[R] Using RSPerl with add-on package ctest and named parameters

[Frank Gibbons]

Hi,.

I've installed RSPerl on my Linux box. It runs all of the test scripts that 
I've been able to find. I've learned that I can pass in vectors of data as 
array-refs, and can use named parameters with R::callWithNames and a hash 
of names and values.

The one problem that I'm left with is how to call a function from an add-on 
package ('ctest' in this case). I know that I need to use 
R::library("ctest") to load the library. I want to run the following R code 
from Perl:

 > library(ctest)
 > x <- c(1.83, .50, 1.62, 2.48, 1.68, 1.88, 1.55, 3.06, 1.3)
 > y <- c(0.878, 0.647, 0.598, 2.95, 1.06, 1.29, 1.06, 3.14, 1.29)
 > wilcox.test(x, y, paired=TRUE, alternative = "greater")

         Wilcoxon signed rank test

data:  x and y
V = 36, p-value = 0.06445
alternative hypothesis: true mu is greater than 0


I had thought that this should do the job:
#!/usr/bin/perl
use strict;
R::library("RSPerl");
R::library("ctest");
my @x = (1.83, .50, 1.62, 2.48, 1.68, 1.88, 1.55, 3.06, 1.3);
my @y = (0.878, 0.647, 0.598, 2.95, 1.06, 1.29, 1.06, 3.14, 1.29);
R::callWithNames('wilcox.test', {'', \@x, '', \@y, 'alternative', "greater"});

The problem is, it doesn't complain, it doesn't return anything at all. 
Shouldn't it print out the results just like the R code does, or does it 
return them in an array? I tried catching the return value, by assigning to 
a scalar, but get an error:

/usr/bin/perl: relocation error: 
/usr/lib/R/library/RSPerl/share/local/lib/perl/5.6.1/auto/R/R.so: undefined 
symbol: userLevelConversionToPerl

I know I'm using the right name ('wilcox.test'), since trying other 
variations ('wilcox', 'ctest::wilcox') gives me an error message. I'd 
really appreciate any suggestions for this problem. I've scoured the web, 
and haven't been able to find any examples in which an add-on package 
function is called using the RSPerl module.

Thanks,

Frank Gibbons

PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons

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