Multiple platform build/check report for BioC 3.22 - BUILD results for epistack on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4749
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4511
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4548
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4489
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4453
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 epistack on lconway

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

Version: 1.15.0

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

StartedAt: 2025-05-18 16:41:52 -0400 (Sun, 18 May 2025)

EndedAt: 2025-05-18 16:42:37 -0400 (Sun, 18 May 2025)

EllapsedTime: 44.5 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data epistack
###
##############################################################################
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* checking for file ‘epistack/DESCRIPTION’ ... OK
* preparing ‘epistack’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘using_epistack.Rmd’ using rmarkdown
2025-05-18 16:42:24.662 R[32513:31077328] XType: com.apple.fonts is not accessible.
2025-05-18 16:42:24.662 R[32513:31077328] XType: XTFontStaticRegistry is enabled.

Quitting from using_epistack.Rmd:233-236 [peak_loading]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://raw.githubusercontent.com/Bioconductor/CSAMA2016/master/lab-5-chipseq/EpigeneticsCSAMA/inst/bedfiles/Rep1_peaks_ucsc_chr6.bed'
---
Backtrace:
     ▆
  1. ├─BiocGenerics::lapply(path_peaks, import)
  2. └─base::lapply(path_peaks, import)
  3.   ├─BiocIO (local) FUN(X[[i]], ...)
  4.   └─BiocIO (local) FUN(X[[i]], ...)
  5.     ├─BiocIO::import(FileForFormat(con), ...)
  6.     └─rtracklayer::import(FileForFormat(con), ...)
  7.       └─rtracklayer (local) .local(con, format, text, ...)
  8.         └─rtracklayer:::queryForConnection(m, con, which)
  9.           └─BiocIO:::connectionForResource(manager, resource, open = "r")
 10.             ├─base::open(con, open)
 11.             └─base::open.connection(con, open)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'using_epistack.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/Bioconductor/CSAMA2016/master/lab-5-chipseq/EpigeneticsCSAMA/inst/bedfiles/Rep1_peaks_ucsc_chr6.bed'
--- failed re-building ‘using_epistack.Rmd’

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

Error: Vignette re-building failed.
Execution halted