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Ricardo Zorzetto Nicoliello Vencio

2004-Feb-01 14:55 UTC

[R] I can't make .C(...) web-page example.

Hi everyone!

I'm trying to lear how to call external C code in R but even the R help
web-page example is drive me crazy.

I copy-paste the example at:

http://stat.ethz.ch/R-manual/R-patched/doc/manual/R-exts.html#Interface%20functions%20.C%20and%20.Fortran

here is the example:

void convolve(double *a, int *na, double *b, int *nb, double *ab)
{
  int i, j, nab = *na + *nb - 1;

  for(i = 0; i < nab; i++)
    ab[i] = 0.0;
  for(i = 0; i < *na; i++)
    for(j = 0; j < *nb; j++)
      ab[i + j] += a[i] * b[j];
}

called from R by

conv <- function(a, b)
  .C("convolve",
     as.double(a),
     as.integer(length(a)),
     as.double(b),
     as.integer(length(b)),
     ab = double(length(a) + length(b) - 1))$ab


but using the conv function in simple examples give me trouble:
> conv(1:10,2:11)Error in conv(1:10, 2:11) : pairlist object cannot be coerced to double
> conv( rnorm(10,10,1) , rnorm(10,11,1) )Segmentation fault
> conv( c(10.53, 8.456, 6.6) , c(10.53, 8.456, 6.6) )Error in conv(c(10.53, 8.456, 6.6), c(10.53, 8.456, 6.6)) :
        cannot allocate vector of length 1717986918
> a = c(1.46756, 5.56456, 2.3646)
> b = a + 5.4
> conv(a,b)Error in conv(a, b) : cannot coerce type promise to double vector


and so on.

These results appear if I have only the .c file or if I use gcc -c conv.c
to create .o file. I cannot create executable because there is no
main(...) in .c file but just the copy-pasted example.


Someone knows what is happening to me ?

Prof Brian Ripley

2004-Feb-01 15:22 UTC

head link

[R] I can't make .C(...) web-page example.

Change the name.  There is a convolve C function in R 1.8.x (but not
R-devel) that is being found rather than yours.


On Sun, 1 Feb 2004, Ricardo Zorzetto Nicoliello Vencio wrote:
> 
> Hi everyone!
> 
> I'm trying to lear how to call external C code in R but even the R help
> web-page example is drive me crazy.
> 
> I copy-paste the example at:
> 
>
http://stat.ethz.ch/R-manual/R-patched/doc/manual/R-exts.html#Interface%20functions%20.C%20and%20.Fortran
> 
> here is the example:
> 
> void convolve(double *a, int *na, double *b, int *nb, double *ab)
> {
>   int i, j, nab = *na + *nb - 1;
> 
>   for(i = 0; i < nab; i++)
>     ab[i] = 0.0;
>   for(i = 0; i < *na; i++)
>     for(j = 0; j < *nb; j++)
>       ab[i + j] += a[i] * b[j];
> }
> 
> called from R by
> 
> conv <- function(a, b)
>   .C("convolve",
>      as.double(a),
>      as.integer(length(a)),
>      as.double(b),
>      as.integer(length(b)),
>      ab = double(length(a) + length(b) - 1))$ab
> 
> 
> but using the conv function in simple examples give me trouble:
> 
> > conv(1:10,2:11)
> Error in conv(1:10, 2:11) : pairlist object cannot be coerced to double
> 
> > conv( rnorm(10,10,1) , rnorm(10,11,1) )
> Segmentation fault
> 
> > conv( c(10.53, 8.456, 6.6) , c(10.53, 8.456, 6.6) )
> Error in conv(c(10.53, 8.456, 6.6), c(10.53, 8.456, 6.6)) :
>         cannot allocate vector of length 1717986918
> 
> > a = c(1.46756, 5.56456, 2.3646)
> > b = a + 5.4
> > conv(a,b)
> Error in conv(a, b) : cannot coerce type promise to double vector
> 
> 
> and so on.
> 
> These results appear if I have only the .c file or if I use gcc -c conv.c
> to create .o file. I cannot create executable because there is no
> main(...) in .c file but just the copy-pasted example.
> 
> 
> Someone knows what is happening to me ?
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
> 
> 
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Rau, Roland

2004-Feb-01 15:32 UTC

head link

[R] I can't make .C(...) web-page example.

Hi!

I am by no means an R-expert nor a C-expert but the document "An
Introduction to .C Interface to R" by Roger D. Peng and  Jan de Leeuw
helped
me a lot to find out how it works in principle to use the .C function call.
You can find it on the homepage of Roger D. Peng
(http://www.biostat.jhsph.edu/~rpeng/ ) at the following URL:
http://www.biostat.jhsph.edu/~rpeng/docs/interface.pdf


Hope this is what you were looking for.

Best,
Roland

> -----Original Message-----
> From:	Ricardo Zorzetto Nicoliello Vencio [SMTP:rvencio at ime.usp.br]
> Sent:	Sunday, February 01, 2004 3:56 PM
> To:	R-help at stat.math.ethz.ch
> Subject:	[R] I can't make .C(...) web-page example.
> 
> 
> Hi everyone!
> 
> I'm trying to lear how to call external C code in R but even the R help
> web-page example is drive me crazy.
> 
> I copy-paste the example at:
> 
> http://stat.ethz.ch/R-manual/R-patched/doc/manual/R-exts.html#Interface%20
> functions%20.C%20and%20.Fortran
> 
> here is the example:
> 
> void convolve(double *a, int *na, double *b, int *nb, double *ab)
> {
>   int i, j, nab = *na + *nb - 1;
> 
>   for(i = 0; i < nab; i++)
>     ab[i] = 0.0;
>   for(i = 0; i < *na; i++)
>     for(j = 0; j < *nb; j++)
>       ab[i + j] += a[i] * b[j];
> }
> 
> called from R by
> 
> conv <- function(a, b)
>   .C("convolve",
>      as.double(a),
>      as.integer(length(a)),
>      as.double(b),
>      as.integer(length(b)),
>      ab = double(length(a) + length(b) - 1))$ab
> 
> 
> but using the conv function in simple examples give me trouble:
> 
> > conv(1:10,2:11)
> Error in conv(1:10, 2:11) : pairlist object cannot be coerced to double
> 
> > conv( rnorm(10,10,1) , rnorm(10,11,1) )
> Segmentation fault
> 
> > conv( c(10.53, 8.456, 6.6) , c(10.53, 8.456, 6.6) )
> Error in conv(c(10.53, 8.456, 6.6), c(10.53, 8.456, 6.6)) :
>         cannot allocate vector of length 1717986918
> 
> > a = c(1.46756, 5.56456, 2.3646)
> > b = a + 5.4
> > conv(a,b)
> Error in conv(a, b) : cannot coerce type promise to double vector
> 
> 
> and so on.
> 
> These results appear if I have only the .c file or if I use gcc -c conv.c
> to create .o file. I cannot create executable because there is no
> main(...) in .c file but just the copy-pasted example.
> 
> 
> Someone knows what is happening to me ?
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html

+++++
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receive a mail that is apparently from a MPI user without this text displayed,
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validity of this message, please check the mail header or ask your system
administrator for assistance.

Uwe Ligges

2004-Feb-01 15:34 UTC

head link

[R] I can't make .C(...) web-page example.

Ricardo Zorzetto Nicoliello Vencio wrote:
> Hi everyone!
> 
> I'm trying to lear how to call external C code in R but even the R help
> web-page example is drive me crazy.
> 
> I copy-paste the example at:
> 
>
http://stat.ethz.ch/R-manual/R-patched/doc/manual/R-exts.html#Interface%20functions%20.C%20and%20.Fortran
> 
> here is the example:
> 
> void convolve(double *a, int *na, double *b, int *nb, double *ab)
> {
>   int i, j, nab = *na + *nb - 1;
> 
>   for(i = 0; i < nab; i++)
>     ab[i] = 0.0;
>   for(i = 0; i < *na; i++)
>     for(j = 0; j < *nb; j++)
>       ab[i + j] += a[i] * b[j];
> }
> 
> called from R by
> 
> conv <- function(a, b)
>   .C("convolve",
>      as.double(a),
>      as.integer(length(a)),
>      as.double(b),
>      as.integer(length(b)),
>      ab = double(length(a) + length(b) - 1))$ab
> 
> 
> but using the conv function in simple examples give me trouble:
> 
> 
> conv(1:10,2:11)
 >> Error in conv(1:10, 2:11) : pairlist object cannot be coerced to double
> 
> 
>>conv( rnorm(10,10,1) , rnorm(10,11,1) )
> 
> Segmentation fault
> 
> 
>>conv( c(10.53, 8.456, 6.6) , c(10.53, 8.456, 6.6) )
> 
> Error in conv(c(10.53, 8.456, 6.6), c(10.53, 8.456, 6.6)) :
>         cannot allocate vector of length 1717986918
> 
> 
>>a = c(1.46756, 5.56456, 2.3646)
>>b = a + 5.4
>>conv(a,b)
> 
> Error in conv(a, b) : cannot coerce type promise to double vector
> 
> 
> and so on.
> 
> These results appear if I have only the .c file or if I use gcc -c conv.c
> to create .o file. I cannot create executable because there is no
> main(...) in .c file but just the copy-pasted example.
Most easily, use the R wrapper to compile and link files as in:

R CMD SHLIB convolve.c
which produces an .so file you can dyn.load().
(If you are on Windows: Rcmd SHLIB makes a dll.)

Uwe Ligges

> 
> Someone knows what is happening to me ?
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

Peter Dalgaard

2004-Feb-01 16:22 UTC

head link

[R] I can't make .C(...) web-page example.

Ricardo Zorzetto Nicoliello Vencio <rvencio at ime.usp.br> writes:
> Hi everyone!
> 
> I'm trying to lear how to call external C code in R but even the R help
> web-page example is drive me crazy.
> 
> I copy-paste the example at:
> 
>
http://stat.ethz.ch/R-manual/R-patched/doc/manual/R-exts.html#Interface%20functions%20.C%20and%20.Fortran
> 
> here is the example:
> 
> void convolve(double *a, int *na, double *b, int *nb, double *ab)
> {
>   int i, j, nab = *na + *nb - 1;
> 
>   for(i = 0; i < nab; i++)
>     ab[i] = 0.0;
>   for(i = 0; i < *na; i++)
>     for(j = 0; j < *nb; j++)
>       ab[i + j] += a[i] * b[j];
> }
> 
> called from R by
> 
> conv <- function(a, b)
>   .C("convolve",
>      as.double(a),
>      as.integer(length(a)),
>      as.double(b),
>      as.integer(length(b)),
>      ab = double(length(a) + length(b) - 1))$ab
> 
> 
> but using the conv function in simple examples give me trouble:
> 
> > conv(1:10,2:11)
> Error in conv(1:10, 2:11) : pairlist object cannot be coerced to double
> 
> > conv( rnorm(10,10,1) , rnorm(10,11,1) )
> Segmentation fault
> 
> > conv( c(10.53, 8.456, 6.6) , c(10.53, 8.456, 6.6) )
> Error in conv(c(10.53, 8.456, 6.6), c(10.53, 8.456, 6.6)) :
>         cannot allocate vector of length 1717986918
> 
> > a = c(1.46756, 5.56456, 2.3646)
> > b = a + 5.4
> > conv(a,b)
> Error in conv(a, b) : cannot coerce type promise to double vector
> 
> 
> and so on.
> 
> These results appear if I have only the .c file or if I use gcc -c conv.c
> to create .o file. I cannot create executable because there is no
> main(...) in .c file but just the copy-pasted example.
> 
> 
> Someone knows what is happening to me ?
Looks like you haven't quite understood how to generate a shared
library (R CMD SHLIB) and load it dynamically (dyn.load), and then
somehow pick up a different convolve entry point (doesn't seem
possible with Linux, but you're not tellig us what your system is...).
Either that or you managed to confuse R badly through some earlier
attempts to load the module.

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907

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