Build/check report for BioC 3.23 - BUILD results for MsBackendMetaboLights on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4013
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BUILD results for MsBackendMetaboLights on kjohnson3

To the developers/maintainers of the MsBackendMetaboLights package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendMetaboLights.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: MsBackendMetaboLights

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MsBackendMetaboLights

StartedAt: 2025-11-12 16:46:59 -0500 (Wed, 12 Nov 2025)

EndedAt: 2025-11-12 16:47:20 -0500 (Wed, 12 Nov 2025)

EllapsedTime: 20.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MsBackendMetaboLights
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* checking for file ‘MsBackendMetaboLights/DESCRIPTION’ ... OK
* preparing ‘MsBackendMetaboLights’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘MsBackendMetaboLights.Rmd’ using rmarkdown

Quitting from MsBackendMetaboLights.Rmd:149-156 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'object' in selecting a method for function 'backendInitialize': The use of 'MsBackendMzR' requires package 'mzR'. Please install with 'BiocInstaller::install("mzR")'
---
Backtrace:
     ▆
  1. ├─Spectra::Spectra("MTBLS39", filePattern = "63A.cdf", source = MsBackendMetaboLights())
  2. ├─Spectra::Spectra("MTBLS39", filePattern = "63A.cdf", source = MsBackendMetaboLights())
  3. │ └─Spectra (local) .local(object, ...)
  4. │   └─Spectra:::.create_spectra(...)
  5. │     ├─ProtGenerics::backendInitialize(...)
  6. │     └─MsBackendMetaboLights::backendInitialize(...)
  7. │       └─MsBackendMetaboLights (local) .local(object, ...)
  8. │         ├─ProtGenerics::backendInitialize(MsBackendMzR(), files = mdata$rpath)
  9. │         └─Spectra::MsBackendMzR()
 10. │           └─base::stop(...)
 11. └─base::.handleSimpleError(...)
 12.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MsBackendMetaboLights.Rmd' failed with diagnostics:
error in evaluating the argument 'object' in selecting a method for function 'backendInitialize': The use of 'MsBackendMzR' requires package 'mzR'. Please install with 'BiocInstaller::install("mzR")'
--- failed re-building ‘MsBackendMetaboLights.Rmd’

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

Error: Vignette re-building failed.
Execution halted