| Back to Build/check report for BioC 3.24: simplified long |
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This page was generated on 2026-05-05 11:33 -0400 (Tue, 05 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" | 4844 |
| 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 892/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Glimma 2.23.1 (landing page) Shian Su
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for Glimma in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Glimma package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Glimma.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: Glimma |
| Version: 2.23.1 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Glimma |
| StartedAt: 2026-05-04 18:00:16 -0400 (Mon, 04 May 2026) |
| EndedAt: 2026-05-04 18:01:43 -0400 (Mon, 04 May 2026) |
| EllapsedTime: 86.1 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 Glimma
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* checking for file ‘Glimma/DESCRIPTION’ ... OK
* preparing ‘Glimma’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘DESeq2.Rmd’ using rmarkdown
--- finished re-building ‘DESeq2.Rmd’
--- re-building ‘limma_edger.Rmd’ using rmarkdown
--- finished re-building ‘limma_edger.Rmd’
--- re-building ‘single_cell_edger.Rmd’ using rmarkdown
Quitting from single_cell_edger.Rmd:41-49 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
▆
1. └─scRNAseq::ZeiselBrainData(ensembl = TRUE)
2. └─scRNAseq:::.convert_to_ensembl(...)
3. └─scRNAseq:::.define_location_from_ensembl(sce, edb = edb, location = location)
4. ├─GenomicFeatures::genes(edb, columns = character(0))
5. └─ensembldb::genes(edb, columns = character(0))
6. └─ensembldb (local) .local(x, ...)
7. ├─ensembldb:::getWhat(...)
8. └─ensembldb:::getWhat(...)
9. └─ensembldb (local) .local(x, ...)
10. └─ensembldb:::.getWhat(...)
11. ├─DBI::dbGetQuery(dbconn(x), Q)
12. └─DBI::dbGetQuery(dbconn(x), Q)
13. └─DBI (local) .local(conn, statement, ...)
14. ├─DBI::dbFetch(rs, n = n, ...)
15. └─RSQLite::dbFetch(rs, n = n, ...)
16. └─RSQLite (local) .local(res, n, ...)
17. └─RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'single_cell_edger.Rmd' failed with diagnostics:
unable to open database file
--- failed re-building ‘single_cell_edger.Rmd’
SUMMARY: processing the following file failed:
‘single_cell_edger.Rmd’
Error: Vignette re-building failed.
Execution halted