Workflows build report for BioC 3.24 - BUILD results for fluentGenomics 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"	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*

BUILD results for fluentGenomics on nebbiolo2

To the developers/maintainers of the fluentGenomics 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: fluentGenomics

Version: 1.25.0

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

StartedAt: 2026-05-05 13:05:04 -0400 (Tue, 05 May 2026)

EndedAt: 2026-05-05 13:06:19 -0400 (Tue, 05 May 2026)

EllapsedTime: 74.0 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 fluentGenomics
###
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* checking for file ‘fluentGenomics/DESCRIPTION’ ... OK
* preparing ‘fluentGenomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘fluentGenomics.Rmd’ using rmarkdown

Quitting from fluentGenomics.Rmd:220-222 [gse]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. ├─tximport::summarizeToGene(se)
  2. └─tximeta::summarizeToGene(se)
  3.   └─tximeta (local) .local(object, ...)
  4.     ├─base::suppressMessages(...)
  5.     │ └─base::withCallingHandlers(...)
  6.     ├─AnnotationDbi::select(txdb, keys(txdb, "TXNAME"), "GENEID", "TXNAME")
  7.     ├─GenomicFeatures (local) select(txdb, keys(txdb, "TXNAME"), "GENEID", "TXNAME")
  8.     │ └─GenomicFeatures:::.select(x, keys, columns, keytype, ...)
  9.     │   └─AnnotationDbi::testSelectArgs(...)
 10.     │     └─AnnotationDbi:::.testForValidKeys(x, keys, keytype, fks)
 11.     ├─AnnotationDbi::keys(txdb, "TXNAME")
 12.     └─GenomicFeatures (local) keys(txdb, "TXNAME")
 13.       └─AnnotationDbi:::smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
 14.         └─GenomicFeatures:::.keys(x, keytype)
 15.           └─AnnotationDbi:::dbQuery(...)
 16.             ├─DBI::dbGetQuery(conn, SQL)
 17.             └─DBI::dbGetQuery(conn, SQL)
 18.               └─DBI (local) .local(conn, statement, ...)
 19.                 ├─DBI::dbFetch(rs, n = n, ...)
 20.                 └─RSQLite::dbFetch(rs, n = n, ...)
 21.                   └─RSQLite (local) .local(res, n, ...)
 22.                     └─RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted