Back to Workflows build report for BioC 3.22

This page was generated on 2025-10-28 16:30 -0400 (Tue, 28 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
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 11/29HostnameOS / ArchINSTALLBUILD
fluentGenomics 1.21.0  (landing page)
Stuart Lee
Snapshot Date: 2025-10-28 12:45 -0400 (Tue, 28 Oct 2025)
git_url: https://git.bioconductor.org/packages/fluentGenomics
git_branch: devel
git_last_commit: b942cf1
git_last_commit_date: 2025-04-15 10:29:43 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK  

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: 1.21.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data fluentGenomics
StartedAt: 2025-10-28 13:04:48 -0400 (Tue, 28 Oct 2025)
EndedAt: 2025-10-28 13:05:59 -0400 (Tue, 28 Oct 2025)
EllapsedTime: 71.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data fluentGenomics
###
##############################################################################
##############################################################################


* checking for file ‘fluentGenomics/DESCRIPTION’ ... OK
* preparing ‘fluentGenomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘fluentGenomics.Rmd’ using rmarkdown

Quitting from fluentGenomics.Rmd:190-195 [tximeta-run]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readRDS()`:
! error reading from connection
---
Backtrace:
    ▆
 1. └─tximeta::tximeta(coldata, dropInfReps = TRUE)
 2.   └─tximeta:::getTxDb(txomeInfo, useHub = useHub, skipFtp = skipFtp)
 3.     ├─AnnotationHub::query(ah, c(srcName, txomeInfo$organism, txomeInfo$release))
 4.     └─AnnotationHub::query(ah, c(srcName, txomeInfo$organism, txomeInfo$release))
 5.       └─AnnotationHub (local) .local(x, pattern, ...)
 6.         └─AnnotationHub:::.db_index_load(x)
 7.           └─base::readRDS(.db_index_file(x))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'fluentGenomics.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building ‘fluentGenomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted