| Back to Build/check report for BioC 3.23 experimental data |
|
This page was generated on 2026-01-22 15:01 -0500 (Thu, 22 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4808 |
| 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 326/432 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| RforProteomics 1.49.0 (landing page) Laurent Gatto
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||
|
To the developers/maintainers of the RforProteomics package: - 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: RforProteomics |
| Version: 1.49.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics |
| StartedAt: 2026-01-22 11:37:48 -0500 (Thu, 22 Jan 2026) |
| EndedAt: 2026-01-22 11:47:06 -0500 (Thu, 22 Jan 2026) |
| EllapsedTime: 557.9 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 RforProteomics
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* checking for file ‘RforProteomics/DESCRIPTION’ ... OK
* preparing ‘RforProteomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘RProtVis.Rmd’ using rmarkdown
Quitting from RProtVis.Rmd:179-210 [makemadata]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.util_download()`:
! bfcadd() failed; see warnings()
---
Backtrace:
▆
1. ├─rpx::pxget(px1, "F063721.dat-mztab.txt")
2. └─rpx::pxget(px1, "F063721.dat-mztab.txt")
3. └─rpx (local) .local(object, ...)
4. └─rpx:::pxget1(uris[i], cache)
5. ├─BiocFileCache::bfcadd(cache, url, url)
6. └─BiocFileCache::bfcadd(cache, url, url)
7. └─BiocFileCache:::.util_download(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
bfcadd() failed; see warnings()
--- failed re-building ‘RProtVis.Rmd’
--- re-building ‘RforProteomics.Rmd’ using rmarkdown
starting worker pid=3118499 on localhost:11706 at 11:43:04.888
starting worker pid=3118498 on localhost:11706 at 11:43:04.888
Loading required package: mzID
Loading required package: mzID
loaded mzID and set parent environment
loaded mzID and set parent environment
reading 55merge_omssa.mzid...
reading 55merge_tandem.mzid...
55merge_omssa.mzid DONE!
55merge_tandem.mzid DONE!
trying URL 'http://www.uniprot.org/uniprot/P00924.fasta'
Content type 'text/plain;format=fasta' length 562 bytes
==================================================
downloaded 562 bytes
--- finished re-building ‘RforProteomics.Rmd’
SUMMARY: processing the following file failed:
‘RProtVis.Rmd’
Error: Vignette re-building failed.
Execution halted