Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-03-28 11:36:59 -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 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: 3.13.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank
StartedAt: 2024-03-27 19:07:26 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 19:14:14 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 408.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-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 [2024-03-27 19:08:31] Loaded compoundlist successfully
INFO [2024-03-27 19:08:31] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%INFO [2024-03-27 19:08:36] msmsWorkflow: Step 2. First analysis pre recalibration

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-03-27 19:08:55] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-03-27 19:08:55] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-27 19:08:56] msmsWorkflow: Done.
INFO [2024-03-27 19:09:58] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-27 19:10:04] msmsWorkflow: Done.
INFO [2024-03-27 19:10:04] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-27 19:10:04] msmsWorkflow: Done.
INFO [2024-03-27 19:10:04] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-03-27 19:10:23] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-03-27 19:10:23] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-03-27 19:12:03] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2024-03-27 19:12:04] msmsWorkflow: Done.
INFO [2024-03-27 19:12:04] mbWorkflow: Step 1. Gather info from several databases
INFO [2024-03-27 19:12:07] 2819: smiles
INFO [2024-03-27 19:12:07] mbWorkflow: Step 2. Export infolist (if required)
INFO [2024-03-27 19:12:07] 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 [2024-03-27 19:12:07] mbWorkflow: Step 1. Gather info from several databases
INFO [2024-03-27 19:12:07] mbWorkflow: Step 2. Export infolist (if required)
INFO [2024-03-27 19:12:07] No new data added.
INFO [2024-03-27 19:12:07] mbWorkflow: Step 3. Data reformatting
INFO [2024-03-27 19:12:07] mbWorkflow: Step 4. Spectra compilation
INFO [2024-03-27 19:12:07] Compiling: 1-(3-Chlorophenyl)piperazine
INFO [2024-03-27 19:12:08] Compiling: 1-(3-Trifluoromethylphenyl)-piperazine
INFO [2024-03-27 19:12:09] mbWorkflow: [Legacy Step 5. Flattening records] ignored
INFO [2024-03-27 19:12:09] mbWorkflow: Step 6. Generate molfiles
INFO [2024-03-27 19:12:10] mbWorkflow: Step 7. Generate subdirs and export
INFO [2024-03-27 19:12:11] mbWorkflow: Step 8. Create list.tsv
--- finished re-building ‘RMassBank.Rmd’

--- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown
INFO [2024-03-27 19:13:20] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-27 19:13:24] msmsWorkflow: Done.
INFO [2024-03-27 19:13:27] Loaded compoundlist successfully
INFO [2024-03-27 19:13:27] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%INFO [2024-03-27 19:13:32] msmsWorkflow: Done.
INFO [2024-03-27 19:13:32] msmsWorkflow: Step 2. First analysis pre recalibration

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-03-27 19:13:34] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-03-27 19:13:34] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-27 19:13:35] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-03-27 19:13:37] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-03-27 19:13:37] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-03-27 19:13:47] msmsWorkflow: Done.
INFO [2024-03-27 19:13:48] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%INFO [2024-03-27 19:13:54] msmsWorkflow: Done.
INFO [2024-03-27 19:13:54] msmsWorkflow: Step 2. First analysis pre recalibration

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-03-27 19:13:55] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-03-27 19:13:55] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-03-27 19:13:56] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-03-27 19:13:58] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-03-27 19:13:58] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-03-27 19:14:08] msmsWorkflow: Done.
INFO [2024-03-27 19:14:08] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2024-03-27 19:14:08] msmsWorkflow: Done.
--- finished re-building ‘RMassBankNonstandard.Rmd’

--- re-building ‘RMassBankXCMS.Rmd’ using rmarkdown
INFO [2024-03-27 19:14:10] Loaded compoundlist successfully

  |                                                                      
  |                                                                |   0%
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