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This page was generated on 2025-03-20 11:42 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4458
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 1778/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 3.17.0  (landing page)
RMassBank at Eawag
Snapshot Date: 2025-03-19 13:40 -0400 (Wed, 19 Mar 2025)
git_url: https://git.bioconductor.org/packages/RMassBank
git_branch: devel
git_last_commit: 8e633a1
git_last_commit_date: 2024-10-29 09:42:07 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for RMassBank on palomino7

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: 3.17.0
Command: chmod a+r RMassBank -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RMassBank
StartedAt: 2025-03-19 21:17:46 -0400 (Wed, 19 Mar 2025)
EndedAt: 2025-03-19 21:28:32 -0400 (Wed, 19 Mar 2025)
EllapsedTime: 645.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r RMassBank -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe 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 [2025-03-19 21:19:54] Loaded compoundlist successfully
INFO [2025-03-19 21:19:54] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================                                |  50%
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  |================================================================| 100%INFO [2025-03-19 21:20:02] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2025-03-19 21:20:38] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-03-19 21:20:38] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-19 21:20:39] msmsWorkflow: Done.
INFO [2025-03-19 21:22:06] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-19 21:22:13] msmsWorkflow: Done.
INFO [2025-03-19 21:22:13] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-19 21:22:13] msmsWorkflow: Done.
INFO [2025-03-19 21:22:14] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2025-03-19 21:22:49] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-03-19 21:22:49] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |================================                                |  50%
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  |================================================================| 100%
INFO [2025-03-19 21:25:07] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2025-03-19 21:25:08] msmsWorkflow: Done.
INFO [2025-03-19 21:25:09] mbWorkflow: Step 1. Gather info from several databases

Quitting from RMassBank.Rmd:432-434 [unnamed-chunk-22]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `strsplit()`:
! non-character argument
---
Backtrace:
    ▆
 1. └─RMassBank::mbWorkflow(mb, infolist_path = "./Narcotics_infolist.csv")
 2.   ├─BiocGenerics::lapply(...)
 3.   └─base::lapply(...)
 4.     └─RMassBank (local) FUN(X[[i]], ...)
 5.       └─RMassBank::gatherData(id)
 6.         └─RMassBank::getCactus(identifier = smiles, representation = "stdinchikey")
 7.           ├─base::unlist(strsplit(ret, "\n"))
 8.           └─base::strsplit(ret, "\n")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RMassBank.Rmd' failed with diagnostics:
non-character argument
--- failed re-building 'RMassBank.Rmd'

--- re-building 'RMassBankNonstandard.Rmd' using rmarkdown
INFO [2025-03-19 21:27:24] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-19 21:27:28] msmsWorkflow: Done.
INFO [2025-03-19 21:27:32] Loaded compoundlist successfully
INFO [2025-03-19 21:27:32] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

  |                                                                      
  |                                                                |   0%
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  |================================                                |  50%
  |                                                                      
  |================================================================| 100%INFO [2025-03-19 21:27:39] msmsWorkflow: Done.
INFO [2025-03-19 21:27:39] msmsWorkflow: Step 2. First analysis pre recalibration

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  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2025-03-19 21:27:42] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-03-19 21:27:42] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-19 21:27:42] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

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  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2025-03-19 21:27:45] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-03-19 21:27:45] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2025-03-19 21:27:58] msmsWorkflow: Done.
INFO [2025-03-19 21:27:59] msmsWorkflow: Step 1. Acquire all MSMS spectra from files

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%INFO [2025-03-19 21:28:06] msmsWorkflow: Done.
INFO [2025-03-19 21:28:06] msmsWorkflow: Step 2. First analysis pre recalibration

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2025-03-19 21:28:08] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-03-19 21:28:08] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-19 21:28:08] msmsWorkflow: Step 5. Reanalyze recalibrated spectra

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2025-03-19 21:28:11] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-03-19 21:28:11] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O

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  |                                                                |   0%
  |                                                                      
  |================================                                |  50%
  |                                                                      
  |================================================================| 100%
INFO [2025-03-19 21:28:27] msmsWorkflow: Done.
INFO [2025-03-19 21:28:28] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2025-03-19 21:28:28] msmsWorkflow: Done.
--- finished re-building 'RMassBankNonstandard.Rmd'

SUMMARY: processing the following file failed:
  'RMassBank.Rmd'

Error: Vignette re-building failed.
Execution halted