| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-26 11:34 -0400 (Thu, 26 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4876 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4574 |
| 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 2355/2372 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| xcms 4.9.2 (landing page) Steffen Neumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| See other builds for xcms in R Universe. | ||||||||||||||
|
To the developers/maintainers of the xcms package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/xcms.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: xcms |
| Version: 4.9.2 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data xcms |
| StartedAt: 2026-03-25 20:55:01 -0400 (Wed, 25 Mar 2026) |
| EndedAt: 2026-03-25 20:59:07 -0400 (Wed, 25 Mar 2026) |
| EllapsedTime: 245.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data xcms
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* checking for file ‘xcms/DESCRIPTION’ ... OK
* preparing ‘xcms’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘LC-MS-feature-grouping.Rmd’ using rmarkdown
--- finished re-building ‘LC-MS-feature-grouping.Rmd’
--- re-building ‘xcms-direct-injection.Rmd’ using rmarkdown
--- finished re-building ‘xcms-direct-injection.Rmd’
--- re-building ‘xcms-lcms-ms.Rmd’ using rmarkdown
Quitting from xcms-lcms-ms.Rmd:83-91 [load-dda-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.local()`:
! File(s) not found
---
Backtrace:
▆
1. └─MsExperiment::readMsExperiment(dda_file)
2. ├─Spectra::Spectra(spectraFiles, ...)
3. └─Spectra::Spectra(spectraFiles, ...)
4. └─Spectra (local) .local(object, ...)
5. └─Spectra:::.create_spectra(...)
6. ├─ProtGenerics::backendInitialize(...)
7. └─Spectra::backendInitialize(...)
8. └─Spectra (local) .local(object, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'xcms-lcms-ms.Rmd' failed with diagnostics:
File(s) not found
--- failed re-building ‘xcms-lcms-ms.Rmd’
--- re-building ‘xcms.Rmd’ using rmarkdown
--- finished re-building ‘xcms.Rmd’
SUMMARY: processing the following file failed:
‘xcms-lcms-ms.Rmd’
Error: Vignette re-building failed.
Execution halted