| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-02-11 11:32 -0500 (Wed, 11 Feb 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" | 4862 |
| 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 291/2351 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cBioPortalData 2.23.4 (landing page) Marcel Ramos
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for cBioPortalData in R Universe. | ||||||||||||||
|
To the developers/maintainers of the cBioPortalData package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cBioPortalData.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: cBioPortalData |
| Version: 2.23.4 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cBioPortalData |
| StartedAt: 2026-02-10 16:53:23 -0500 (Tue, 10 Feb 2026) |
| EndedAt: 2026-02-10 16:54:42 -0500 (Tue, 10 Feb 2026) |
| EllapsedTime: 79.0 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 cBioPortalData
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* checking for file ‘cBioPortalData/DESCRIPTION’ ... OK
* preparing ‘cBioPortalData’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘cBioPortalData.Rmd’ using rmarkdown
Quitting from cBioPortalData.Rmd:118-122 [cbiodatapack]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Unable to download file.
reason: 'wget' call had nonzero exit status
---
Backtrace:
▆
1. └─cBioPortalData::cBioDataPack("laml_tcga", ask = FALSE)
2. └─cBioPortalData::downloadStudy(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
7. └─cBioPortalData:::.altDownload(url_file, cancer_study_id, verbose = TRUE)
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'cBioPortalData.Rmd' failed with diagnostics:
Unable to download file.
reason: 'wget' call had nonzero exit status
--- failed re-building ‘cBioPortalData.Rmd’
--- re-building ‘cBioPortalDataErrors.Rmd’ using rmarkdown
--- finished re-building ‘cBioPortalDataErrors.Rmd’
--- re-building ‘cBioPortalRClient.Rmd’ using rmarkdown
--- finished re-building ‘cBioPortalRClient.Rmd’
--- re-building ‘cgdsrMigration.Rmd’ using rmarkdown
--- finished re-building ‘cgdsrMigration.Rmd’
SUMMARY: processing the following file failed:
‘cBioPortalData.Rmd’
Error: Vignette re-building failed.
Execution halted