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BUILD report for FELLA on merida2

This page was generated on 2019-04-09 13:36:38 -0400 (Tue, 09 Apr 2019).

Package 535/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FELLA 1.3.1
Sergio Picart-Armada
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/FELLA
Branch: master
Last Commit: 3fca6aa
Last Changed Date: 2019-02-15 03:55:59 -0400 (Fri, 15 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: FELLA
Version: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA
StartedAt: 2019-04-08 22:24:51 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:31:44 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 412.3 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/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
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, 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, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, 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 object is masked from 'package:base':

    expand.grid



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...
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/RtmptjTtnN/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/RtmptjTtnN/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/RtmptjTtnN/my_database/pagerank.rowSums.RData. Z-scores won't be available for pagerank.
Done.
Data successfully loaded.
Warning: LaTeX Warning: You have requested package `/Library/Frameworks/R.framework/Vers
ions/3.6/Resources/library/BiocStyle/resources/tex/Bioconductor',
               but the package provides `Bioconductor'.
Package geometry Warning: Over-specification in `h'-direction.
    `width' (384.1122pt) is ignored.
Package Fancyhdr Warning: \fancyhead's `E' option without twoside option is use
less on input line 173.
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.
sh: line 1: 92772 Abort trap: 6           'convert' 'quickstart_files/figure-html/unnamed-chunk-12-1.png' -trim 'quickstart_files/figure-html/unnamed-chunk-12-1.png' > /dev/null
sh: line 1: 92783 Abort trap: 6           'convert' 'quickstart_files/figure-html/unnamed-chunk-13-1.png' -trim 'quickstart_files/figure-html/unnamed-chunk-13-1.png' > /dev/null
sh: line 1: 92809 Abort trap: 6           'convert' 'quickstart_files/figure-html/unnamed-chunk-14-1.png' -trim 'quickstart_files/figure-html/unnamed-chunk-14-1.png' > /dev/null
Building through KEGGREST...
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/RtmptjTtnN/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/RtmptjTtnN/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/RtmptjTtnN/my_database/pagerank.rowSums.RData. Z-scores won't be available for pagerank.
Done.
Data successfully loaded.
Warning: LaTeX Warning: You have requested package `/Library/Frameworks/R.framework/Vers
ions/3.6/Resources/library/BiocStyle/resources/tex/Bioconductor',
               but the package provides `Bioconductor'.
Package geometry Warning: Over-specification in `h'-direction.
    `width' (384.1122pt) is ignored.
Package Fancyhdr Warning: \fancyhead's `E' option without twoside option is use
less on input line 173.
Building through KEGGREST...
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/RtmptjTtnN/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/RtmptjTtnN/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/RtmptjTtnN/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.
262 nodes below the threshold have been limited to 150 nodes.
262 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 bmAttrFilt("filters", mart, verbose = verbose) : 
  biomaRt error: looks like we're connecting to incompatible version of BioMart suite.
Execution halted