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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data linkSet
###
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* 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
zcat: can't stat: /private/tmp/RtmpxUmdSl/Rinsta28234e668c5/linkSet/extdata/toyExample.pair.gz (/private/tmp/RtmpxUmdSl/Rinsta28234e668c5/linkSet/extdata/toyExample.pair.gz.Z): No such file or directory
zcat: can't stat: /private/tmp/RtmpxUmdSl/Rinsta28234e668c5/linkSet/extdata/toyExample.pair.gz (/private/tmp/RtmpxUmdSl/Rinsta28234e668c5/linkSet/extdata/toyExample.pair.gz.Z): No such file or directory

Quitting from hic_workthrough.Rmd:94-132 [setup-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readvalidPairs()`:
! File has fewer columns than expected minimum
---
Backtrace:
    ▆
 1. └─linkSet::readvalidPairs(hic_file, format = "pair")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'hic_workthrough.Rmd' failed with diagnostics:
File has fewer columns than expected minimum
--- failed re-building ‘hic_workthrough.Rmd’

--- re-building ‘linkSet.Rmd’ using rmarkdown
2025-08-21 17:23:22.348 R[45585:81399098] XType: com.apple.fonts is not accessible.
2025-08-21 17:23:22.348 R[45585:81399098] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘linkSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted