| 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 901/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GmicR 1.27.0 (landing page) Richard Virgen-Slane
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for GmicR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the GmicR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GmicR.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: GmicR |
| Version: 1.27.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 GmicR |
| StartedAt: 2026-05-04 18:01:46 -0400 (Mon, 04 May 2026) |
| EndedAt: 2026-05-04 18:02:46 -0400 (Mon, 04 May 2026) |
| EllapsedTime: 60.0 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 GmicR
###
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* checking for file ‘GmicR/DESCRIPTION’ ... OK
* preparing ‘GmicR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘GmicR_vignette.Rmd’ using rmarkdown
Quitting from GmicR_vignette.Rmd:184-189 [GO enrichment]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
▆
1. └─GmicR::GSEAGO_Builder(...)
2. ├─AnnotationDbi::GOAllFrame(AnnotationDbi::GOFrame(GOdf, organism = species))
3. └─AnnotationDbi::GOAllFrame(AnnotationDbi::GOFrame(GOdf, organism = species))
4. └─AnnotationDbi:::.convertGOtoGO2ALL(x@data, "BP")
5. ├─DBI::dbSendQuery(con, sqlIns, params = unclass(unname(clnVals)))
6. └─RSQLite::dbSendQuery(con, sqlIns, params = unclass(unname(clnVals)))
7. └─RSQLite (local) .local(conn, statement, ...)
8. ├─DBI::dbBind(rs, params)
9. └─RSQLite::dbBind(rs, params)
10. └─RSQLite:::db_bind(res, as.list(params), ..., allow_named_superset = FALSE)
11. └─RSQLite:::result_bind(res@ptr, params)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GmicR_vignette.Rmd' failed with diagnostics:
unable to open database file
--- failed re-building ‘GmicR_vignette.Rmd’
SUMMARY: processing the following file failed:
‘GmicR_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted