DeSousa2013

Package: DeSousa2013
Type: Package
Title: Poor prognosis colon cancer is defined by a molecularly distinct
subtype and precursor lesion
Version: 1.8.0
Date: 2013-04-10
Author: Xin Wang <Xin.Wang@cruk.cam.ac.uk>
Maintainer: Xin Wang <Xin.Wang@cruk.cam.ac.uk>
Depends: R (>= 2.15),
Imports: affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs,
sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr,
survival, gplots, AnnotationDbi, Biobase
Description: This package reproduces the main pipeline to analyze the
AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature
Medicine in 2013.
License: Artistic-2.0
biocViews: CancerData, ColonCancerData, MicroarrayData
Collate: preprocessing.R consensusClustering.R featureSelection.R
classification.R prognosis.R figures.R pipeline.R
LazyLoad: yes
NeedsCompilation: no
Packaged: 2016-05-07 20:34:37 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'DeSousa2013' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DeSousa2013'
    finding HTML links ... done
    CRCPipeLine                             html  
Rd warning: /tmp/RtmpwZKZlz/R.INSTALL3260648ae181/DeSousa2013/man/CRCPipeLine.Rd:23: missing file link 'AMC_sample_head'
Rd warning: /tmp/RtmpwZKZlz/R.INSTALL3260648ae181/DeSousa2013/man/CRCPipeLine.Rd:26: missing file link 'AMC_CRC_clinical'
    buildClassifier                         html  
    compGapStats                            html  
    conClust                                html  
    data-AMC                                html  
    filterDiffGenes                         html  
    filterSamples                           html  
    findDiffGenes                           html  
    geneExpPre                              html  
Rd warning: /tmp/RtmpwZKZlz/R.INSTALL3260648ae181/DeSousa2013/man/geneExpPre.Rd:18: missing file link 'AMC_sample_head'
    getCentroids                            html  
    pamClassify                             html  
Rd warning: /tmp/RtmpwZKZlz/R.INSTALL3260648ae181/DeSousa2013/man/pamClassify.Rd:33: missing file link 'AMC_CRC_clinical'
    pbs2unigenes                            html  
    progAMC                                 html  
Rd warning: /tmp/RtmpwZKZlz/R.INSTALL3260648ae181/DeSousa2013/man/progAMC.Rd:17: missing file link 'AMC_CRC_clinical'
Rd warning: /tmp/RtmpwZKZlz/R.INSTALL3260648ae181/DeSousa2013/man/progAMC.Rd:21: missing file link 'AMC_sample_head'
    selTopVarGenes                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DeSousa2013)
Making 'packages.html' ... done