:09:49] msmsWorkflow: Done.
INFO [2024-03-28 01:11:31] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-28 01:11:39] msmsWorkflow: Done.
INFO [2024-03-28 01:11:39] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-28 01:11:40] msmsWorkflow: Done.
INFO [2024-03-28 01:11:40] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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INFO [2024-03-28 01:12:10] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-03-28 01:12:10] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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INFO [2024-03-28 01:14:44] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2024-03-28 01:14:46] msmsWorkflow: Done.
INFO [2024-03-28 01:14:46] mbWorkflow: Step 1. Gather info from several databases
INFO [2024-03-28 01:15:02] 2819: smiles
INFO [2024-03-28 01:15:02] mbWorkflow: Step 2. Export infolist (if required)
INFO [2024-03-28 01:15:02] 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 [2024-03-28 01:15:03] mbWorkflow: Step 1. Gather info from several databases
INFO [2024-03-28 01:15:03] mbWorkflow: Step 2. Export infolist (if required)
INFO [2024-03-28 01:15:03] No new data added.
INFO [2024-03-28 01:15:03] mbWorkflow: Step 3. Data reformatting
INFO [2024-03-28 01:15:03] mbWorkflow: Step 4. Spectra compilation
INFO [2024-03-28 01:15:03] Compiling: 1-(3-Chlorophenyl)piperazine
INFO [2024-03-28 01:15:04] Compiling: 1-(3-Trifluoromethylphenyl)-piperazine
INFO [2024-03-28 01:15:06] mbWorkflow: [Legacy Step 5. Flattening records] ignored
INFO [2024-03-28 01:15:06] mbWorkflow: Step 6. Generate molfiles
INFO [2024-03-28 01:15:19] mbWorkflow: Step 7. Generate subdirs and export
INFO [2024-03-28 01:15:20] mbWorkflow: Step 8. Create list.tsv
--- finished re-building ‘RMassBank.Rmd’

--- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown
INFO [2024-03-28 01:17:07] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-28 01:17:13] msmsWorkflow: Done.
INFO [2024-03-28 01:17:17] Loaded compoundlist successfully
INFO [2024-03-28 01:17:17] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================================================| 100%INFO [2024-03-28 01:17:25] msmsWorkflow: Done.
INFO [2024-03-28 01:17:25] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================================================| 100%
INFO [2024-03-28 01:17:28] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-03-28 01:17:28] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-28 01:17:29] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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INFO [2024-03-28 01:17:32] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-03-28 01:17:32] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================================================| 100%
INFO [2024-03-28 01:17:48] msmsWorkflow: Done.
INFO [2024-03-28 01:17:49] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================================================| 100%INFO [2024-03-28 01:17:58] msmsWorkflow: Done.
INFO [2024-03-28 01:17:58] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================================================| 100%
INFO [2024-03-28 01:18:00] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-03-28 01:18:00] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-28 01:18:01] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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INFO [2024-03-28 01:18:04] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-03-28 01:18:04] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================================================| 100%
INFO [2024-03-28 01:18:20] msmsWorkflow: Done.
INFO [2024-03-28 01:18:20] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2024-03-28 01:18:21] msmsWorkflow: Done.
--- finished re-building ‘RMassBankNonstandard.Rmd’

--- re-building ‘RMassBankXCMS.Rmd’ using rmarkdown
INFO [2024-03-28 01:18:24] Loaded compoundlist successfully

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Quitting from lines 138-142 [unnamed-chunk-9] (RMassBankXCMS.Rmd)
Error: processing vignette 'RMassBankXCMS.Rmd' failed with diagnostics:
could not find function "bpstopOnError"
--- failed re-building ‘RMassBankXCMS.Rmd’

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

Error: Vignette re-building failed.
Execution halted