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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GOFunction
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* checking for file ‘GOFunction/DESCRIPTION’ ... OK
* preparing ‘GOFunction’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GOFunction.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, 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, 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: graph
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:Rgraphviz’:

    from, to

The following object is masked from ‘package:base’:

    expand.grid


Loading required package: SparseM

Attaching package: ‘SparseM’

The following object is masked from ‘package:base’:

    backsolve

Loading required package: org.Hs.eg.db


Error: processing vignette 'GOFunction.Rnw' failed with diagnostics:
 chunk 1 (label = Example) 
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'

--- failed re-building ‘GOFunction.Rnw’

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

Error: Vignette re-building failed.
Execution halted