affy

Package: affy
Version: 1.50.0
Title: Methods for Affymetrix Oligonucleotide Arrays
Author: Rafael A. Irizarry <rafa@jhu.edu>, Laurent Gautier
<lgautier@gmail.com>, Benjamin Milo Bolstad
<bmb@bmbolstad.com>, and Crispin Miller
<cmiller@picr.man.ac.uk> with contributions from Magnus
Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope
<cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad
Halling <challing@agilixcorp.com>, Wolfgang Huber, James
MacDonald <jmacdon@u.washington.edu>, Benjamin I. P. Rubinstein,
Christopher Workman <workman@cbs.dtu.dk>, John Zhang
Maintainer: Rafael A. Irizarry <rafa@jhu.edu>
Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5)
Imports: affyio (>= 1.13.3), BiocInstaller, graphics, grDevices,
methods, preprocessCore, stats, utils, zlibbioc
Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools
LinkingTo: preprocessCore
Description: The package contains functions for exploratory
oligonucleotide array analysis. The dependence on tkWidgets
only concerns few convenience functions. 'affy' is fully
functional without it.
License: LGPL (>= 2.0)
Collate: ProgressBarText.R ppset.ttest.R ppsetApply.R expressoWidget.R
getCDFenv.R AffyRNAdeg.R avdiff.R barplot.ProbeSet.R
bg.Affy.chipwide.R bg.R expresso.R fit.li.wong.R
generateExprVal.method.avgdiff.R
generateExprVal.method.liwong.R generateExprVal.method.mas.R
generateExprVal.method.medianpolish.R
generateExprVal.method.playerout.R hlog.R justrma.R
loess.normalize.R maffy.R mas5.R merge.AffyBatch.R
normalize.constant.R normalize.contrasts.R
normalize.invariantset.R normalize.loess.R normalize.qspline.R
normalize.quantiles.R pairs.AffyBatch.R plot.density.R
plotLocation.R plot.ProbeSet.R pmcorrect.mas.R AffyBatch.R
mva.pairs.R ProbeSet.R read.affybatch.R rma.R summary.R
tukey.biweight.R whatcdf.R xy2indices.R zzz.R
biocViews: Microarray, OneChannel, Preprocessing
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2016-05-04 02:38:27 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c chipbackground.c -o chipbackground.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c getall_locations.c -o getall_locations.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c mas5calls.c -o mas5calls.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c rma2.c -o rma2.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c rma_common.c -o rma_common.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'open' from package 'base' in package 'affy'
Creating a generic function for 'close' from package 'base' in package 'affy'
Creating a generic function for 'barplot' from package 'graphics' in package 'affy'
** help
*** installing help indices
  converting help for package 'affy'
    finding HTML links ... done
    AffyBatch-class                         html  
    finding level-2 HTML links ... done

    AffyRNAdeg                              html  
    MAplot                                  html  
    ProbeSet-class                          html  
    ProgressBarText-class                   html  
    SpikeIn                                 html  
    affy-deprecated                         html  
    affy-options                            html  
    affy.scalevalue.exprSet                 html  
    barplot.ProbeSet                        html  
    bg.adjust                               html  
    bgc                                     html  
    cdfFromBioC                             html  
    cdfenv.example                          html  
    cleancdfname                            html  
    debug.affy123                           html  
    expresso                                html  
    expressoWidget                          html  
    fit.li.wong                             html  
    generateExprSet-methods                 html  
    generateExprVal-methods                 html  
    generateExprVal.method.avgdiff          html  
    generateExprVal.method.playerout        html  
    hlog                                    html  
    justrma                                 html  
    list.celfiles                           html  
    maffy.subset                            html  
    mas5                                    html  
    mas5calls                               html  
    merge.AffyBatch                         html  
    mva.pairs                               html  
    normalize-methods                       html  
    normalize.constant                      html  
    normalize.contrast                      html  
    normalize.invariantset                  html  
    normalize.loess                         html  
    normalize.qspline                       html  
    normalize.quantiles                     html  
    normalize.quantiles.robust              html  
    pairs.AffyBatch                         html  
    plot.ProbeSet                           html  
    plot.density                            html  
    plotLocation                            html  
    pmcorrect                               html  
    ppsetApply                              html  
    probeMatch-methods                      html  
    probeNames-methods                      html  
    read.affybatch                          html  
    read.probematrix                        html  
    rma                                     html  
    setAffyOptions                          html  
    summary                                 html  
    tukey.biweight                          html  
    whatcdf                                 html  
    xy2indices                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affy)
Making 'packages.html' ... done