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This page was generated on 2022-08-12 11:04:57 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4167
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for FELLA on nebbiolo2


To the developers/maintainers of the FELLA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FELLA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 657/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FELLA 1.17.0  (landing page)
Sergio Picart-Armada
Snapshot Date: 2022-08-11 14:00:04 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/FELLA
git_branch: master
git_last_commit: 5797113
git_last_commit_date: 2022-04-26 11:47:52 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.2.1 Monterey / x86_64  OK    ERROR  skippedskipped

Summary

Package: FELLA
Version: 1.17.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA
StartedAt: 2022-08-11 16:39:54 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 16:50:40 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 646.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-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
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname



Attaching package: 'igraph'

The following object is masked from 'package:IRanges':

    union

The following object is masked from 'package:S4Vectors':

    union

The following objects are masked from 'package:BiocGenerics':

    normalize, path, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

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/RtmpPyIjOf/my_database does not exist. Creating it...
Done.
Done.
Computing diffusion.matrix... (this may take a while and use some memory)
Computing diffusion.rowSums...
Done.
Loading KEGG graph data...
Done.
Loading hypergeom data...
Loading matrix...
'hypergeom.matrix.RData' not present in:/tmp/RtmpPyIjOf/my_database/hypergeom.matrix.RData. Hypergeometric test won't execute.
Done.
Loading diffusion data...
Loading matrix...
'diffusion.matrix.RData' not loaded. Simulated permutations may execute slower for diffusion.
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/RtmpPyIjOf/my_database/pagerank.rowSums.RData. Z-scores won't be available for pagerank.
Done.
Data successfully loaded.
Warning: LaTeX Warning: You have requested package `/home/biocbuild/bbs-3.16-bioc/R/libr
Warning: ary/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.
--- finished re-building ‘musmusculus.Rmd’

--- re-building ‘quickstart.Rmd’ using rmarkdown
No background compounds specified. Default background will be used.
Warning in defineCompounds(compounds = input.fail, data = FELLA.sample) :
  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.
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 hypergeom...
Starting hypergeometric p-values calculation...
Done.
Running diffusion...
Computing p-scores through the specified distribution.
Done.
Running PageRank...
Computing p-scores through the specified distribution.
Using provided damping factor...
Done.
--- finished re-building ‘quickstart.Rmd’

--- re-building ‘zebrafish.Rmd’ using rmarkdown
Building through KEGGREST...
Available gene annotations: ncbi-geneid, ncbi-proteinid. Using ncbi-geneid
Done.
Building graph...
Filtering 1 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/RtmpPyIjOf/my_database does not exist. Creating it...
Done.
Done.
Computing diffusion.matrix... (this may take a while and use some memory)
Computing diffusion.rowSums...
Done.
Loading KEGG graph data...
Done.
Loading hypergeom data...
Loading matrix...
'hypergeom.matrix.RData' not present in:/tmp/RtmpPyIjOf/my_database/hypergeom.matrix.RData. Hypergeometric test won't execute.
Done.
Loading diffusion data...
Loading matrix...
'diffusion.matrix.RData' not loaded. Simulated permutations may execute slower for diffusion.
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/RtmpPyIjOf/my_database/pagerank.rowSums.RData. Z-scores won't be available for pagerank.
Done.
Data successfully loaded.
Warning: LaTeX Warning: You have requested package `/home/biocbuild/bbs-3.16-bioc/R/libr
Warning: ary/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.
--- 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/RtmpPyIjOf/my_database does not exist. Creating it...
Done.
Done.
Computing diffusion.matrix... (this may take a while and use some memory)
Done
Computing diffusion.rowSums...
Done.
Loading KEGG graph data...
Done.
Loading hypergeom data...
Loading matrix...
'hypergeom.matrix.RData' not present in:/tmp/RtmpPyIjOf/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/RtmpPyIjOf/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.

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 10001 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