Back to Workflows build report for BioC 3.23

This page was generated on 2025-11-14 16:30 -0500 (Fri, 14 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4826
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Package 11/28HostnameOS / ArchINSTALLBUILD
fluentGenomics 1.23.0  (landing page)
Stuart Lee
Snapshot Date: 2025-11-14 12:45 -0500 (Fri, 14 Nov 2025)
git_url: https://git.bioconductor.org/packages/fluentGenomics
git_branch: devel
git_last_commit: 4891059
git_last_commit_date: 2025-10-29 09:47:28 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  

BUILD results for fluentGenomics on nebbiolo1

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: 1.23.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data fluentGenomics
StartedAt: 2025-11-14 13:04:23 -0500 (Fri, 14 Nov 2025)
EndedAt: 2025-11-14 13:09:30 -0500 (Fri, 14 Nov 2025)
EllapsedTime: 307.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.23-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:190-195 [tximeta-run]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readRDS()`:
! embedded nul in string: 'E005-H3K4me2.imputed.pval.signal.bigwig\rBroadInstitute\rHomo sapiens\r9606\rhg19\rBigwig File containing -log10(p-value) signal tracks from EpigenomeRoadMap Project\r0\rBioconductor Maintainer <maintainer@bioconductor.org>\r2015-05-08\rEpigenomeRoadMapPreparer\rc("EpigenomeRoadMap", "signal", "consolidatedImputed", "H3K4me2", "E005", "ES-deriv", "ESDR.H1.BMP4.TAted.pval.signal.bigwig\rhttp://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidatedImputed/H3K4me2/E004-H3K4me2.imputed.pval.signal.bigwig\rBigWig\0\004\0\t\0\0\002kE005-H3K4me2.imputed.pval.signal.bigwig\rBroadInstitute\rHomo sapiens\r9606\rhg19\rBigwig File containing -log1'
---
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:
embedded nul in string: 'E005-H3K4me2.imputed.pval.signal.bigwig\rBroadInstitute\rHomo sapiens\r9606\rhg19\rBigwig File containing -log10(p-value) signal tracks from EpigenomeRoadMap Project\r0\rBioconductor Maintainer <maintainer@bioconductor.org>\r2015-05-08\rEpigenomeRoadMapPreparer\rc("EpigenomeRoadMap", "signal", "consolidatedImputed", "H3K4me2", "E005", "ES-deriv", "ESDR.H1.BMP4.TAted.pval.signal.bigwig\rhttp://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidatedImputed/H3K4me2/E004-H3K4me2.imputed.pval.signal.bigwig\rBigWig\0\004\0\t\0\0\002kE005-H3K4me2.imputed.pval.signal.bigwig\rBroadInstitute\rHomo sapiens\r9606\rhg19\rBigwig File containing -log1'
--- failed re-building ‘fluentGenomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted