| Back to Multiple platform build/check report for BioC 3.24: simplified long |
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This page was generated on 2026-05-19 12:53 -0400 (Tue, 19 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4898 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4617 |
| 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 275/2377 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CAGEr 2.19.0 (landing page) Charles Plessy
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | ||||||||||
| See other builds for CAGEr in R Universe. | ||||||||||||||
|
To the developers/maintainers of the CAGEr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.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: CAGEr |
| Version: 2.19.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 CAGEr |
| StartedAt: 2026-05-18 16:42:36 -0400 (Mon, 18 May 2026) |
| EndedAt: 2026-05-18 16:45:02 -0400 (Mon, 18 May 2026) |
| EllapsedTime: 145.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 CAGEr
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* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* preparing ‘CAGEr’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘CAGE_Resources.Rmd’ using rmarkdown
--- finished re-building ‘CAGE_Resources.Rmd’
--- re-building ‘CAGEexp.Rmd’ using rmarkdown
Quitting from CAGEexp.Rmd:708-713 [unnamed-chunk-21]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `table()`:
! the table() method for Rle objects only takes one input object at the moment
---
Backtrace:
▆
1. ├─BiocGenerics::table(consensusClustersGR(ce)$exprClass, useNA = "always")
2. └─S4Vectors (local) table(consensusClustersGR(ce)$exprClass, useNA = "always")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'CAGEexp.Rmd' failed with diagnostics:
the table() method for Rle objects only takes one input object at the moment
--- failed re-building ‘CAGEexp.Rmd’
SUMMARY: processing the following file failed:
‘CAGEexp.Rmd’
Error: Vignette re-building failed.
Execution halted