[R] Installing RSPerl and Statistics::R
Luc.Vereecken at chem.kuleuven.ac.be
Tue Jul 12 18:28:26 CEST 2005
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
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
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
R INSTALL -c -l <wherever> --configure-args='--with-in-perl'
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>
Hope this is of use to anyone,
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