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###
### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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
Warning: LaTeX Warning: You have requested package `/home/biocbuild/bbs-3.22-bioc/R/site
Warning: -library/BiocStyle/resources/tex/Bioconductor',
Warning:                but the package provides `Bioconductor'.
--- finished 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]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
---
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>`(2L)
  5. |     \-FELLA (local) .fun(piece, ...)
  6. |       \-KEGGREST::keggList(database = category)
  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]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
--- failed re-building ‘zebrafish.Rmd’

--- re-building ‘FELLA.Rnw’ using Sweave
Building through KEGGREST...
Available gene annotations: ncbi-geneid, ncbi-proteinid. Using ncbi-geneid
Done.
Building graph...
Filtering 5 pathways.
Done.
Pruning graph...
Current weight: 1 out of 4...
Current weight: 2 out of 4...
Current weight: 3 out of 4...
Current weight: 4 out of 4...
Done.
Computing probabilities for random subgraphs... (this may take a while)
Directory /tmp/Rtmp66DOEP/my_database does not exist. Creating it...
Done.
Done.
Computing diffusion.matrix... (this may take a while and use some memory)
Warning in asMethod(object) :
  sparse->dense coercion: allocating vector of size 1.1 GiB
Done
Computing diffusion.rowSums...
Done.
Loading KEGG graph data...
Done.
Loading hypergeom data...
Loading matrix...
'hypergeom.matrix.RData' not present in:/tmp/Rtmp66DOEP/my_database/hypergeom.matrix.RData. Hypergeometric test won't execute.
Done.
Loading diffusion data...
Loading matrix...
Done.
Loading rowSums...
Done.
Loading pagerank data...
Loading matrix...
'pagerank.matrix.RData' not loaded. Simulated permutations may execute slower for pagerank.
Done.
Loading rowSums...
'pagerank.rowSums.RData' not present in:/tmp/Rtmp66DOEP/my_database/pagerank.rowSums.RData. Z-scores won't be available for pagerank.
Done.
Data successfully loaded.
No background compounds specified. Default background will be used.
Warning in defineCompounds(compounds = compounds.epithelial, data = fella.data) :
  Some compounds were introduced as affected but they do not belong to the background. These compounds will be excluded from the analysis. Use 'getExcluded' to see them.
Running diffusion...
Computing p-scores through the specified distribution.
Done.
288 nodes below the threshold have been limited to 150 nodes.
288 nodes below the threshold have been limited to 150 nodes.

Warning in (function (OrgDb = NULL, annoDb = NULL, keytype = "ENTREZID",  :
  use 'annoDb' instead of 'OrgDb'

preparing gene to GO mapping data...
preparing IC data...
Writing diffusion results...
Done.
Writing diffusion enzymes...
Null GOterm provided to addGOToGraph. Only the GO labels will be added. To include similarity values as well, please specify a GOterm
Done.
Exporting to a csv file...
Writing diffusion results...
Done.
Done
288 nodes below the threshold have been limited to 250 nodes.
Exporting to the format pajek using igraph...
Done
No background compounds specified. Default background will be used.
Warning in defineCompounds(compounds = compounds, compoundsBackground = compoundsBackground,  :
  Some compounds were introduced as affected but they do not belong to the background. These compounds will be excluded from the analysis. Use 'getExcluded' to see them.
Running diffusion...
Computing p-scores through the specified distribution.
Done.
169 nodes below the threshold have been limited to 150 nodes.
No background compounds specified. Default background will be used.
Warning in defineCompounds(compounds = compounds, compoundsBackground = compoundsBackground,  :
  Some compounds were introduced as affected but they do not belong to the background. These compounds will be excluded from the analysis. Use 'getExcluded' to see them.
Running diffusion...
Computing p-scores through the specified distribution.
Done.
179 nodes below the threshold have been limited to 50 nodes.
--- finished re-building ‘FELLA.Rnw’

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

Error: Vignette re-building failed.
Execution halted