Rapid builds (Linux only) of a subset of BioC 3.21<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	869
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BUILD results for ensembldb on teran2

To the developers/maintainers of the ensembldb package:
- 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.

raw results

Summary

Package: ensembldb

Version: 2.31.0

Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data ensembldb

StartedAt: 2025-03-21 12:31:02 -0400 (Fri, 21 Mar 2025)

EndedAt: 2025-03-21 12:32:35 -0400 (Fri, 21 Mar 2025)

EllapsedTime: 92.8 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data ensembldb
###
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* checking for file ‘ensembldb/DESCRIPTION’ ... OK
* preparing ‘ensembldb’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MySQL-backend.Rmd’ using rmarkdown
--- finished re-building ‘MySQL-backend.Rmd’

--- re-building ‘coordinate-mapping-use-cases.Rmd’ using rmarkdown
--- finished re-building ‘coordinate-mapping-use-cases.Rmd’

--- re-building ‘coordinate-mapping.Rmd’ using rmarkdown
--- finished re-building ‘coordinate-mapping.Rmd’

--- re-building ‘ensembldb.Rmd’ using rmarkdown

Quitting from ensembldb.Rmd:368-381 [example-AnnotationFilterList]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'mean': database or disk is full
---
Backtrace:
     ▆
  1. ├─base::mean(...)
  2. ├─ensembldb::lengthOf(...)
  3. ├─ensembldb::lengthOf(...)
  4. │ └─ensembldb (local) .local(x, ...)
  5. │   ├─base::suppressWarnings(GRL <- exonsBy(x, by = of, filter = filter))
  6. │   │ └─base::withCallingHandlers(...)
  7. │   ├─GenomicFeatures::exonsBy(x, by = of, filter = filter)
  8. │   └─ensembldb::exonsBy(x, by = of, filter = filter)
  9. │     └─ensembldb (local) .local(x, by, ...)
 10. │       ├─ensembldb:::getWhat(...)
 11. │       └─ensembldb:::getWhat(...)
 12. │         └─ensembldb (local) .local(x, ...)
 13. │           └─ensembldb:::.getWhat(...)
 14. │             ├─DBI::dbGetQuery(dbconn(x), Q)
 15. │             └─DBI::dbGetQuery(dbconn(x), Q)
 16. │               └─DBI (local) .local(conn, statement, ...)
 17. │                 ├─DBI::dbSendQuery(conn, statement, ...)
 18. │                 └─RSQLite::dbSendQuery(conn, statement, ...)
 19. │                   └─RSQLite (local) .local(conn, statement, ...)
 20. │                     ├─methods::new(...)
 21. │                     │ ├─methods::initialize(value, ...)
 22. │                     │ └─methods::initialize(value, ...)
 23. │                     └─RSQLite:::result_create(conn@ptr, statement)
 24. └─base::.handleSimpleError(...)
 25.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ensembldb.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'mean': database or disk is full
--- failed re-building ‘ensembldb.Rmd’

--- re-building ‘proteins.Rmd’ using rmarkdown
--- finished re-building ‘proteins.Rmd’

SUMMARY: processing the following file failed:
  ‘ensembldb.Rmd’

Error: Vignette re-building failed.
Execution halted