puma

Package: puma
Type: Package
Title: Propagating Uncertainty in Microarray Analysis(including
Affymetrix tranditional 3' arrays and exon arrays and Human
Transcriptome Array 2.0)
Version: 3.14.0
Date: 2015-7-29
Author: Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D.
Lawrence, Guido Sanguinetti, Li Zhang
Maintainer: Xuejun Liu <xuejun.liu@nuaa.edu.cn>
Depends: R (>= 3.2.0), oligo (>= 1.32.0), graphics, grDevices, methods,
stats, utils, mclust, oligoClasses
Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses
Suggests: pumadata, affydata, snow, limma, ROCR, annotate
Description: Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.
License: LGPL
biocViews: Microarray, OneChannel, Preprocessing,
DifferentialExpression, Clustering, ExonArray, GeneExpression,
mRNAMicroarray, ChipOnChip, AlternativeSplicing,
DifferentialSplicing, Bayesian, TwoChannel, DataImport, HTA2.0
URL: http://umber.sbs.man.ac.uk/resources/puma
Packaged: 2016-05-04 03:02:05 UTC; biocbuild
NeedsCompilation: yes

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'puma' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c PMmultimgmos.c -o PMmultimgmos.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cregistration.c -o cregistration.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c donlp2.c -o donlp2.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c gme.c -o gme.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ipplr_c.c -o ipplr_c.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c multimgmos.c -o multimgmos.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c newx.c -o newx.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pplr_c.c -o pplr_c.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pumaclust_c.c -o pumaclust_c.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pumaclustii_c.c -o pumaclustii_c.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c user_eval.c -o user_eval.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/puma/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'puma'
    finding HTML links ... done
    Clust.exampleE                          html  
    Clust.exampleStd                        html  
    Clustii.exampleE                        html  
    Clustii.exampleStd                      html  
    DEResult-class                          html  
    PMmmgmos                                html  
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/PMmmgmos.Rd:5: missing file link 'FeatureSet-class'
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/PMmmgmos.Rd:22: missing file link 'FeatureSet-class'
    bcomb                                   html  
    calcAUC                                 html  
    calculateFC                             html  
    calculateLimma                          html  
    calculateTtest                          html  
    clusterApplyLBDots                      html  
    clusterNormE                            html  
    clusterNormVar                          html  
    compareLimmapumaDE                      html  
    createContrastMatrix                    html  
    createDesignMatrix                      html  
    create_eset_r                           html  
    erfc                                    html  
    eset_mmgmos                             html  
    exampleE                                html  
    exampleStd                              html  
    exprReslt-class                         html  
    gmhta                                   html  
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/gmhta.Rd:5: missing file link 'FeatureSet-class'
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/gmhta.Rd:23: missing file link 'FeatureSet-class'
    gmoExon                                 html  
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/gmoExon.Rd:5: missing file link 'FeatureSet-class'
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/gmoExon.Rd:24: missing file link 'FeatureSet-class'
    hcomb                                   html  
    hgu95aphis                              html  
    igmoExon                                html  
    justmgMOS                               html  
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/justmgMOS.Rd:33: missing file link 'FeatureSet-class'
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/justmgMOS.Rd:46: missing file link 'FeatureSet-class'
    justmmgMOS                              html  
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/justmmgMOS.Rd:33: missing file link 'FeatureSet-class'
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/justmmgMOS.Rd:46: missing file link 'FeatureSet-class'
    legend2                                 html  
    license.puma                            html  
    matrixDistance                          html  
    mgmos                                   html  
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/mgmos.Rd:5: missing file link 'FeatureSet-class'
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/mgmos.Rd:21: missing file link 'FeatureSet-class'
    mmgmos                                  html  
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/mmgmos.Rd:5: missing file link 'FeatureSet-class'
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/mmgmos.Rd:22: missing file link 'FeatureSet-class'
    normalisation.gs                        html  
    numFP                                   html  
    numOfFactorsToUse                       html  
    numTP                                   html  
    orig_pplr                               html  
    plot-methods                            html  
    plotErrorBars                           html  
    plotHistTwoClasses                      html  
    plotROC                                 html  
    plotWhiskers                            html  
    pplr                                    html  
    pplrUnsorted                            html  
    puma-package                            html  
    pumaClustii                             html  
    pumaComb                                html  
    pumaCombImproved                        html  
    pumaDE                                  html  
    pumaDEUnsorted                          html  
    pumaFull                                html  
Rd warning: /tmp/RtmpIBQTLc/R.INSTALL262a6b145d37/puma/man/pumaFull.Rd:20: missing file link 'FeatureSet-class'
    pumaNormalize                           html  
    pumaPCA                                 html  
    pumaPCAExpectations-class               html  
    pumaPCAModel-class                      html  
    pumaPCARes-class                        html  
    pumaclust                               html  
    removeUninformativeFactors              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (puma)
Making 'packages.html' ... done