BioC 3.2: BUILD report for HTSanalyzeR on oaxaca

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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 HTSanalyzeR
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* checking for file ‘HTSanalyzeR/DESCRIPTION’ ... OK
* preparing ‘HTSanalyzeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: igraph

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

Warning: replacing previous import by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
/////////////////////////////////////////////////////////////////////////////

//------------------    Thanks for using HTSanalyzeR    -------------------//
 
//------------please use function changes() to see new changes-------------//

//------------please report any bug to xinwang2hms@gmail.com---------------//

/////////////////////////////////////////////////////////////////////////////
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:igraph’:

    normalize, union

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

    IQR, mad, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated,
    append, as.data.frame, as.vector, cbind, colnames,
    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,
    rep.int, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unlist, unsplit

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: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    compare


Attaching package: ‘IRanges’

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

    simplify

Loading required package: XML
Loading required package: graph

Attaching package: ‘graph’

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

    addNode

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

    degree, edges, intersection

Loading required package: RColorBrewer
Loading required package: genefilter

Attaching package: ‘genefilter’

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

    anyNA

Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
Loading required package: DBI



KEGG.db contains mappings based on older data because the
  original resource was removed from the the public domain
  before the most recent update was produced. This package
  should now be considered deprecated and future versions of
  Bioconductor may not have it available.  Users who want more
  current data are encouraged to look at the KEGGREST or
  reactome.db packages

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_MF of HyperGeo.results, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_BP of HyperGeo.results, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_CC of HyperGeo.results, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection PW_KEGG of HyperGeo.results, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_MF of GSEA.results, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_BP of GSEA.results, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_CC of GSEA.results, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection PW_KEGG of GSEA.results, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_MF of Sig.pvals.in.both, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_BP of Sig.pvals.in.both, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_CC of Sig.pvals.in.both, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection PW_KEGG of Sig.pvals.in.both, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_MF of Sig.adj.pvals.in.both, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_BP of Sig.adj.pvals.in.both, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection GO_CC of Sig.adj.pvals.in.both, and will be overwritten by new gene set terms!

Warning in FUN(X[[i]], ...) :
  --Gene Set terms already exsit in gene set collection PW_KEGG of Sig.adj.pvals.in.both, and will be overwritten by new gene set terms!

Loading required package: RBGL

Attaching package: ‘RBGL’

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

    bfs, dfs, transitivity

Warning in bumOptim(x = x, starts) :
  One or both parameters are on the limit of the defined parameter space

Error: processing vignette 'HTSanalyzeR-Vignette.Rnw' failed with diagnostics:
 chunk 36 (label = fitBUMplot) 
Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected
Execution halted
BioC 3.2: BUILD report for HTSanalyzeR on oaxaca

Summary

Command output
