Multiple platform build/check report for BioC 3.23 - BUILD results for ChIPseeker on nebbiolo1

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"	4874
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4582
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 ChIPseeker on nebbiolo1

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

Version: 1.47.1

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ChIPseeker

StartedAt: 2025-12-12 16:47:43 -0500 (Fri, 12 Dec 2025)

EndedAt: 2025-12-12 16:57:52 -0500 (Fri, 12 Dec 2025)

EllapsedTime: 608.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ChIPseeker
###
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* checking for file ‘ChIPseeker/DESCRIPTION’ ... OK
* preparing ‘ChIPseeker’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘ChIPseeker.Rmd’ using rmarkdown

Quitting from ChIPseeker.Rmd:488-496 [unnamed-chunk-41]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://rest.kegg.jp/link/hsa/pathway'
---
Backtrace:
     ▆
  1. └─clusterProfiler::compareCluster(...)
  2.   └─plyr::llply(...)
  3.     ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
  4.     └─base::lapply(pieces, .fun, ...)
  5.       └─clusterProfiler (local) FUN(X[[i]], ...)
  6.         ├─base::suppressMessages(fun(i, ...))
  7.         │ └─base::withCallingHandlers(...)
  8.         └─clusterProfiler (local) fun(i, ...)
  9.           └─clusterProfiler:::prepare_KEGG(species, "KEGG", keyType)
 10.             └─clusterProfiler::download_KEGG(species, KEGG_Type, keyType)
 11.               └─clusterProfiler:::download.KEGG.Path(species)
 12.                 └─clusterProfiler:::kegg_link(species, "pathway")
 13.                   └─clusterProfiler:::kegg_rest(url)
 14.                     └─yulab.utils::yread(rest_url)
 15.                       ├─base::do.call(reader, args = c(file, params))
 16.                       └─base (local) `<fn>`("https://rest.kegg.jp/link/hsa/pathway")
 17.                         └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ChIPseeker.Rmd' failed with diagnostics:
cannot open the connection to 'https://rest.kegg.jp/link/hsa/pathway'
--- failed re-building ‘ChIPseeker.Rmd’

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

Error: Vignette re-building failed.
Execution halted