Back to Workflows build report for BioC 3.24

This page was generated on 2026-05-06 14:17 -0400 (Wed, 06 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4878
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 28/28HostnameOS / ArchINSTALLBUILD
variants 1.37.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2026-05-05 12:45 -0400 (Tue, 05 May 2026)
git_url: https://git.bioconductor.org/packages/variants
git_branch: devel
git_last_commit: 03e91df
git_last_commit_date: 2026-04-28 08:43:22 -0400 (Tue, 28 Apr 2026)
nebbiolo2Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    ERROR  

BUILD results for variants on nebbiolo2

To the developers/maintainers of the variants 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: variants
Version: 1.37.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data variants
StartedAt: 2026-05-05 13:11:04 -0400 (Tue, 05 May 2026)
EndedAt: 2026-05-05 13:11:46 -0400 (Tue, 05 May 2026)
EllapsedTime: 42.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data variants
###
##############################################################################
##############################################################################


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

Quitting from Annotating_Genomic_Variants.Rmd:103-110 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. ├─AnnotationDbi::select(...)
  2. └─AnnotationDbi::select(...)
  3.   └─AnnotationDbi:::.select(...)
  4.     └─AnnotationDbi::testSelectArgs(...)
  5.       └─AnnotationDbi:::.testForValidKeys(x, keys, keytype, fks)
  6.         ├─AnnotationDbi::keys(x, keytype)
  7.         └─AnnotationDbi::keys(x, keytype)
  8.           └─AnnotationDbi:::smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
  9.             └─AnnotationDbi:::.keys(x, keytype)
 10.               └─AnnotationDbi:::.legacyKeys(x, keytype)
 11.                 └─AnnotationDbi:::.queryForKeys(x, keytype)
 12.                   └─AnnotationDbi:::dbQuery(dbconn(x), sql)
 13.                     ├─DBI::dbGetQuery(conn, SQL)
 14.                     └─DBI::dbGetQuery(conn, SQL)
 15.                       └─DBI (local) .local(conn, statement, ...)
 16.                         ├─DBI::dbFetch(rs, n = n, ...)
 17.                         └─RSQLite::dbFetch(rs, n = n, ...)
 18.                           └─RSQLite (local) .local(res, n, ...)
 19.                             └─RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted