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This page was generated on 2025-10-31 08:34 -0400 (Fri, 31 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4428
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Package 1500/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.31.0  (landing page)
Haakon Tjeldnes
Snapshot Date: 2025-10-30 13:40 -0400 (Thu, 30 Oct 2025)
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: devel
git_last_commit: 1c0375d
git_last_commit_date: 2025-10-29 10:45:22 -0400 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for ORFik on nebbiolo1

To the developers/maintainers of the ORFik package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ORFik.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: ORFik
Version: 1.31.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ORFik
StartedAt: 2025-10-30 18:17:31 -0400 (Thu, 30 Oct 2025)
EndedAt: 2025-10-30 18:19:59 -0400 (Thu, 30 Oct 2025)
EllapsedTime: 147.1 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 ORFik
###
##############################################################################
##############################################################################


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

--- re-building ‘Importing_Data.Rmd’ using rmarkdown

Quitting from Importing_Data.Rmd:164-177 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `S4Vectors:::load_package_gracefully()`:
! Could not load package GenomeInfoDbData. Is it installed?

  Note that the GenomeInfoDbData package is required by loadTaxonomyDb().
  Please install it with:

    BiocManager::install("GenomeInfoDbData")
---
Backtrace:
     ▆
  1. └─ORFik::getGenomeAndAnnotation(...)
  2.   └─ORFik:::get_genome_gtf(...)
  3.     └─ORFik::makeTxdbFromGenome(...)
  4.       └─ORFik:::makeTxdbTemplate(gtf, genome, organism)
  5.         └─ORFik::loadTxdb(gtf, organism = organismCapital, chrominfo = fa.seqinfo)
  6.           └─txdbmaker::makeTxDbFromGFF(txdb, organism = organism, chrominfo = chrominfo)
  7.             └─txdbmaker:::.prepareGFFMetadata(...)
  8.               └─GenomeInfoDb:::lookup_tax_id_by_organism(organism)
  9.                 └─GenomeInfoDb::loadTaxonomyDb()
 10.                   └─S4Vectors:::load_package_gracefully("GenomeInfoDbData", "by loadTaxonomyDb()")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Importing_Data.Rmd' failed with diagnostics:
Could not load package GenomeInfoDbData. Is it installed?

  Note that the GenomeInfoDbData package is required by loadTaxonomyDb().
  Please install it with:

    BiocManager::install("GenomeInfoDbData")
--- failed re-building ‘Importing_Data.Rmd’

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

--- re-building ‘ORFikOverview.Rmd’ using rmarkdown

Quitting from ORFikOverview.Rmd:60-65 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
---
Backtrace:
    ▆
 1. └─base::library(BSgenome.Hsapiens.UCSC.hg19)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ORFikOverview.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
--- failed re-building ‘ORFikOverview.Rmd’

--- re-building ‘Ribo-seq_pipeline-human.Rmd’ using rmarkdown
--- finished re-building ‘Ribo-seq_pipeline-human.Rmd’

--- re-building ‘Ribo-seq_pipeline-yeast.Rmd’ using rmarkdown
--- finished re-building ‘Ribo-seq_pipeline-yeast.Rmd’

--- re-building ‘Working_with_transcripts.Rmd’ using rmarkdown

Quitting from Working_with_transcripts.Rmd:28-42 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `S4Vectors:::load_package_gracefully()`:
! Could not load package GenomeInfoDbData. Is it installed?

  Note that the GenomeInfoDbData package is required by loadTaxonomyDb().
  Please install it with:

    BiocManager::install("GenomeInfoDbData")
---
Backtrace:
     ▆
  1. └─ORFik::getGenomeAndAnnotation(...)
  2.   └─ORFik:::get_genome_gtf(...)
  3.     └─ORFik::makeTxdbFromGenome(...)
  4.       └─ORFik:::makeTxdbTemplate(gtf, genome, organism)
  5.         └─ORFik::loadTxdb(gtf, organism = organismCapital, chrominfo = fa.seqinfo)
  6.           └─txdbmaker::makeTxDbFromGFF(txdb, organism = organism, chrominfo = chrominfo)
  7.             └─txdbmaker:::.prepareGFFMetadata(...)
  8.               └─GenomeInfoDb:::lookup_tax_id_by_organism(organism)
  9.                 └─GenomeInfoDb::loadTaxonomyDb()
 10.                   └─S4Vectors:::load_package_gracefully("GenomeInfoDbData", "by loadTaxonomyDb()")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Working_with_transcripts.Rmd' failed with diagnostics:
Could not load package GenomeInfoDbData. Is it installed?

  Note that the GenomeInfoDbData package is required by loadTaxonomyDb().
  Please install it with:

    BiocManager::install("GenomeInfoDbData")
--- failed re-building ‘Working_with_transcripts.Rmd’

SUMMARY: processing the following files failed:
  ‘Importing_Data.Rmd’ ‘ORFikOverview.Rmd’
  ‘Working_with_transcripts.Rmd’

Error: Vignette re-building failed.
Execution halted