Difference between revisions of "R installation"

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This page describes how to install {{R}} for BioUML. You need to perform the following steps:
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This page describes how to install {{R}} for BioUML. There is a special script in BioUML source tree scripts/R/install that will install R and required packages (only for ubuntu):
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You need to perform the following steps:
  
* R itself:
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* Change directory to BioUML/scripts/R
  yum install R
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  cd BioUML/scripts/R
or
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* run install script as root user
apt-get install r-recommended
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  sudo ./install
* Rserve:
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apt-get install r-cran-rserve
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=== See also ===
* Set high enough socket connection timeout, add following line to /etc/R/Rprofile.site
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* [[Using R in BioUML]]
options(timeout=864000L);
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* BioConductor (from R-console):
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  source("http://bioconductor.org/biocLite.R")
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biocLite()
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biocLite("makecdfenv", lib="/usr/local/lib/R/site-library")
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* Illumina normalization (from R-console):
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biocLite("lumi")
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Note that this step may require installation of additional packages in the system like libxml2-dev, libglut3-dev, libcurl4-gnutls-dev.
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* Agilent normalization (from R-console):
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biocLite("limma")
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[[Category:Installation]]
 
[[Category:Installation]]
 
[[Category:R]]
 
[[Category:R]]

Latest revision as of 16:21, 4 June 2015

This page describes how to install R for BioUML. There is a special script in BioUML source tree scripts/R/install that will install R and required packages (only for ubuntu): You need to perform the following steps:

  • Change directory to BioUML/scripts/R
cd BioUML/scripts/R
  • run install script as root user
sudo ./install

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