[BioC] Biostrings C interface :: example not compiling

[Charles C. Berry]

On Fri, 2 Apr 2010, Erik Wright wrote:

> Hello all,
>
> I am trying to interface Biostrings from C for the first time.  I 
> followed the example given in the header of Biostrings_interface.h to 
> the letter (quite literally).  In step "e" I paste the example function 
> into myFile.c, register it as a .Call entry point and compile with R CMD 
> CHECK.  I get the following errors:
>
> myFile.c:13: warning: implicit declaration of function ~Qcache_XRaw~R
> myFile.c:13: error: incompatible types in assignment
> myFile.c:14: error: ~QcachedCharSeq~R has no member named ~Qelts~R
> myFile.c:14: error: ~QcachedCharSeq~R has no member named ~Qnelt~R
>
> Based on the error, it seems like I still don't have access to any of 
> the Biostrings variable definitions.  I have tried everything that I can 
> think of, so I am quite stuck.  Does anyone know what I am doing 
> incorrectly?  I have pasted myFile.c below for reference.


Erik,

I have encountered difficulty getting cache_XRaw() to work myself, but 
last December I did get it to go.

IIRC, putting together a standalone .so was a nightmare in which I ended 
up with hard coded paths and other hacks.

I found the path of least resistance was to set up a package and have 
this:


Depends: IRanges
Imports: methods, IRanges
LinkingTo: IRanges

in the description file. (you get cache_XRaw from IRanges.) And I placed a 
file called IRanges_subs.c containing one-line:

#include "_IRanges_stubs.c"

in the src/ directory along with this .c file (beware line wrapping!):


/* read some XRaw as integer */

#include <R.h>
#include <Rdefines.h>
#include <R_ext/Error.h>
#include <R_ext/Rdynload.h>

#include "IRanges_interface.h"


SEXP tryXRaw ( SEXP x ) {

   SEXP ans;
   int i,len;
   const char *x_char;
   cachedCharSeq X;

   X = cache_XRaw(x);

   for (i = 0, x_char = X.seq; i < X.length; i++, x_char++)
   Rprintf("%x ", *x_char);
   Rprintf("\n");


   PROTECT( ans = NEW_INTEGER( X.length ) );
   for (i = 0, x_char = X.seq; i < X.length; i++, x_char++) INTEGER(ans)[i]=X.seq[i];
   UNPROTECT( 1);
   return ans;
}


R_CMethodDef cMethods[] =
   {
     {"tryXRaw", (DL_FUNC)&tryXRaw, 1, NULL},
     {NULL,NULL, 0}
   };

void R_init_tryXRaw(DllInfo *dll)
{
   R_registerRoutines(dll,cMethods,NULL,NULL,NULL);
}

/* end of file */

If this doesn't get you going I can build the package and send the tgz to 
you privately as .tgz

HTH,

Chuck

p.s. In the course of researching how to get this going I encountered 
alphabetFrequency() which solved the problem I was planning to use 
cache_XRaw() for, so I never bothered to go any further.


>
> Thanks!,
> Erik
>
>
>
>
> //myFile.c
>
> #include <Rdefines.h>
> #include <R_ext/Rdynload.h>
> #include <stdio.h>
> #include <stdlib.h>
> #include "Biostrings_interface.h"
>
> SEXP print_XString_bytes(SEXP xstring)
> {
> 	cachedCharSeq x;
> 	int i;
> 	const char *x_char;
>
> 	x = cache_XRaw(xstring);
> 	for (i = 0, x_char = x.elts; i < x.nelt; i++, x_char++)
> 		Rprintf("%x ", *x_char);
> 	Rprintf("\n");
> 	return R_NilValue;
> }
>
> /*
> * -- REGISTRATION OF THE .Call ENTRY POINTS ---
> */
> static const R_CallMethodDef callMethods[] = {
> 	{"print_XString_bytes", (DL_FUNC) &print_XString_bytes, 1},
> 	{NULL, NULL, 0}
> };
>
> void R_init_GoneFISHing(DllInfo *info)
> {
> 	R_registerRoutines(info, NULL, callMethods, NULL, NULL);
> }
> 	[[alternative HTML version deleted]]
>
>
>
>    [ Part 3.2: "Included Message" ]
>

Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901