Multiple platform build/check report for BioC 3.9 - BUILD report for SeqGSEA on tokay2

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### Running command:
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###   chmod a+r SeqGSEA -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data SeqGSEA
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* checking for file 'SeqGSEA/DESCRIPTION' ... OK
* preparing 'SeqGSEA':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'SeqGSEA.Rnw' using Sweave
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: DESeq
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
Warning: executing %dopar% sequentially: no parallel backend registered
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in phifun(x, ctable, mu) :
  closing unused connection 6 (<-TOKAY2:11031)
Warning in phifun(x, ctable, mu) :
  closing unused connection 5 (<-TOKAY2:11031)
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.

Error: processing vignette 'SeqGSEA.Rnw' failed with diagnostics:
 chunk 38 (label = main_gsea_DE) 
Error in getBM(values = ensembl.genes, attributes = c("ensembl_gene_id",  : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. 
Please report this on the support site at http://support.bioconductor.org

--- failed re-building 'SeqGSEA.Rnw'

Warning in file.remove(f) :
  cannot remove file 'Rplots.pdf', reason 'Permission denied'
Warning in file.remove(f) :
  cannot remove file 'SeqGSEA.tex', reason 'Permission denied'
SUMMARY: processing the following file failed:
  'SeqGSEA.Rnw'

Error: Vignette re-building failed.
Execution halted
BUILD report for SeqGSEA on tokay2

Summary

Command output
