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This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| 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 |
| 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 1641/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PSMatch 1.15.0 (landing page) Laurent Gatto
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | ||||||||
|
To the developers/maintainers of the PSMatch package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PSMatch.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. |
| Package: PSMatch |
| Version: 1.15.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data PSMatch |
| StartedAt: 2025-11-12 16:59:39 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 16:59:57 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 17.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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 PSMatch
###
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* checking for file ‘PSMatch/DESCRIPTION’ ... OK
* preparing ‘PSMatch’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘AdjacencyMatrix.Rmd’ using rmarkdown
Failed with error: 'there is no package called 'mzR''
Quitting from AdjacencyMatrix.Rmd:42-49 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'metadata': error in evaluating the argument 'x' in selecting a method for function 'metadata': requireNamespace("mzR") is not TRUE
---
Backtrace:
▆
1. ├─PSMatch::filterPsmRank(...)
2. │ └─PSMatch::psmVariables(x)
3. │ └─S4Vectors::metadata(object)
4. ├─PSMatch::filterPsmDecoy(...)
5. │ └─PSMatch::psmVariables(x)
6. │ └─S4Vectors::metadata(object)
7. ├─PSMatch::PSM(msdata::ident(full.names = TRUE, pattern = "TMT"))
8. │ └─PSMatch:::readPSMsMzR(x, BPPARAM)
9. │ └─base::stopifnot(requireNamespace("mzR"))
10. │ └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
11. ├─base (local) `<fn>`(`<smplErrr>`)
12. └─base::.handleSimpleError(...)
13. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'AdjacencyMatrix.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'metadata': error in evaluating the argument 'x' in selecting a method for function 'metadata': requireNamespace("mzR") is not TRUE
--- failed re-building ‘AdjacencyMatrix.Rmd’
--- re-building ‘Fragments.Rmd’ using rmarkdown
Quitting from Fragments.Rmd:43-47 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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(spf)
2. ├─Spectra::Spectra(spf)
3. │ └─Spectra (local) .local(object, ...)
4. │ ├─Spectra:::.create_spectra(...)
5. │ │ └─ProtGenerics::backendInitialize(...)
6. │ └─Spectra::MsBackendMzR()
7. │ └─base::stop(...)
8. └─base::.handleSimpleError(...)
9. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Fragments.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 ‘Fragments.Rmd’
--- re-building ‘PSM.Rmd’ using rmarkdown
Failed with error: 'there is no package called 'mzR''
Quitting from PSM.Rmd:64-68 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readPSMsMzR()`:
! requireNamespace("mzR") is not TRUE
---
Backtrace:
▆
1. └─PSMatch::PSM(f)
2. └─PSMatch:::readPSMsMzR(x, BPPARAM)
3. └─base::stopifnot(requireNamespace("mzR"))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'PSM.Rmd' failed with diagnostics:
requireNamespace("mzR") is not TRUE
--- failed re-building ‘PSM.Rmd’
SUMMARY: processing the following files failed:
‘AdjacencyMatrix.Rmd’ ‘Fragments.Rmd’ ‘PSM.Rmd’
Error: Vignette re-building failed.
Execution halted