affycoretools

Package: affycoretools
Date: 2008-12-15
Title: Functions useful for those doing repetitive analyses with
Affymetrix GeneChips
Version: 1.44.2
Author: James W. MacDonald
Description: Various wrapper functions that have been written to
streamline the more common analyses that a core Biostatistician
might see.
Maintainer: James W. MacDonald <jmacdon@u.washington.edu>
License: Artistic-2.0
Depends: Biobase, methods
Imports: affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi,
ggplot2, gplots, oligoClasses, ReportingTools, hwriter,
lattice, S4Vectors, edgeR
Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl
biocViews: ReportWriting, Microarray, OneChannel, GeneExpression
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 01:36:27 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'affycoretools' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
** help
*** installing help indices
  converting help for package 'affycoretools'
    finding HTML links ... done
    affycoretools-defunct                   html  
    affycoretools                           html  
    affystart                               html  
    annotateEset                            html  
Rd warning: /tmp/RtmpKo7i8Y/R.INSTALL66b7471d2d6c/affycoretools/man/annotateEset.Rd:43: missing file link 'columns'
Rd warning: /tmp/RtmpKo7i8Y/R.INSTALL66b7471d2d6c/affycoretools/man/annotateEset.Rd:46: missing file link 'mapIds'
Rd warning: /tmp/RtmpKo7i8Y/R.INSTALL66b7471d2d6c/affycoretools/man/annotateEset.Rd:51: missing file link 'rma'
    dataAndHeatmapPage                      html  
    finding level-2 HTML links ... done

    entrezLinks                             html  
    fixHeaderAndGo                          html  
    geneSetPage                             html  
    getCols                                 html  
    getMainProbes                           html  
    gsHeatmap                               html  
    intNames                                html  
    make.cl                                 html  
    makeGoGeneTable                         html  
Rd warning: /tmp/RtmpKo7i8Y/R.INSTALL66b7471d2d6c/affycoretools/man/makeGoGeneTable.Rd:11: missing file link 'topTable'
    makeGoTable                             html  
Rd warning: /tmp/RtmpKo7i8Y/R.INSTALL66b7471d2d6c/affycoretools/man/makeGoTable.Rd:12: missing file link 'topTable'
    makeHmap                                html  
    makeImages                              html  
    makeIndices                             html  
    makeVenn                                html  
    maplot                                  html  
    mirna2mrna                              html  
    outputRomer                             html  
    pca.legend                              html  
    plotDeg                                 html  
    plotPCA                                 html  
    runRomer                                html  
    tableFilt                               html  
    venn4Way                                html  
    vennCounts2                             html  
    vennPage                                html  
    vennSelect2                             html  
    writeFit                                html  
Rd warning: /tmp/RtmpKo7i8Y/R.INSTALL66b7471d2d6c/affycoretools/man/writeFit.Rd:38: missing file link 'write.fit'
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* DONE (affycoretools)
Making 'packages.html' ... done