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

Quitting from musmusculus.Rmd:74-84 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [rest.kegg.jp]: Send failure: Broken pipe
---
Backtrace:
    x
 1. +-KEGGREST::keggLink("enzyme", "mmu")
 2. | \-KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
 3. |   \-httr::GET(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 'musmusculus.Rmd' failed with diagnostics:
Timeout was reached [rest.kegg.jp]: Send failure: Broken pipe
--- failed re-building ‘musmusculus.Rmd’

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

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

Quitting from zebrafish.Rmd:50-74 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [rest.kegg.jp]: Connection timed out after 10002 milliseconds
---
Backtrace:
     x
  1. +-FELLA::buildGraphFromKEGGREST(organism = "dre", filter.path = c("01100"))
  2. | \-plyr::llply(...)
  3. |   +-plyr:::loop_apply(n, do.ply)
  4. |   \-plyr (local) `<fn>`(1L)
  5. |     \-FELLA (local) .fun(piece, ...)
  6. |       \-KEGGREST::keggList(database = category, organism = organism)
  7. |         \-KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
  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 'zebrafish.Rmd' failed with diagnostics:
Timeout was reached [rest.kegg.jp]: Connection timed out after 10002 milliseconds
--- failed re-building ‘zebrafish.Rmd’

--- re-building ‘FELLA.Rnw’ using Sweave
Building through KEGGREST...

Error: processing vignette 'FELLA.Rnw' failed with diagnostics:
 chunk 2 (label = 01_graph) 
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [rest.kegg.jp]: Connection timed out after 10002 milliseconds

--- failed re-building ‘FELLA.Rnw’

SUMMARY: processing the following files failed:
  ‘musmusculus.Rmd’ ‘zebrafish.Rmd’ ‘FELLA.Rnw’

Error: Vignette re-building failed.
Execution halted