R help - May 2008 - Calling C code from R...wrapping C structures

Hi everyone,

I am currently trying to call some C code from R, specifically calling a
function which populates a C struct.

typedef struct{
   // contents
} Model;

void test(Model *m){
   // fill the struct with crap
}

I compile the C code into a shared library, which loads into R properly. My
simple test functions work (i.e adding numbers etc)
setModel <- function(){
   model<-vector("list", 6)
   name(model) <- c( SET THE NAMES OF THE MODEL HERE )
   model
}
t <- setModel()
testcode <- function(setModel){


dyn.load("Simulation.so")

foo <- .C("test", Model=setModel)
foo
}

testcode(t)

However I get segfaults whenever I try to access any of the variables
contained in Model. So my question is: am I doing something wrong here? Is
list the right data type to wrap a structure in? I cant see any
documentation about wrapping structs in R.

Also when I pass strings to C from R they dont seem to be passed at all? Is
this a problem with R or a problem with me and if so how do I fix it?



Many Thanks in advance,

Nathan

	[[alternative HTML version deleted]]

On 5/13/2008 7:51 AM, Nathan Harmston wrote:
> Hi everyone,
> 
> I am currently trying to call some C code from R, specifically calling a
> function which populates a C struct.
> 
> typedef struct{
>    // contents
> } Model;
> 
> void test(Model *m){
>    // fill the struct with crap
> }
> 
> I compile the C code into a shared library, which loads into R properly. My
> simple test functions work (i.e adding numbers etc)
> setModel <- function(){
>    model<-vector("list", 6)
>    name(model) <- c( SET THE NAMES OF THE MODEL HERE )
>    model
> }
> t <- setModel()
> testcode <- function(setModel){
> 
> 
> dyn.load("Simulation.so")
> 
> foo <- .C("test", Model=setModel)
> foo
> }
> 
> testcode(t)
> 
> However I get segfaults whenever I try to access any of the variables
> contained in Model. So my question is: am I doing something wrong here? Is
> list the right data type to wrap a structure in? I cant see any
> documentation about wrapping structs in R.
> 
> Also when I pass strings to C from R they dont seem to be passed at all? Is
> this a problem with R or a problem with me and if so how do I fix it?
It is a problem in your C code.  The .C interface doesn't know about the 
C declaration of the Model structure; it can only pass things it knows 
about.  So your C function test() should have its header set to accept 
what gets passed to it.  In your case, that's a list, so your C function 
receives an array of pointers to SEXP structures; not the easiest things 
to work with.  Most people using .C() pass in simple vectors (numeric, 
integer, etc.), and use the .Call() interface if they really need R 
internals.

Duncan Murdoch

> 
> Many Thanks in advance,
> 
> Nathan
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Dear Nathan,

How is you C function "test" defined? What type of argument is it
expecting? The mappings between R and C type of arguments you can pass
is explained in:

http://cran.r-project.org/doc/manuals/R-exts.html#Interface-functions-_002eC-and-_002eFortran

which also provides some examples. If you want to pass a list, you'll
probably have to use .Call, not .C.

HTH,

R.



On Tue, May 13, 2008 at 1:51 PM, Nathan Harmston
<iwanttobeabadger at googlemail.com> wrote:
> Hi everyone,
>
>  I am currently trying to call some C code from R, specifically calling a
>  function which populates a C struct.
>
>  typedef struct{
>    // contents
>  } Model;
>
>  void test(Model *m){
>    // fill the struct with crap
>  }
>
>  I compile the C code into a shared library, which loads into R properly.
My
>  simple test functions work (i.e adding numbers etc)
>  setModel <- function(){
>    model<-vector("list", 6)
>    name(model) <- c( SET THE NAMES OF THE MODEL HERE )
>    model
>  }
>  t <- setModel()
>  testcode <- function(setModel){
>
>
>  dyn.load("Simulation.so")
>
>  foo <- .C("test", Model=setModel)
>  foo
>  }
>
>  testcode(t)
>
>  However I get segfaults whenever I try to access any of the variables
>  contained in Model. So my question is: am I doing something wrong here? Is
>  list the right data type to wrap a structure in? I cant see any
>  documentation about wrapping structs in R.
>
>  Also when I pass strings to C from R they dont seem to be passed at all?
Is
>  this a problem with R or a problem with me and if so how do I fix it?
>
>
>
>  Many Thanks in advance,
>
>  Nathan
>
>         [[alternative HTML version deleted]]
>
>  ______________________________________________
>  R-help at r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>


-- 
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz