Overview

The RMark package can be installed and run under recent distrubutions of the GNU/Linux operating system (hereafter, Linux). There are several reasons that doing so might be of interest. First, Linux is a very stable operating system, and RMark and mark.exe under Linux is less "crash-prone" than running RMark and MARK under Windows. Second, and most importantly, some of the inherent efficiencies in Linux make running RMark under Linux faster than under Windows (all other things being equal).

   The following assumes you have a basic familiarity with Linux, and have at least sudo access to specific directories (if you don't know what that is, then you should probably stop now...). It also assumes that the machine you're planning on using has (i) the latest verion of R installed (at least 2.13) and running, and (ii) at least gfortran 4.4 (or newer) installed (including all the libs).

There are two steps to install MARK and RMark under Linux, described below.

Step (1) - installing MARK executable

  • download the g'zip'd tarball containing the 32- and 64-bit builds of the MARK numerical routines executable - here
  • extract the file (mark32 or mark64) that is suitable for your machine/distribution
  • rename the file 'mark' (i.e, drop the 32 or 64 part), copy it to a directory in the path (typically, /usr/local/bin), and make it executable
  • make sure it runs by typing mark from the command line (or ./mark if trying to run it from the directory in which you placed the executable)

Step (2) - installing RMark under Linux...

Here are the basic steps...

  • Install the RMark package from CRAN.
  • For the Linux version of RMark, it expects the executable for mark to be named mark and to be found in the search path. The variable MarkPath is ignored. If you store it some place not in your path you can create a symbolic link (Linux is a wonderful thing - as if being 'free' wasn't enough). For example, you can install the executable for Mark where you want (e.g. ~/Programs/MARK/ ) and in /usr/local/bin you'd type

    ln -s ~/Programs/MARK/mark mark

  • One other setting is the name of the editor/file viewer. The default is pico. If you want to use something other than pico or your machine does not have pico. Simply type MarkViewer="myviewer" in your R session before using RMark, where myviewer is the name of an editor or file viewer that is in your path. You can put the library call and the MarkViewer assignment into a function .First() and they will be run each time you start the R session in that directory.

Misc notes...

The Linux-compiled version of MARK was built using gfortran 4.4 and dynamic (shared) libraries. (Most modern distros will have gfortran 4.4 installed -- for other less bleeding-edge distros like CentOS or Redhat -- you might need to install gfortran 4.4 alongside the older version that comes bundled). There is some chance that the libraries on your distribution may be in different locations than the MARK executable is expecting.

   You can LDD the MARK executable to find out what it 'requires', then tweak the LD_LIBRARY_PATH as needed (if the preceding sentence doesn't make sense to you, you should either quit now, ask a local 'Linux' guru for help, or go back to some 'easier' operating system like Windows or OS/X... ;-)