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This page was generated on 2024-05-09 11:41:22 -0400 (Thu, 09 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4748
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4484
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4514
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 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 3.14.0  (landing page)
RMassBank at Eawag
Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024)
git_url: https://git.bioconductor.org/packages/RMassBank
git_branch: RELEASE_3_19
git_last_commit: 8ec7b0f
git_last_commit_date: 2024-04-30 10:28:27 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 3.14.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank
StartedAt: 2024-05-09 03:04:14 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 03:15:08 -0000 (Thu, 09 May 2024)
EllapsedTime: 653.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/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 [2024-05-09 03:05:43] Loaded compoundlist successfully
INFO [2024-05-09 03:05:43] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================================================| 100%INFO [2024-05-09 03:05:52] msmsWorkflow: Step 2. First analysis pre recalibration

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INFO [2024-05-09 03:06:23] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-05-09 03:06:23] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-05-09 03:06:24] msmsWorkflow: Done.
INFO [2024-05-09 03:08:06] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-05-09 03:08:15] msmsWorkflow: Done.
INFO [2024-05-09 03:08:15] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-05-09 03:08:16] msmsWorkflow: Done.
INFO [2024-05-09 03:08:17] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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INFO [2024-05-09 03:08:47] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-05-09 03:08:47] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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INFO [2024-05-09 03:11:23] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2024-05-09 03:11:25] msmsWorkflow: Done.
INFO [2024-05-09 03:11:25] mbWorkflow: Step 1. Gather info from several databases

Quitting from lines  at lines 433-434 [unnamed-chunk-22] (RMassBank.Rmd)
Error: processing vignette 'RMassBank.Rmd' failed with diagnostics:
not all data was parsed (0 chars were parsed out of a total of 573 chars)
--- failed re-building ‘RMassBank.Rmd’

--- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown
INFO [2024-05-09 03:13:45] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-05-09 03:13:52] msmsWorkflow: Done.
INFO [2024-05-09 03:13:57] Loaded compoundlist successfully
INFO [2024-05-09 03:13:58] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================                                |  50%
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  |================================================================| 100%INFO [2024-05-09 03:14:06] msmsWorkflow: Done.
INFO [2024-05-09 03:14:06] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================================================| 100%
INFO [2024-05-09 03:14:09] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-05-09 03:14:09] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-05-09 03:14:10] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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  |================================================================| 100%
INFO [2024-05-09 03:14:13] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-05-09 03:14:13] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-05-09 03:14:30] msmsWorkflow: Done.
INFO [2024-05-09 03:14:31] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================                                |  50%
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  |================================================================| 100%INFO [2024-05-09 03:14:42] msmsWorkflow: Done.
INFO [2024-05-09 03:14:42] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-05-09 03:14:44] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2024-05-09 03:14:44] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2024-05-09 03:14:45] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2024-05-09 03:14:48] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2024-05-09 03:14:48] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2024-05-09 03:15:04] msmsWorkflow: Done.
INFO [2024-05-09 03:15:05] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2024-05-09 03:15:06] msmsWorkflow: Done.
--- finished re-building ‘RMassBankNonstandard.Rmd’

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

Error: Vignette re-building failed.
Execution halted