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Installation instructions for the rjags package
-----------------------------------------------

The rjags package is an interface to the JAGS library.  In order to
build a binary package, or install from source, you must have a matching
installation of the JAGS library.

1 Windows
---------

If you are installing the Windows binary rjags package, then R will
consult the Windows registry to find the location of JAGS.

If you are compiling the rjags package from source then you must
supply the location of JAGS yourself using the make variable
JAGS_ROOT, defining it in the file HOME/.R/Makevars.win, e.g.

JAGS_ROOT=c:\Program Files\JAGS\JAGS-3.3.0

2 Unix/Linux
------------

The configure script will try to guess the location of the JAGS
library. It does this by querying the R and jags executables, and
should work if both are on your PATH.

Recall that most Linux distributions divide software into `user' and
`developer' versions, so if you are using a pre-built JAGS binary
package for your Linux distribution then remember to install the
developer version.

If you have installed JAGS in a non-standard place then you may need
to supply hints to the configure script.  This can be done by 
passing configure arguments or setting environment variables (see below).

The options/environment variables correspond to options that were
used when JAGS was installed. They are shown in the table below:

JAGS configure  rjags configure        Environmnent     default
option          option                 variable
--------------  ---------------        ------------     -------
--prefix        --with-jags-prefix     JAGS_PREFIX      /usr/local
--libdir        --with-jags-libdir     JAGS_LIBDIR      ${prefix}/${LIBnn}
--includedir    --with-jags-includedir JAGS_INCLUDEDIR  ${prefix}/include

By default LIBnn is the value returned by `R CMD config LIBnn`.
This can be overridden by setting the environment variable LIBnn.

Example 1
---------

Suppose that when you installed JAGS, you used the configure argument
'--prefix=/opt' to install JAGS in the directory /opt instead of the
default /usr/local.  If /opt/bin is on your PATH then the configure
script should still automatically detect JAGS for you.  Otherwise, you
need to supply the configure argument '--with-jags-prefix=/opt' when
installing rjags.

Alternatively you can set the environment variable JAGS_PREFIX
before building rjags:

export JAGS_PREFIX=/opt

Example 2
---------

Suppose you are on a 64-bit system and installed the JAGS library in
in /usr/local/lib64 instead of the default /usr/local/lib.  If R_HOME
is /usr/lib64/R then the configure script should automatically look in
the right place for the JAGS library.  Otherwise, you need to supply
the configure argument '--with-jags-libdir=/usr/local/lib64' when
installing rjags.

Alternatively you can set the environment variable JAGS_LIBDIR
before building rjags:

export JAGS_LIBDIR=/usr/local/lib64

or set the variable LIBnn

export LIBnn=lib64

2.1 Passing configure arguments
-------------------------------

Configure options for rjags are passed via the --configure-args
argument to R CMD INSTALL:

  R CMD INSTALL --configure-args='--with-jags...'

or, using the install.packages() function from within R, using
the configure.args argument:

  install.packages("rjags", configure.args="--with-jags...")

If configure arguments are set, they always override the corresponding
environment variables.

2.2 Failure to load 
-------------------

Even with the above options, the rjags package may compile and install
correctly, but then fail with the message "ERROR:loading failed".

On some systems it is possible to hard-code the location of the JAGS
library at compile time so that the linker knows where to look. This
can be done by adding the configure argument --enable-rpath, e.g.

R CMD INSTALL --configure-args="--prefix=/opt --enable-rpath" rjags

However, please note that this is not portable and may not work on
your system. In this case you need to set the environment variable
LD_LIBRARY_PATH to include the directory containing the jags libraries
before starting R, e.g

LD_LIBRARY_PATH=/opt/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH