| Back to Build/check report for BioC 3.22: simplified long |
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This page was generated on 2026-02-05 11:57 -0500 (Thu, 05 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4888 |
| 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 521/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Damsel 1.6.0 (landing page) Caitlin Page
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for Damsel in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Damsel package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Damsel.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: Damsel |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Damsel |
| StartedAt: 2026-02-03 16:53:07 -0500 (Tue, 03 Feb 2026) |
| EndedAt: 2026-02-03 16:57:20 -0500 (Tue, 03 Feb 2026) |
| EllapsedTime: 253.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Damsel
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* checking for file ‘Damsel/DESCRIPTION’ ... OK
* preparing ‘Damsel’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Damsel-workflow.Rmd’ using rmarkdown
Warning in doTryCatch(return(expr), name, parentenv, handler) :
"panel.first" is not a graphical parameter
Quitting from Damsel-workflow.Rmd:317-320 [unnamed-chunk-20]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/httr2_http_500>
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
---
Backtrace:
▆
1. └─Damsel::collateGenes(...)
2. └─Damsel:::..accessBiomart(species = genes, regions, version)
3. └─biomaRt::useEnsembl(biomart = "genes", dataset = species, version = version)
4. └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
5. └─biomaRt:::.getFilters(mart, verbose = verbose)
6. └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "filters")
7. └─biomaRt:::bmRequest(...)
8. └─httr2::req_perform(request)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Damsel-workflow.Rmd' failed with diagnostics:
HTTP 500 Internal Server Error.
--- failed re-building ‘Damsel-workflow.Rmd’
SUMMARY: processing the following file failed:
‘Damsel-workflow.Rmd’
Error: Vignette re-building failed.
Execution halted