Wednesday, February 6, 2013

Installing JAGS and rjags on Ubuntu 12.04

I ran into a few issues earlier trying to install JAGS/rjags on Ubuntu. This set of instructions assumes you already have R installed on your system

  • Download and Install R (32/64) -bit
  • Download the Bayesian Sampling Program JAGS from here : Extract the contents of the tar file and install the JAGS program by running the following commands from the JAGS root folder.
  • Download and install the rjags package : I tried install.packages('rjags') in R, which failed initially on my system (Ubuntu). Now, this may work if you're on a Mac or Windows. If you experience the same problems, you need to download the appropriate rjags tar file and and then install it manually.
  • The second line configures rjags for (32/64) bit R. If you are running 32-bit R be sure to replace \lib{64} with \lib and for 64-bit R replace \lib{64} with \lib64. This is very important as you could lose a few nights of sleep here trying to figure out why you can't link the rjags library with the JAGS program. This comes courtesy of Rrasch
    JAGS is a program that is used for the analysis of Bayesian Hierarchical Models using MCMC (Markov Chain Monte Carlo) Simulations. I used JAGS over BUGS(WinBUGS/OpenBUGS) because it is cross platform, runs on Linux and it appears to be more robust among other reasons.

3 comments:

  1. Hi, I am not used to dealing with linux nor programing, may be someone could give me a hint here... I am trying to install JAGS on "ubuntu, precise", I have dowloaded the file jags_3.1.0.orig.tar.gz from https://launchpad.net/ubuntu/+source/jags/3.1.0-1 but I don know what to do next...where am I supposed to run the commands "./configure; make; make install"? I tried on the terminal but nothing happens...
    thanks in advance!
    Carolina

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  2. You should run those commands in the same directory as the uncompressed JAGS file

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  3. Hi, sorry bother you but I am getting a weird error and I am stuck

    Running your command last command

    sudo R CMD INSTALL --configure-args='--with-jags-include=/usr/local/include/JAGS --with-jags-lib=/usr/local/lib --enable-rpath' rjags_3-4.tar.gz

    I am getting this error

    Error : .onLoad failed in loadNamespace() for 'rjags', details:
    call: dyn.load(file)
    error: unable to load shared object '/usr/local/lib/JAGS/modules-3/bugs.so':
    libjrmath.so.0: cannot open shared object file: No such file or directory
    Error: loading failed
    Execution halted
    ERROR: loading failed

    I checked libjrmath.so.0 is indeed in /usr/local/lib so I cannot go on installing rjags

    Any help?

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