| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-10-31 08:34 -0400 (Fri, 31 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4428 |
| 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 180/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Bioc.gff 1.1.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the Bioc.gff package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Bioc.gff.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: Bioc.gff |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Bioc.gff |
| StartedAt: 2025-10-30 16:14:15 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 16:15:02 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 47.1 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 Bioc.gff
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* checking for file ‘Bioc.gff/DESCRIPTION’ ... OK
* preparing ‘Bioc.gff’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Bioc.gff.Rmd’ using rmarkdown
Quitting from Bioc.gff.Rmd:194-209 [make-txdb-from-gff]
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<error/rlang_error>
Error in `S4Vectors:::load_package_gracefully()`:
! Could not load package GenomeInfoDbData. Is it installed?
Note that the GenomeInfoDbData package is required by loadTaxonomyDb().
Please install it with:
BiocManager::install("GenomeInfoDbData")
---
Backtrace:
▆
1. └─txdbmaker::makeTxDbFromGFF(...)
2. └─txdbmaker:::.prepareGFFMetadata(...)
3. └─GenomeInfoDb:::check_tax_id(taxonomyId)
4. └─GenomeInfoDb::loadTaxonomyDb()
5. └─S4Vectors:::load_package_gracefully("GenomeInfoDbData", "by loadTaxonomyDb()")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Bioc.gff.Rmd' failed with diagnostics:
Could not load package GenomeInfoDbData. Is it installed?
Note that the GenomeInfoDbData package is required by loadTaxonomyDb().
Please install it with:
BiocManager::install("GenomeInfoDbData")
--- failed re-building ‘Bioc.gff.Rmd’
SUMMARY: processing the following file failed:
‘Bioc.gff.Rmd’
Error: Vignette re-building failed.
Execution halted