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### Running command:
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###   /Library/Frameworks/R.framework/Resources/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
Warning: LaTeX Warning: You have requested package `/Library/Frameworks/R.framework/Vers
Warning: ions/4.2-arm64/Resources/library/BiocStyle/resources/tex/Bioconductor',
Warning:                but the package provides `Bioconductor'.
Warning: Package geometry Warning: Over-specification in `h'-direction.
Warning:     `width' (384.1122pt) is ignored.
Warning: Package fancyhdr Warning: \fancyhead's `E' option without twoside option is use
Warning: less on input line 162.
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
--- finished re-building ‘musmusculus.Rmd’

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

--- re-building ‘zebrafish.Rmd’ using rmarkdown
Warning: LaTeX Warning: You have requested package `/Library/Frameworks/R.framework/Vers
Warning: ions/4.2-arm64/Resources/library/BiocStyle/resources/tex/Bioconductor',
Warning:                but the package provides `Bioconductor'.
Warning: Package geometry Warning: Over-specification in `h'-direction.
Warning:     `width' (384.1122pt) is ignored.
Warning: Package fancyhdr Warning: \fancyhead's `E' option without twoside option is use
Warning: less on input line 162.
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
--- finished 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/Rtmpc2wsPT/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 1.0 GiB
Done
Computing diffusion.rowSums...
Done.
Loading KEGG graph data...
Done.
Loading hypergeom data...
Loading matrix...
'hypergeom.matrix.RData' not present in:/tmp/Rtmpc2wsPT/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/Rtmpc2wsPT/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.
290 nodes below the threshold have been limited to 150 nodes.
290 nodes below the threshold have been limited to 150 nodes.

Error: processing vignette 'FELLA.Rnw' failed with diagnostics:
 chunk 15 (label = 04_go) 
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [www.ensembl.org:443] Operation timed out after 10133 milliseconds with 0 bytes received

--- failed re-building ‘FELLA.Rnw’

SUMMARY: processing the following file failed:
  ‘FELLA.Rnw’

Error: Vignette re-building failed.
Execution halted