fella.build

[Yikun]

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA
###
##############################################################################
##############################################################################

* 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
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'musmusculus.Rmd' failed with diagnostics:
LaTeX failed to compile /tmp/RtmpjthNsZ/Rbuild16700d24a5b97e/FELLA/vignettes/musmusculus.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See musmusculus.log for more info.
--- failed re-building ‘musmusculus.Rmd’

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

--- re-building ‘zebrafish.Rmd’ using rmarkdown
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'zebrafish.Rmd' failed with diagnostics:
LaTeX failed to compile /tmp/RtmpjthNsZ/Rbuild16700d24a5b97e/FELLA/vignettes/zebrafish.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See zebrafish.log for more info.
--- 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/RtmpcUbJg8/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/RtmpcUbJg8/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/RtmpcUbJg8/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 10000 milliseconds with 79678 bytes received

--- failed re-building ‘FELLA.Rnw’

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

Error: Vignette re-building failed.
Execution halted

[martin-g]

The fella package has been deprecated in 3.17 and removed for 3.18.