Tiago Chedraoui Silva
| Snapshot Date: 2026-01-22 13:40 -0500 (Thu, 22 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/TCGAbiolinks |
| git_branch: devel |
| git_last_commit: 2072af1 |
| git_last_commit_date: 2025-10-29 10:27:16 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-23 11:35 -0500 (Fri, 23 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 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4542 |
| 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 2177/2345 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.39.0 (landing page) Tiago Chedraoui Silva
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the TCGAbiolinks package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCGAbiolinks.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: TCGAbiolinks |
| Version: 2.39.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAbiolinks |
| StartedAt: 2026-01-22 17:53:44 -0500 (Thu, 22 Jan 2026) |
| EndedAt: 2026-01-22 17:57:29 -0500 (Thu, 22 Jan 2026) |
| EllapsedTime: 224.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAbiolinks
###
##############################################################################
##############################################################################
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* preparing ‘TCGAbiolinks’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘analysis.Rmd’ using rmarkdown
--- finished re-building ‘analysis.Rmd’
--- re-building ‘casestudy.Rmd’ using rmarkdown
--- finished re-building ‘casestudy.Rmd’
--- re-building ‘classifiers.Rmd’ using rmarkdown
--- finished re-building ‘classifiers.Rmd’
--- re-building ‘clinical.Rmd’ using rmarkdown
--- finished re-building ‘clinical.Rmd’
--- re-building ‘download_prepare.Rmd’ using rmarkdown
--- finished re-building ‘download_prepare.Rmd’
--- re-building ‘extension.Rmd’ using rmarkdown
--- finished re-building ‘extension.Rmd’
--- re-building ‘index.Rmd’ using rmarkdown
--- finished re-building ‘index.Rmd’
--- re-building ‘mutation.Rmd’ using rmarkdown
2026-01-22 17:56:31.164 R[88737:812435510] XType: Using static font registry.
Quitting from mutation.Rmd:98-104 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─maftools::plotmafSummary(...)
2. └─maftools:::dashboard(...)
3. └─maftools::titv(maf = maf, useSyn = TRUE, plot = FALSE)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'mutation.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘mutation.Rmd’
--- re-building ‘query.Rmd’ using rmarkdown
--- finished re-building ‘query.Rmd’
--- re-building ‘stemness_score.Rmd’ using rmarkdown
--- finished re-building ‘stemness_score.Rmd’
--- re-building ‘subtypes.Rmd’ using rmarkdown
--- finished re-building ‘subtypes.Rmd’
SUMMARY: processing the following file failed:
‘mutation.Rmd’
Error: Vignette re-building failed.
Execution halted