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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 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:112-122 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! GDC server down, try to use this package later
---
Backtrace:
    ▆
 1. └─TCGAbiolinks::GDCprepare(query_biospecimen)
 2.   └─TCGAbiolinks::isServeOK() at TCGAbiolinks/R/prepare.R:60:5
 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
--- finished re-building ‘download_prepare.Rmd’

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

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

--- re-building ‘mutation.Rmd’ using rmarkdown
2025-10-30 18:58:13.250 R[61846:684295625] XType: com.apple.fonts is not accessible.
2025-10-30 18:58:13.250 R[61846:684295625] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘mutation.Rmd’

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

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

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

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

Error: Vignette re-building failed.
Execution halted