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

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

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

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

Quitting from clinical.Rmd:67-77 [BCR_Biotab]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! GDC server down, try to use this package later
---
Backtrace:
    ▆
 1. └─TCGAbiolinks::GDCquery(...)
 2.   └─TCGAbiolinks::isServeOK() at TCGAbiolinks/R/query.R:162:5
 3.     └─base::tryCatch(...) at TCGAbiolinks/R/internal.R:32:5
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'clinical.Rmd' failed with diagnostics:
GDC server down, try to use this package later
--- failed re-building ‘clinical.Rmd’

--- re-building ‘download_prepare.Rmd’ using rmarkdown
[WARNING] Could not fetch resource https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/fonts/fontawesome-webfont.eot?v=4.4.0: HttpExceptionRequest Request {
    host                 = "maxcdn.bootstrapcdn.com"
    port                 = 443
    secure               = True
    requestHeaders       = []
    path                 = "/font-awesome/4.4.0/fonts/fontawesome-webfont.eot"
    queryString          = "?v=4.4.0"
    method               = "GET"
    proxy                = Nothing
    rawBody              = False
    redirectCount        = 10
    responseTimeout      = ResponseTimeoutDefault
    requestVersion       = HTTP/1.1
    proxySecureMode      = ProxySecureWithConnect
  }
   (InternalException (HandshakeFailed (Error_Misc "Network.Socket.recvBuf: resource vanished (Connection reset by peer)")))
--- finished re-building ‘download_prepare.Rmd’

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

Quitting from extension.Rmd:46-49 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [api.gdc.cancer.gov]:
Connection timed out after 10003 milliseconds
---
Backtrace:
     ▆
  1. ├─TCGAbiolinks::getGDCprojects()
  2. │ ├─jsonlite::fromJSON(...) at TCGAbiolinks/R/internal.R:143:5
  3. │ ├─httr::content(GET(url), as = "text", encoding = "UTF-8")
  4. │ │ ├─base::stopifnot(is.response(x))
  5. │ │ └─httr:::is.response(x)
  6. │ └─httr::GET(url)
  7. │   └─httr:::request_perform(req, hu$handle$handle)
  8. │     ├─httr:::request_fetch(req$output, req$url, handle)
  9. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 10. │       └─curl::curl_fetch_memory(url, handle = handle)
 11. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'extension.Rmd' failed with diagnostics:
Timeout was reached [api.gdc.cancer.gov]:
Connection timed out after 10003 milliseconds
--- failed re-building ‘extension.Rmd’

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

--- re-building ‘mutation.Rmd’ using rmarkdown
2025-12-12 18:00:15.521 R[91139:378362549] XType: Using static font registry.
--- finished re-building ‘mutation.Rmd’

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

Quitting from query.Rmd:95-103 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [api.gdc.cancer.gov]:
Connection timed out after 10003 milliseconds
---
Backtrace:
     ▆
  1. ├─DT::datatable(...)
  2. │ └─crosstalk::is.SharedData(data)
  3. ├─TCGAbiolinks:::getGDCprojects()
  4. │ ├─jsonlite::fromJSON(...) at TCGAbiolinks/R/internal.R:143:5
  5. │ ├─httr::content(GET(url), as = "text", encoding = "UTF-8")
  6. │ │ ├─base::stopifnot(is.response(x))
  7. │ │ └─httr:::is.response(x)
  8. │ └─httr::GET(url)
  9. │   └─httr:::request_perform(req, hu$handle$handle)
 10. │     ├─httr:::request_fetch(req$output, req$url, handle)
 11. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 12. │       └─curl::curl_fetch_memory(url, handle = handle)
 13. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'query.Rmd' failed with diagnostics:
Timeout was reached [api.gdc.cancer.gov]:
Connection timed out after 10003 milliseconds
--- failed re-building ‘query.Rmd’

--- re-building ‘stemness_score.Rmd’ using rmarkdown
[WARNING] Could not fetch resource https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/fonts/fontawesome-webfont.woff?v=4.4.0: HttpExceptionRequest Request {
    host                 = "maxcdn.bootstrapcdn.com"
    port                 = 443
    secure               = True
    requestHeaders       = []
    path                 = "/font-awesome/4.4.0/fonts/fontawesome-webfont.woff"
    queryString          = "?v=4.4.0"
    method               = "GET"
    proxy                = Nothing
    rawBody              = False
    redirectCount        = 10
    responseTimeout      = ResponseTimeoutDefault
    requestVersion       = HTTP/1.1
    proxySecureMode      = ProxySecureWithConnect
  }
   NoResponseDataReceived
--- finished re-building ‘stemness_score.Rmd’

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

SUMMARY: processing the following files failed:
  ‘clinical.Rmd’ ‘extension.Rmd’ ‘query.Rmd’

Error: Vignette re-building failed.
Execution halted