Build/check report for BioC 3.22 - BUILD results for CNVRanger on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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 CNVRanger on kjohnson3

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

Version: 1.25.4

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

StartedAt: 2025-10-26 16:00:38 -0400 (Sun, 26 Oct 2025)

EndedAt: 2025-10-26 16:06:02 -0400 (Sun, 26 Oct 2025)

EllapsedTime: 324.4 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 CNVRanger
###
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* checking for file ‘CNVRanger/DESCRIPTION’ ... OK
* preparing ‘CNVRanger’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CNVRanger.Rmd’ using rmarkdown

Quitting from CNVRanger.Rmd:384-386 [recurrViz]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
---
Backtrace:
     ▆
  1. └─CNVRanger::plotRecurrentRegions(cnvrs, genome = "bosTau6", chr = "chr1")
  2.   └─Gviz::IdeogramTrack(genome = genome, chr = chr, fontsize = 15)
  3.     └─methods::new(...)
  4.       ├─methods::initialize(value, ...)
  5.       └─Gviz::initialize(value, ...)
  6.         └─Gviz (local) .local(.Object, ...)
  7.           └─Gviz:::.cacheGenomes(genome = genome)
  8.             └─Gviz::.doCache(...)
  9.               ├─BiocGenerics::eval(expression, envir = callEnv)
 10.               ├─base::eval(expression, envir = callEnv)
 11.               │ └─base::eval(expression, envir = callEnv)
 12.               └─rtracklayer::ucscGenomes()
 13.                 ├─restfulr::read(url$list$ucscGenomes)
 14.                 └─restfulr::read(url$list$ucscGenomes)
 15.                   ├─base::tryCatch(...)
 16.                   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 17.                   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 18.                   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 19.                   └─x@protocol$read(x, cacheInfo)
 20.                     └─restfulr:::handleResponse(content, reader, cache.info, x@errorHandler)
 21.                       └─restfulr (local) errorHandler(responseError)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CNVRanger.Rmd' failed with diagnostics:

--- failed re-building ‘CNVRanger.Rmd’

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

Error: Vignette re-building failed.
Execution halted