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

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

Version: 1.59.0

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

StartedAt: 2026-05-04 20:45:06 -0400 (Mon, 04 May 2026)

EndedAt: 2026-05-04 20:47:52 -0400 (Mon, 04 May 2026)

EllapsedTime: 166.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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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 VariantAnnotation
###
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* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* preparing ‘VariantAnnotation’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘VariantAnnotation.Rmd’ using rmarkdown

Quitting from VariantAnnotation.Rmd:281-288 [locate_rename_seqlevels]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. ├─VariantAnnotation::locateVariants(rd, txdb, CodingVariants())
  2. └─VariantAnnotation::locateVariants(rd, txdb, CodingVariants())
  3.   └─VariantAnnotation (local) .local(query, subject, region, ...)
  4.     ├─AnnotationDbi::select(...)
  5.     └─GenomicFeatures (local) select(subject, as.character(res$TXID), "GENEID", "TXID")
  6.       └─GenomicFeatures:::.select(x, keys, columns, keytype, ...)
  7.         └─AnnotationDbi:::dbQuery(dbconn(x), sql)
  8.           ├─DBI::dbGetQuery(conn, SQL)
  9.           └─DBI::dbGetQuery(conn, SQL)
 10.             └─DBI (local) .local(conn, statement, ...)
 11.               ├─DBI::dbSendQuery(conn, statement, ...)
 12.               └─RSQLite::dbSendQuery(conn, statement, ...)
 13.                 └─RSQLite (local) .local(conn, statement, ...)
 14.                   ├─methods::new(...)
 15.                   │ ├─methods::initialize(value, ...)
 16.                   │ └─methods::initialize(value, ...)
 17.                   └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

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

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

Error: Vignette re-building failed.
Execution halted