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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RTopper
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* checking for file ‘RTopper/DESCRIPTION’ ... OK
* preparing ‘RTopper’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RTopper.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.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: AnnotationDbi
Loading required package: stats4
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: ‘limma’

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

    plotMA


Error: processing vignette 'RTopper.Rnw' failed with diagnostics:
 chunk 21 (label = runBatchGSE.format3) 
Error in data.frame(fisher = gseUP.int.3$integrated$kegg, wilcoxon = gseUP.int$integrated$kegg) : 
  row names contain missing values

--- failed re-building ‘RTopper.Rnw’

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

Error: Vignette re-building failed.
Execution halted