Monday, August 9, 2010

R::Install::ClassDiscovery::ClassComparision
Install R
$ sudo apt-get install r-base
$ sudo apt-get install r-base-dev r-base-core

Go to R
$ sudo R
> install.packages(repos="http://bioinformatics.mdanderson.org/OOMPA", dependencies=TRUE)
- ran into warnings and errors
- Error : package 'Biobase' could not be loaded
- Information to install biobase, http://www.bioconductor.org/packages/2.2/bioc/html/Biobase.html
> source("http://bioconductor.org/biocLite.R")
> biocLite("Biobase")
> install.packages(repos="http://bioinformatics.mdanderson.org/OOMPA", dependencies=TRUE)
- select ClassComparison
- you should get the following sentence
* DONE (ClassComparison)
check if the package is installed
> library('ClassComparison')
> install.packages(repos="http://bioinformatics.mdanderson.org/OOMPA", dependencies=TRUE)
- select ClassDiscovery
- Error : package 'mclust' could not be loaded
To install mclust
> install.packages("Rserve")
* Done (Rserve)

On unix:
$ wget http://bioconductor.org/packages/1.9/bioc/src/contrib/vsn_1.12.0.tar.gz
$ sudo R CMD INSTALL vsn_1.12.0.tar.gz
* Done (vsn)

Go to R
$ sudo R
> install.packages('mclust')
* Done (mclust)
> install.packages(repos="http://bioinformatics.mdanderson.org/OOMPA", dependencies=TRUE)
* DONE (ClassDiscovery)

check installation
> library('ClassDiscovery')

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