BioC 3.1: BUILD report for a4 on petty

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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 a4
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* checking for file ‘a4/DESCRIPTION’ ... OK
* preparing ‘a4’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: a4Base
Loading required package: grid
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 object is masked from ‘package:stats’:

    xtabs

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

    anyDuplicated, append, as.data.frame,
    as.vector, cbind, colnames, do.call,
    duplicated, eval, evalq, Filter, Find,
    get, intersect, is.unsorted, lapply,
    Map, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unlist, unsplit

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: GenomeInfoDb
Loading required package: S4Vectors
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Loading required package: IRanges
Loading required package: annaffy
Loading required package: GO.db
Loading required package: DBI

Loading required package: KEGG.db

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

Loading required package: mpm
Loading required package: MASS

Attaching package: ‘MASS’

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

    select

Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

mpm version 1.0-22

Loading required package: genefilter

Attaching package: ‘genefilter’

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

    area

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

    anyNA

Loading required package: limma

Attaching package: ‘limma’

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

    plotMA

Loading required package: multtest
Loading required package: glmnet
Loading required package: Matrix

Attaching package: ‘Matrix’

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

    expand

Loading required package: foreach
Loaded glmnet 2.0-2

Loading required package: a4Preproc
Loading required package: a4Core

Attaching package: ‘a4Core’

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

    topTable

Loading required package: gplots

Attaching package: ‘gplots’

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

    wapply

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

    space

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

    lowess


a4Base version 1.16.0

Loading required package: a4Classif
Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: XML
Loading required package: cluster
Loading required package: ROCR
Loading required package: pamr
Loading required package: survival
Loading required package: varSelRF
Loading required package: randomForest
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.

Attaching package: ‘randomForest’

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

    combine

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

    combine


a4Classif version 1.16.0

Loading required package: a4Reporting

a4 version 1.16.0

Loading required package: ALL
Loading required package: nlcv
Loading required package: RColorBrewer
Loading required package: xtable

Attaching package: ‘xtable’

The following object is masked from ‘package:a4Reporting’:

    xtable

Loading required package: ipred

Attaching package: ‘ipred’

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

    cv


nlcv version 0.2-0

Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


Warning in plotCombination2genes(geneSymbol1 = featResultLasso$topList[1,  :
  Gene2 ABL1 corresponds to 6 probesets; only the first probeset ( 1635_at ) has been displayed on the plot.
Warning in logReg(geneSymbol = "ABL1", object = bcrAblOrNeg, groups = "mol.biol") :
  Gene ABL1 corresponds to 6 probesets; only the first probeset ( 1635_at ) has been displayed on the plot.
Warning in ROCcurve(geneSymbol = "ABL1", object = bcrAblOrNeg, groups = "mol.biol") :
  Gene ABL1 corresponds to 6 probesets; only the first probeset ( 1635_at ) has been displayed on the plot.
Warning in plotCombination2genes(geneSymbol1 = featResultLasso$topList[1,  :
  Gene2 ABL1 corresponds to 6 probesets; only the first probeset ( 1635_at ) has been displayed on the plot.
Loading required package: Cairo
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "axes" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "axes" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "axes" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "axes" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "axes" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "axes" is not a graphical parameter
Loading required package: MLP
Loading required package: affy
Loading required package: plotrix

Attaching package: ‘plotrix’

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

    plotCI

Loading required package: gmodels
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: ‘gdata’

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

    combine

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

    trim

The following object is masked from ‘package:stats4’:

    nobs

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

    combine

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

    combine

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

    nobs

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

    object.size

Loading required package: gtools
Loading required package: Rgraphviz
Loading required package: graph

Attaching package: ‘graph’

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

    acc

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

    addNode


Attaching package: ‘Rgraphviz’

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

    toFile

Loading required package: GOstats
Loading required package: Category

Attaching package: ‘GOstats’

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

    makeGOGraph

Warning: 'smartlegend' is deprecated.
Use 'legend' instead.
See help("Deprecated") and help("graphics-deprecated").
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'a4vignette.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./plotComb2Samples.png): reading image file faile
d
 ==> Fatal error occurred, no output PDF file produced!
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted
BioC 3.1: BUILD report for a4 on petty

Summary

Command output
