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### Running command:
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###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/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
--- finished re-building ‘clinical.Rmd’

--- re-building ‘download_prepare.Rmd’ using rmarkdown
--- 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()`:
! Failure when receiving data from the peer [api.gdc.cancer.gov]:
Recv failure: Connection reset by peer
---
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:
Failure when receiving data from the peer [api.gdc.cancer.gov]:
Recv failure: Connection reset by peer
--- failed re-building ‘extension.Rmd’

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

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

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

Quitting from query.Rmd:219-294 [queries]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://api.gdc.cancer.gov/projects/TCGA-ACC?expand=summary,summary.data_categories&pretty=true'
---
Backtrace:
     ▆
  1. └─TCGAbiolinks::GDCquery(...)
  2.   └─TCGAbiolinks:::getGDCquery(...) at TCGAbiolinks/R/query.R:223:9
  3.     ├─base::paste0("size=", getNbFiles(project, data.category)) at TCGAbiolinks/R/query.R:621:5
  4.     └─TCGAbiolinks:::getNbFiles(project, data.category) at TCGAbiolinks/R/query.R:621:5
  5.       └─TCGAbiolinks::getProjectSummary(project) at TCGAbiolinks/R/api.R:327:5
  6.         └─jsonlite::fromJSON(url, simplifyDataFrame = TRUE) at TCGAbiolinks/R/api.R:291:5
  7.           └─jsonlite:::parse_and_simplify(...)
  8.             └─jsonlite:::parseJSON(txt, bigint_as_char)
  9.               └─jsonlite:::parse_con(txt, bigint_as_char)
 10.                 ├─base::open(con, "rb")
 11.                 └─base::open.connection(con, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'query.Rmd' failed with diagnostics:
cannot open the connection to 'https://api.gdc.cancer.gov/projects/TCGA-ACC?expand=summary,summary.data_categories&pretty=true'
--- failed re-building ‘query.Rmd’

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

Quitting from stemness_score.Rmd:51-83 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! EDASeq package is needed for this function to work. Please install it.
---
Backtrace:
    ▆
 1. └─TCGAbiolinks::TCGAanalyze_Normalization(tabDF = dataBRCA, geneInfo = geneInfo)
 2.   └─TCGAbiolinks:::check_package("EDASeq") at TCGAbiolinks/R/analyze.R:585:5
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'stemness_score.Rmd' failed with diagnostics:
EDASeq package is needed for this function to work. Please install it.
--- failed re-building ‘stemness_score.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted