How to setup R and JAGS on Amazon EC2Posted: July 8, 2011
Yesterday I setup a Amazon EC2 machine and installed R, JAGS and rjags. Unfortunately I was unable to compile the latest version of JAGS. The configuration step failed with an error that says that a specific LAPACK library is missing. I tried to install the missing library manually but for some reason JAGS doesn’t recognize the new version. After an hour, I decided to go with the older JAGS version. Here is how I installed all three packages.
ssh. In a first step we install an older version of
R. It is necessary to use the older version in order to get JAGS 1.0.4 running later. After downloading the R source file, we unzip it, cd into the folder and start installing a couple of additional libraries and compilers that we need to compile R (and later JAGS). We then configure the R installer without any x-window support and install everything. The last line makes sure that you can start R with simply typing ‘R’.
cd ~ wget http://cran.r-project.org/src/base/R-2/R-2.10.0.tar.gz tar xf R-2.10.0.tar.gz cd ~/R-2.10.0 sudo yum install gcc sudo yum install gcc-c++ sudo yum install gcc-gfortran sudo yum install readline-devel sudo yum install make ./configure --with-x=no make PATH=$PATH:~/download/R-2.10.0/bin/
Next, try to start R and install the coda package.
R install.packages('coda') q()
Now, we proceed with installing JAGS. First, get some libraries and the JAGS source code. Unzip, cd into the folder and run configure with specifying the shared library folder. The specification of the shared library path is crucial, otherwise rjags fails to load in R.
sudo yum install blas-devel lapack-devel cd ~/download/ wget http://sourceforge.net/projects/mcmc-jags/files/JAGS/1.0/JAGS-1.0.4.tar.gz/download tar xf JAGS-1.0.4.tar.gz cd ~/download/JAGS-1.0.4 ./configure --libdir=/usr/local/lib64 make sudo make install
In a last step, download the appropriate rjags version and install it it.
cd ~/download/ wget http://cran.r-project.org/src/contrib/Archive/rjags/rjags_1.0.3-13.tar.gz R --with-jags-modules=/usr/local/lib/JAGS/modules/ CMD INSTALL rjags_1.0.3-13.tar.gz