Build/check report for BioC 3.24 - BUILD results for OrganismDbi on nebbiolo2

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
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BUILD results for OrganismDbi on nebbiolo2

To the developers/maintainers of the OrganismDbi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OrganismDbi.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.

raw results

Summary

Package: OrganismDbi

Version: 1.55.1

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 OrganismDbi

StartedAt: 2026-05-04 19:14:33 -0400 (Mon, 04 May 2026)

EndedAt: 2026-05-04 19:15:56 -0400 (Mon, 04 May 2026)

EllapsedTime: 83.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 OrganismDbi
###
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* checking for file ‘OrganismDbi/DESCRIPTION’ ... OK
* preparing ‘OrganismDbi’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘OrganismDbi.Rmd’ using rmarkdown

Quitting from OrganismDbi.Rmd:88-90 [transcripts]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. ├─GenomicFeatures::transcripts(...)
  2. └─OrganismDbi::transcripts(...)
  3.   └─OrganismDbi (local) .local(x, ...)
  4.     └─OrganismDbi:::.transcripts(x, columns, filter)
  5.       ├─AnnotationDbi::select(...)
  6.       └─OrganismDbi::select(...)
  7.         └─OrganismDbi:::.select(x, keys, columns, keytype, ...)
  8.           └─OrganismDbi:::.getSelects(x, keytype, keys, needCols, visitNodes)
  9.             ├─base::suppressMessages(...)
 10.             │ └─base::withCallingHandlers(...)
 11.             ├─AnnotationDbi::select(...)
 12.             └─GenomicFeatures (local) select(...)
 13.               └─GenomicFeatures:::.select(x, keys, columns, keytype, ...)
 14.                 └─AnnotationDbi:::dbQuery(dbconn(x), sql)
 15.                   ├─DBI::dbGetQuery(conn, SQL)
 16.                   └─DBI::dbGetQuery(conn, SQL)
 17.                     └─DBI (local) .local(conn, statement, ...)
 18.                       ├─DBI::dbSendQuery(conn, statement, ...)
 19.                       └─RSQLite::dbSendQuery(conn, statement, ...)
 20.                         └─RSQLite (local) .local(conn, statement, ...)
 21.                           ├─methods::new(...)
 22.                           │ ├─methods::initialize(value, ...)
 23.                           │ └─methods::initialize(value, ...)
 24.                           └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'OrganismDbi.Rmd' failed with diagnostics:
unable to open database file
--- failed re-building ‘OrganismDbi.Rmd’

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

Error: Vignette re-building failed.
Execution halted