Multiple platform build/check report for BioC 3.23 - BUILD results for GenomicRanges on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4826
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4491
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4562
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 GenomicRanges on lconway

To the developers/maintainers of the GenomicRanges package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicRanges.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: GenomicRanges

Version: 1.63.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicRanges

StartedAt: 2025-11-16 22:09:44 -0500 (Sun, 16 Nov 2025)

EndedAt: 2025-11-16 22:11:29 -0500 (Sun, 16 Nov 2025)

EllapsedTime: 104.8 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘GenomicRangesIntroduction.Rmd’ using rmarkdown
--- finished re-building ‘GenomicRangesIntroduction.Rmd’

--- re-building ‘ExtendingGenomicRanges.Rnw’ using Sweave
--- finished 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.)
2025-11-16 22:10:45.327 R[73914:4807488] XType: Using static font registry.

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

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

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

Error: processing vignette 'GenomicRangesHOWTOs.Rnw' failed with diagnostics:
 chunk 3 (label = pasillaBamSubset) 
Error in library(pasillaBamSubset) : 
  there is no package called ‘pasillaBamSubset’

--- 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

Loading required package: BiocIO
Loading required package: rtracklayer
--- finished re-building ‘Ten_things_slides.Rnw’

SUMMARY: processing the following files failed:
  ‘GRanges_and_GRangesList_slides.Rnw’ ‘GenomicRangesHOWTOs.Rnw’

Error: Vignette re-building failed.
Execution halted