Multiple platform build/check report for BioC 3.20 - BUILD results for ELMER on nebbiolo2

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 ELMER on nebbiolo2

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

Version: 2.30.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ELMER

StartedAt: 2025-03-17 17:58:28 -0400 (Mon, 17 Mar 2025)

EndedAt: 2025-03-17 18:03:47 -0400 (Mon, 17 Mar 2025)

EllapsedTime: 319.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ELMER
###
##############################################################################
##############################################################################


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

--- re-building ‘analysis_diff_meth.Rmd’ using rmarkdown
--- finished re-building ‘analysis_diff_meth.Rmd’

--- re-building ‘analysis_get_pair.Rmd’ using rmarkdown
--- finished re-building ‘analysis_get_pair.Rmd’

--- re-building ‘analysis_gui.Rmd’ using rmarkdown
--- finished re-building ‘analysis_gui.Rmd’

--- re-building ‘analysis_motif_enrichment.Rmd’ using rmarkdown
--- finished re-building ‘analysis_motif_enrichment.Rmd’

--- re-building ‘analysis_regulatory_tf.Rmd’ using rmarkdown
--- finished re-building ‘analysis_regulatory_tf.Rmd’

--- re-building ‘index.Rmd’ using rmarkdown
--- finished re-building ‘index.Rmd’

--- re-building ‘input.Rmd’ using rmarkdown
--- finished re-building ‘input.Rmd’

--- re-building ‘pipe.Rmd’ using rmarkdown
--- finished re-building ‘pipe.Rmd’

--- re-building ‘plots_TF.Rmd’ using rmarkdown
Warning: ggrepel: 66 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘plots_TF.Rmd’

--- re-building ‘plots_heatmap.Rmd’ using rmarkdown
--- finished re-building ‘plots_heatmap.Rmd’

--- re-building ‘plots_motif_enrichment.Rmd’ using rmarkdown
--- finished re-building ‘plots_motif_enrichment.Rmd’

--- re-building ‘plots_scatter.Rmd’ using rmarkdown
--- finished re-building ‘plots_scatter.Rmd’

--- re-building ‘plots_schematic.Rmd’ using rmarkdown

Quitting from plots_schematic.Rmd:43-51 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
! Internal Server Error
---
Backtrace:
     ▆
  1. └─ELMER::schematic.plot(...)
  2.   ├─base::suppressWarnings(...)
  3.   │ └─base::withCallingHandlers(...)
  4.   └─ELMER:::schematic(...)
  5.     └─Gviz::IdeogramTrack(genome = metadata(data)$genome, chromosome = chr)
  6.       └─methods::new(...)
  7.         ├─methods::initialize(value, ...)
  8.         └─Gviz::initialize(value, ...)
  9.           └─Gviz (local) .local(.Object, ...)
 10.             └─Gviz:::.cacheGenomes(genome = genome)
 11.               ├─Gviz::.doCache(...)
 12.               │ ├─BiocGenerics::eval(expression, envir = callEnv)
 13.               │ └─base::eval(expression, envir = callEnv)
 14.               │   └─base::eval(expression, envir = callEnv)
 15.               ├─rtracklayer::getTable(query)
 16.               └─rtracklayer::getTable(query)
 17.                 └─rtracklayer (local) .local(object, ...)
 18.                   ├─restfulr::read(url$getData$track, query)
 19.                   └─restfulr::read(url$getData$track, query)
 20.                     ├─base::tryCatch(...)
 21.                     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 22.                     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 23.                     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 24.                     └─x@protocol$read(x, cacheInfo)
 25.                       └─restfulr:::handleResponse(content, reader, cache.info, x@errorHandler)
 26.                         └─restfulr (local) errorHandler(responseError)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'plots_schematic.Rmd' failed with diagnostics:
Internal Server Error

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

--- re-building ‘usecase.Rmd’ using rmarkdown
--- finished re-building ‘usecase.Rmd’

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

Error: Vignette re-building failed.
Execution halted