##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data AlphaMissenseR
###
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* checking for file ‘AlphaMissenseR/DESCRIPTION’ ... OK
* preparing ‘AlphaMissenseR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘alphafold.Rmd’ using rmarkdown

Quitting from alphafold.Rmd:50-52 [am_available]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/records/10813168'
---
Backtrace:
    ▆
 1. └─AlphaMissenseR::am_available()
 2.   └─AlphaMissenseR:::am_available_from_internet(record, bfc)
 3.     ├─AlphaMissenseR:::am_record_json(record)
 4.     │ ├─base::withVisible(eval(mc, parent.frame()))
 5.     │ └─base::eval(mc, parent.frame())
 6.     │   └─base::eval(mc, parent.frame())
 7.     └─AlphaMissenseR (local) `<fn>`(record = record)
 8.       └─base::readLines(url, warn = FALSE)
 9.         └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'alphafold.Rmd' failed with diagnostics:
cannot open the connection to 'https://zenodo.org/api/records/10813168'
--- failed re-building ‘alphafold.Rmd’

--- re-building ‘benchmarking.Rmd’ using rmarkdown
2025-12-18 19:01:35.737 R[97160:323075054] XType: Using static font registry.
--- finished re-building ‘benchmarking.Rmd’

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

Quitting from clinvar.Rmd:60-62 [plot_P37023]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
---
Backtrace:
     ▆
  1. └─AlphaMissenseR::clinvar_plot(uniprotId = "P37023")
  2.   └─AlphaMissenseR:::clinvar_filter_am_table(...)
  3.     └─AlphaMissenseR::am_data("aa_substitutions")
  4.       └─AlphaMissenseR::am_available(record = record)
  5.         └─AlphaMissenseR:::am_available_from_internet(record, bfc)
  6.           ├─AlphaMissenseR:::am_record_is_latest(record)
  7.           │ ├─base::withVisible(eval(mc, parent.frame()))
  8.           │ └─base::eval(mc, parent.frame())
  9.           │   └─base::eval(mc, parent.frame())
 10.           └─AlphaMissenseR (local) `<fn>`(record = record)
 11.             └─base::readLines(latest_version_url, warn = FALSE)
 12.               └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'clinvar.Rmd' failed with diagnostics:
cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
--- failed re-building ‘clinvar.Rmd’

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

Quitting from introduction.Rmd:82-84 [am_available]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
---
Backtrace:
    ▆
 1. └─AlphaMissenseR::am_available()
 2.   └─AlphaMissenseR:::am_available_from_internet(record, bfc)
 3.     ├─AlphaMissenseR:::am_record_is_latest(record)
 4.     │ ├─base::withVisible(eval(mc, parent.frame()))
 5.     │ └─base::eval(mc, parent.frame())
 6.     │   └─base::eval(mc, parent.frame())
 7.     └─AlphaMissenseR (local) `<fn>`(record = record)
 8.       └─base::readLines(latest_version_url, warn = FALSE)
 9.         └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
--- failed re-building ‘introduction.Rmd’

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

Quitting from issues.Rmd:73-75 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
---
Backtrace:
     ▆
  1. └─AlphaMissenseR::am_data("gene_hg38")
  2.   └─AlphaMissenseR::am_available(record = record)
  3.     └─AlphaMissenseR:::am_available_from_internet(record, bfc)
  4.       ├─AlphaMissenseR:::am_record_is_latest(record)
  5.       │ ├─base::withVisible(eval(mc, parent.frame()))
  6.       │ └─base::eval(mc, parent.frame())
  7.       │   └─base::eval(mc, parent.frame())
  8.       └─AlphaMissenseR (local) `<fn>`(record = record)
  9.         └─base::readLines(latest_version_url, warn = FALSE)
 10.           └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'issues.Rmd' failed with diagnostics:
cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
--- failed re-building ‘issues.Rmd’

SUMMARY: processing the following files failed:
  ‘alphafold.Rmd’ ‘clinvar.Rmd’ ‘introduction.Rmd’ ‘issues.Rmd’

Error: Vignette re-building failed.
Execution halted