Multiple platform build/check report for BioC 3.22 - BUILD results for coMET on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 beta (2025-04-02 r88102) -- "How About a Twenty-Six"	4737
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-03 r88103 ucrt) -- "How About a Twenty-Six"	4524
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 coMET on palomino8

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

Version: 1.39.1

Command: chmod a+r coMET -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data coMET

StartedAt: 2025-04-08 18:18:16 -0400 (Tue, 08 Apr 2025)

EndedAt: 2025-04-08 18:20:53 -0400 (Tue, 08 Apr 2025)

EllapsedTime: 157.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r coMET -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data coMET
###
##############################################################################
##############################################################################


* checking for file 'coMET/DESCRIPTION' ... OK
* preparing 'coMET':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'coMET.Rnw' using knitr

Quitting from coMET.Rnw:336-345 [cometwebPlot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
! Internal Server Error
---
Backtrace:
     x
  1. \-coMET::comet.web(...)
  2.   \-coMET:::draw.plot.comet.web(config.var, gbl.var, newpage = TRUE)
  3.     \-coMET:::draw.plot.grid.setup(config.var, gbl.var)
  4.       \-Gviz::IdeogramTrack(genome = gbl.var$mydata.gen, chromosome = gbl.var$mydata.chr)
  5.         \-methods::new(...)
  6.           +-methods::initialize(value, ...)
  7.           \-Gviz::initialize(value, ...)
  8.             \-Gviz (local) .local(.Object, ...)
  9.               \-Gviz:::.cacheGenomes(genome = genome)
 10.                 +-Gviz::.doCache(...)
 11.                 | +-BiocGenerics::eval(expression, envir = callEnv)
 12.                 | \-base::eval(expression, envir = callEnv)
 13.                 |   \-base::eval(expression, envir = callEnv)
 14.                 +-rtracklayer::getTable(query)
 15.                 \-rtracklayer::getTable(query)
 16.                   \-rtracklayer (local) .local(object, ...)
 17.                     +-restfulr::read(url$getData$track, query)
 18.                     \-restfulr::read(url$getData$track, query)
 19.                       +-base::tryCatch(...)
 20.                       | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
 21.                       |   \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 22.                       |     \-base (local) doTryCatch(return(expr), name, parentenv, handler)
 23.                       \-x@protocol$read(x, cacheInfo)
 24.                         \-restfulr:::handleResponse(content, reader, cache.info, x@errorHandler)
 25.                           \-restfulr (local) errorHandler(responseError)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'coMET.Rnw' failed with diagnostics:
Internal Server Error

--- failed re-building 'coMET.Rnw'

SUMMARY: processing the following file failed:
  'coMET.Rnw'

Error: Vignette re-building failed.
Execution halted