[R] Installing RSPerl and Statistics::R

From: Luc Vereecken <Luc.Vereecken_at_chem.kuleuven.ac.be>
Date: Wed 13 Jul 2005 - 02:28:26 EST


Hi list,

For my research, I started using R as a statistics engine, driven by perl scripts that manage my data and computational jobs. I recently upgraded my cluster to Suse 9.2, and obviously wanted to upgrade R to it's latest version, 2.1.1. Installation of R-2.1.1 went flawlessly thanks to the rpm's created by Detlef Steuer (see cran, thanks Detlef).

To interface perl and R, two packages are available: RSPerl and Statistics::R. Neither of the two installed out of the box, so I describe the problems here, as well as their solutions, for use by others.

My scripts are based on a perl package Statistics::R, available from the perl CPAN in version 0.02. Installation of such a perl package is normally performed by doing:

         perl -MCPAN -e 'install Statistics::R' but the installation failed due to errors in the tests requiring me to ctrl-C the test program. I was able to force an install of this package by entering the CPAN shell:

         perl -MCPAN -e shell
and executing a forced install:

         force install Statistics::R
killing the test program halfway the install. Some investigation learned that Statistics::R as it is available at this time can not possible run as R is invoked as

         R --slave --vanilla --gui=none
which used to work in older version of R, but the current versions no longer support --gui=none causing an error "ERROR: unknown GUI none". Strangely, invoking "R BATCH" sets the gui to none according to the manual, so either gui=none still exists internally but is simply no longer supported by the R script, or the R BATCH manual is not correctly updated.
Statistics::R can be installed and made to work by using the forced install described above, and by editing the startup perl routines removing the gui=none option from the command line. This command line can be found in
/usr/lib/perl5/site_perl/5.8.5/Statistics/R/Bridge/Linux.pm for my installation, it should be similar for other perl versions and library-locations.

RSPerl 0.7, available from www.omagahat.org/RSPerl/ , gives on it's main page the command

         R INSTALL -c -l <wherever> RSPerl_0.7-0.tar.gz or

         R INSTALL -c -l <wherever> --configure-args='--with-in-perl' RSPerl_0.7-0.tar.gz
as installation command. In the "calling R from perl" PDF document, the command given is:

         R CMD INSTALL -c -configure-args='-with-in-perl' RSPerl None of these commands work due to typo's. A working command line is:

         R CMD INSTALL -c -l <installdir> --configure-args='--with-in-perl' RSPerl_0.7-0.tar.gz

Hope this is of use to anyone,

Luc Vereecken



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