Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/linkSet

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)/x86_64	ERROR	skipped	skipped	skipped

nebbiolo1 Summary

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Package: linkSet

Version: 0.99.5

RVersion: 4.5

BiocVersion: 3.21

BuildCommand: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data linkSet

BuildTime: 1 minutes 57.23 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: linkSet_20250317113021

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: linkSet. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 1.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

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

Quitting from hic_workthrough.Rmd:48-58 [setup_data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'http://www.enhanceratlas.org/data/download/enhancer/mm/Embryo_body.bed'
---
Backtrace:
    ▆
 1. ├─rtracklayer::import(file_url, format = "BED")
 2. └─rtracklayer::import(file_url, format = "BED")
 3.   ├─BiocIO::import(FileForFormat(con, format), ...)
 4.   └─rtracklayer::import(FileForFormat(con, format), ...)
 5.     └─rtracklayer (local) .local(con, format, text, ...)
 6.       └─rtracklayer:::queryForConnection(m, con, which)
 7.         └─BiocIO:::connectionForResource(manager, resource, open = "r")
 8.           ├─base::open(con, open)
 9.           └─base::open.connection(con, open)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'hic_workthrough.Rmd' failed with diagnostics:
cannot open the connection to 'http://www.enhanceratlas.org/data/download/enhancer/mm/Embryo_body.bed'
--- failed re-building ‘hic_workthrough.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output

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