[R] pchisq error

Thomas Lumley tlumley at u.washington.edu
Mon Jan 19 10:40:17 CET 2009


I don't get the error, but I assume it's because your C function returns a double and .C() assumes it is a void function.

     -thomas


On Mon, 19 Jan 2009, Jeremy Silver wrote:

> Dear R experts,
>
> I'm trying to call 'pchisq' from within a C subroutine. The following
> error is returned:
>
>   ** NON-convergence in pgamma()'s pd_lower_cf() f= nan.
>
> This error message is not printed the first time I call 'pchisq' from
> the C subroutine, but the second time or the next time I call 'pchisq'
> from within R.
>
> My session output is shown below:
>
> ######################
>
>> system('R CMD SHLIB reproduceError.c')
>
> make: `reproduceError.so' is up to date.
>
>>
>
>> reproduceError <- function(x){
>
> +   dyn.load('reproduceError.so')
>
> +   .C('tempCfunction',as.double(x))
>
> +   dyn.unload('reproduceError.so')
>
> +   invisible(NULL)
>
> + }
>
>>
>
>> pchisq(5.464342,1,lower.tail = FALSE)
>
> [1] 0.01940836
>
>> reproduceError(5.464342)
>
> stat = 5.464342, p = 0.019408
>
>> pchisq(5.464342,1,lower.tail = FALSE)
>
> [1] NaN
>
> Warning messages:
>
> 1: In pchisq(5.464342, 1, lower.tail = FALSE) :
>
>   ** NON-convergence in pgamma()'s pd_lower_cf() f= nan.
>
> 2: In pchisq(q, df, lower.tail, log.p) : NaNs produced
>
>> reproduceError(5.464342)
>
> stat = 5.464342, p = 0.019408
>
>> reproduceError(5.464342)
>
> stat = 5.464342, p = nan
>
> Warning message:
>
> In reproduceError(5.464342) :
>
>   ** NON-convergence in pgamma()'s pd_lower_cf() f= nan.
>
>> pchisq(5.464342,1,lower.tail = FALSE)
>
> [1] NaN
>
> Warning messages:
>
> 1: In pchisq(5.464342, 1, lower.tail = FALSE) :
>
>   ** NON-convergence in pgamma()'s pd_lower_cf() f= nan.
>
> 2: In pchisq(q, df, lower.tail, log.p) : NaNs produced
>
>> pchisq(5.464342,1,lower.tail = FALSE)
>
> [1] 0.01940836
>
>> pchisq(5.464342,1,lower.tail = FALSE)
>
> [1] 0.01940836
>
>>
>
>> sessionInfo()
>
> R version 2.8.0 (2008-10-20)
>
> i686-pc-linux-gnu
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> #############################
>
>
> The C file (reproduceError.c) with the subroutine tempCfunction is:
>
> #############################
>
> #include <stdio.h>
>
> #include <Rmath.h>
>
> #include <R.h>
>
> #include <Rinternals.h>
>
> #include <string.h>
>
> double tempCfunction(double *x){
>
>  double stat = x[0];
>
>  double pval = pchisq(stat, 1.0 , 0, 0);
>
>  printf("stat = %f, p = %f\n",stat,pval);
>
>
>
>  return pval;
>
> }
>
> #############################
>
> Can anybody explain this behaviour?
>
> Thanks,
>
> Jeremy
>
> --
> /****************************************
> Jeremy Silver
> Research Assistant
> University of Copenhagen, Denmark
> ph: +45 3532 7917
> email: j.silver at biostat.ku.dk or jere at pubhealth.ku.dk
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle




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