Multiple platform build/check report for BioC 3.20 - BUILD results for DMRcate on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4756
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4514
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4441
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4406
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 DMRcate on merida1

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

Version: 3.2.1

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

StartedAt: 2025-03-17 19:17:23 -0400 (Mon, 17 Mar 2025)

EndedAt: 2025-03-17 19:40:51 -0400 (Mon, 17 Mar 2025)

EllapsedTime: 1408.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DMRcate
###
##############################################################################
##############################################################################


* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* preparing ‘DMRcate’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘EPICv1_and_450K.Rnw’ using knitr

Quitting from EPICv1_and_450K.Rnw:125-132 [plotting]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
! Internal Server Error
---
Backtrace:
     x
  1. \-DMRcate::DMR.plot(...)
  2.   \-Gviz::IdeogramTrack(genome = genome, chromosome = as.character(seqnames(ranges.inplot)))
  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::getTable(query)
 13.             \-rtracklayer::getTable(query)
 14.               \-rtracklayer (local) .local(object, ...)
 15.                 +-restfulr::read(url$getData$track, query)
 16.                 \-restfulr::read(url$getData$track, query)
 17.                   +-base::tryCatch(...)
 18.                   | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
 19.                   |   \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 20.                   |     \-base (local) doTryCatch(return(expr), name, parentenv, handler)
 21.                   \-x@protocol$read(x, cacheInfo)
 22.                     \-restfulr:::handleResponse(content, reader, cache.info, x@errorHandler)
 23.                       \-restfulr (local) errorHandler(responseError)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'EPICv1_and_450K.Rnw' failed with diagnostics:
Internal Server Error

--- failed re-building ‘EPICv1_and_450K.Rnw’

--- re-building ‘EPICv2.Rnw’ using knitr
--- finished re-building ‘EPICv2.Rnw’

--- re-building ‘sequencing.Rnw’ using knitr

Quitting from sequencing.Rnw:122-132 [seqDMRplot1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
! Internal Server Error
---
Backtrace:
     x
  1. \-DMRcate::DMR.plot(...)
  2.   \-Gviz::IdeogramTrack(genome = genome, chromosome = as.character(seqnames(ranges.inplot)))
  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::getTable(query)
 13.             \-rtracklayer::getTable(query)
 14.               \-rtracklayer (local) .local(object, ...)
 15.                 +-restfulr::read(url$getData$track, query)
 16.                 \-restfulr::read(url$getData$track, query)
 17.                   +-base::tryCatch(...)
 18.                   | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
 19.                   |   \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 20.                   |     \-base (local) doTryCatch(return(expr), name, parentenv, handler)
 21.                   \-x@protocol$read(x, cacheInfo)
 22.                     \-restfulr:::handleResponse(content, reader, cache.info, x@errorHandler)
 23.                       \-restfulr (local) errorHandler(responseError)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

SUMMARY: processing the following files failed:
  ‘EPICv1_and_450K.Rnw’ ‘sequencing.Rnw’

Error: Vignette re-building failed.
Execution halted