##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi
###
##############################################################################
##############################################################################


* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* preparing ‘pgxRpi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction_1_load_metadata.Rmd’ using rmarkdown

Quitting from Introduction_1_load_metadata.Rmd:183-188 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (nrow(meta.sel.df) == 0) ...`:
! argument is of length zero
---
Backtrace:
    ▆
 1. └─pgxRpi::pgxMetaplot(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Introduction_1_load_metadata.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Introduction_1_load_metadata.Rmd’

--- re-building ‘Introduction_2_query_variants.Rmd’ using rmarkdown

Quitting from Introduction_2_query_variants.Rmd:76-79 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (grepl("^https?://", domain)) ...`:
! argument is of length zero
---
Backtrace:
    ▆
 1. └─pgxRpi::pgxLoader(type = "g_variants", biosample_id = biosample_id)
 2.   └─pgxRpi:::pgxVariantLoader(...)
 3.     └─pgxRpi:::read_variant_beacon(...)
 4.       └─pgxRpi:::normalize_domain(domain, use_https)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Introduction_2_query_variants.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Introduction_2_query_variants.Rmd’

--- re-building ‘Introduction_3_access_cnv_frequency.Rmd’ using rmarkdown

Quitting from Introduction_3_access_cnv_frequency.Rmd:49-54 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Could not resolve hostname [progenetix.org]:
Could not resolve host: progenetix.org
---
Backtrace:
    ▆
 1. ├─pgxRpi::pgxLoader(...)
 2. │ └─pgxRpi:::pgxFreqLoader(output = output, filters = filters, domain = domain)
 3. │   └─httr::GET(encoded_url)
 4. │     └─httr:::request_perform(req, hu$handle$handle)
 5. │       ├─httr:::request_fetch(req$output, req$url, handle)
 6. │       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 7. │         └─curl::curl_fetch_memory(url, handle = handle)
 8. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Introduction_3_access_cnv_frequency.Rmd' failed with diagnostics:
Could not resolve hostname [progenetix.org]:
Could not resolve host: progenetix.org
--- failed re-building ‘Introduction_3_access_cnv_frequency.Rmd’

--- re-building ‘Introduction_4_process_pgxseg.Rmd’ using rmarkdown
2025-10-26 17:33:18.267 R[98662:550850972] XType: Using static font registry.
--- finished re-building ‘Introduction_4_process_pgxseg.Rmd’

SUMMARY: processing the following files failed:
  ‘Introduction_1_load_metadata.Rmd’
  ‘Introduction_2_query_variants.Rmd’
  ‘Introduction_3_access_cnv_frequency.Rmd’

Error: Vignette re-building failed.
Execution halted