HowToInstallRSPerl

Short Installation Instructions for RSPerl

NOTE

RSPerl -- The Omegahat interface for R and Perl.

Follow these instructions to install the RSPerl bidirections interface for use with the EMMA 2 software.

The RSPerl software is written and copyrighted by Duncan Temple Lang and distributed under the FreeBSD license. See the RSPerl homepage: http://www.omegahat.org/RSPerl/index.html

Please report any problems related to RSPerl to the omega help mailing list: omega-help@eeyore.ucdavis.edu

If you also want to use RSPerl for another purpose (e.g. Perl from R), you should also consider the original installation instructions.

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! This page is meant for internal use at the CeBiTec. Any information in this document is provided without any warranty. !

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Prerequisites

• Perl >= 5.8.x
• R >= 2.7.2

both installed and working.

R needs to be configured with --enable-R-shlib switch (which is the case by default).

Obtaining the Sources

Changed: -- MichaelDondrup DateTime(2009-04-09T12:06:56Z)

/!\ Do not download the version from omegahat. The official version has not been updated since 2007. In the meantime we provide our own derived version which has an important new feature: It allows to create complex data structures as RReferences in Perl. Furthermore it contains several Bugfixes in addition. This package is released under the same license as the original (the BSD-license). EMMA is not compatible with the original version 0.9-1 any more! Report any problems with the derived package to the emma-devel mailing list.

You can also he original package ca nbe downloaded from: http://www.omegahat.org/RSPerl/index.html.

Version 0.9 has been locally tested with

• FreeBSD 5.4
• Solaris 9 and 10 (sparc and i386)
• R 2.2.1, R 2.3.0 (test on sparc solaris only)
• Perl 5.8.x

(Versions of RSPerl prior to 0.9-1 had a bug that prevents EMMA to function with it)

Installation

You need to be a privileged user to install RSPerl in the standard location of R libraries and Perl modules. At the console, type:

radmin#  R CMD INSTALL --configure-args='--with-in-perl --with-modules=""' RSPerl_X.tar.gz 

(replace X with the actual version) or

somebody# R CMD INSTALL -l <whereever> --configure-args='--with-in-perl --with-modules=""' RSPerl_X.tar.gz 

to install to another directory. This is recommended, for a first test of the package, and if you do not want to or cannot become privileged user.

Setting up the Environment

For RSPerl to execute R commands from within Perl you have to set LD_LIBRARY_PATH, PERL5LIB, and R_HOME.

export R_HOME=/usr/local/lib/R 
# or wherever you installed it
RSPERLDIR=$R_HOME/library/RSPerl 
# or wherever you put RSPerl 

export LD_LIBRARY_PATH=$RSPERLDIR/libs:$R_HOME/lib

export PERL5LIB=$RSPERLDIR/share/lib/site_perl
# check, that this directory contains R.pm and RReferences.pm

To avoid having to set PERL5LIB you could also copy the content of $RSPERLDIR/share/lib/site_perl/ to the site_perl directory of your local perl installation.

Testing R from Perl

After setting up the environment, try to execute the perl scripts in the tests/ subdirectory of the RSPerl installation.

somebody# perl test.pl
RSPERL 0.8.0 - May 23 2006, 12:27:13 initialized
[...no error message...] 
somebody# perl test1.pl; perl test2.pl; perl test3.pl; perl plot.pl

Issues

• All resolved :)) Thanx Duncan

System specific issues

Debian based Linux

The perl distribution in Debian-based Linux distributions (Debian, Ubuntu, ...) has been split in two. To build Rsperl you need the shared object libperl.so. Make sure you have the package libperl installed:

apt-get install libperl

Solaris

There is a patch kindly provided by Björn Fischer from the CeBiTec support group, that will remove the need to set the LD_LIBRARY_PATH. The patch will appear here soon.

FreeBSD

RSPerl uses GNU make features. To be able to install RSPerl on systems, where make is not GNU make by default, do the following prior to running R CMD INSTALL (provided you are using bash):

radmin#  export MAKE=gmake