Rapid builds (Linux only) of a subset of BioC 3.22<BR>Report updated every 6 hours - BUILD results for GenomicRanges on teran2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	896
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BUILD results for GenomicRanges on teran2

To the developers/maintainers of the GenomicRanges 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: GenomicRanges

Version: 1.63.0

Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicRanges

StartedAt: 2025-10-30 12:42:43 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 12:43:04 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 20.9 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicRanges
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* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* preparing ‘GenomicRanges’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GenomicRangesIntroduction.Rmd’ using rmarkdown

Quitting from GenomicRangesIntroduction.Rmd:663-673 [subjectx_declaration]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package 'GenomicFeatures' required by 'TxDb.Hsapiens.UCSC.hg38.knownGene' could not be found
---
Backtrace:
    ▆
 1. └─base::library(TxDb.Hsapiens.UCSC.hg38.knownGene)
 2.   └─base::.getRequiredPackages2(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GenomicRangesIntroduction.Rmd' failed with diagnostics:
package 'GenomicFeatures' required by 'TxDb.Hsapiens.UCSC.hg38.knownGene' could not be found
--- failed re-building ‘GenomicRangesIntroduction.Rmd’

--- re-building ‘ExtendingGenomicRanges.Rnw’ using Sweave

Error: processing vignette 'ExtendingGenomicRanges.Rnw' failed with diagnostics:
 chunk 6 (label = vranges) 
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'extraColumnSlotNames': there is no package called ‘VariantAnnotation’

--- failed re-building ‘ExtendingGenomicRanges.Rnw’

--- re-building ‘GRanges_and_GRangesList_slides.Rnw’ using Sweave
Warning in .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

Error: processing vignette 'GRanges_and_GRangesList_slides.Rnw' failed with diagnostics:
 chunk 28 (label = findOverlaps1) 
Error in library(GenomicAlignments) : 
  there is no package called ‘GenomicAlignments’

--- failed re-building ‘GRanges_and_GRangesList_slides.Rnw’

--- re-building ‘GenomicRangesHOWTOs.Rnw’ using Sweave

Error: processing vignette 'GenomicRangesHOWTOs.Rnw' failed with diagnostics:
 chunk 6 (label = readGAlignments_2) 
Error in library(GenomicAlignments) : 
  there is no package called ‘GenomicAlignments’

--- failed re-building ‘GenomicRangesHOWTOs.Rnw’

--- re-building ‘Ten_things_slides.Rnw’ using Sweave
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit


Error: processing vignette 'Ten_things_slides.Rnw' failed with diagnostics:
 chunk 1 (label = setup) 
Error in library(BSgenome) : there is no package called ‘BSgenome’

--- failed re-building ‘Ten_things_slides.Rnw’

SUMMARY: processing the following files failed:
  ‘GenomicRangesIntroduction.Rmd’ ‘ExtendingGenomicRanges.Rnw’
  ‘GRanges_and_GRangesList_slides.Rnw’ ‘GenomicRangesHOWTOs.Rnw’
  ‘Ten_things_slides.Rnw’

Error: Vignette re-building failed.
Execution halted