R help - Jun 2002 - Using RSPerl with add-on package ctest and named parameters

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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At 11:41 AM 6/13/2002, you wrote:
> > 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
>
>It would if you called print() on the return value (which is not a
>scalar).
Brian,

I tried that already, and get the same result as if I had tried assigning 
to a scalar (see below).

Can you suggest something else? Do you know for sure that it should return 
a value (rather than printing out its own results)? If so, is there 
possibly a problem with my installation of R.so, the library mentioned in 
the error message, which is apparently unable to find the symbol to convert 
the result (whatever it is) to Perl?

Thanks for your help,

Frank
> > 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
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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r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at
stat.math.ethz.ch
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