R help - Jul 2010 - calling a c function from R

Hi,
I am trying to call a C function, that I wrote to parse a flat file,  into
R. The argument that will go into this function is an input file that I need
to parse and write the desired output in an output file.  I used some hit
and trial approach but i keep on getting the "file not found" or
"segmentation fault" error. I know that the error is in passing the
argument
but I could not solve it.

After reading  some of the tutorials, I understood how to do this if the
arguments are integers or floats. I am stuck when i am trying to send the
files. I am attaching stub of each file.
Help appreciated.
Thanks

---------------------------------------
My function call would be:
source("parse.R")
parseGBest('./gbest/inFile.seq',   './gbest/outFile.out');
---------------------------------------
I wrote a wrapper function (parse.R) as follows:

dyn.load("parse.so");
parseGBest = function(inFile, outFile)
{
.C( "parse" , inFile , outFile);
}

How to write receive the filenames in function( , ) above. and how to call
.C

----------------------------------------
parse.c file is as below:  How to receive the argument in funcion and how to
make it compatible with my argv[ ].


void parse( int argc, char *argv[] )  //This is working as standalone C
program. How to receive
                                                  // the above files so that
it become compatible with my argv[ ]
    {

    FILE *fr, *of;
    char line[81];


 if ( *argc == 3 )*/
        {
        if ( ( fr = fopen( argv[0], "r" )) == NULL )
            {
            puts( "Can't open input file.\n" );
            exit( 0 );
            }
        if ( ( of = fopen( argv[1], "w" )) == NULL )
            {
            puts( "Output file not given.\n" );
            }
      }
   else
        {printf("wrong usage: Try Agay!!! correct usage is:=  functionName
inputfileToParse outFileToWriteInto\n");
       }
    while(fgets(line, 81, fr) != NULL)

--
---
--
}



Thanks again
Fahim

-- 
Fahim Mohammad
Bioinforformatics Lab
University of Louisville
Louisville, KY, USA
Ph:  +1-502-409-1167

	[[alternative HTML version deleted]]

Fahim, 

Please see the Writing R Extensions manual
http://cran.r-project.org/doc/manuals/R-exts.pdf

There are simple instructions in this document under the heading "System
and foreign language interfaces."

-Matt


On Wed, 2010-07-14 at 01:21 -0400, Fahim Md wrote:
> Hi,
> I am trying to call a C function, that I wrote to parse a flat file,  into
> R. The argument that will go into this function is an input file that I
need
> to parse and write the desired output in an output file.  I used some hit
> and trial approach but i keep on getting the "file not found" or
> "segmentation fault" error. I know that the error is in passing
the argument
> but I could not solve it.
> 
> After reading  some of the tutorials, I understood how to do this if the
> arguments are integers or floats. I am stuck when i am trying to send the
> files. I am attaching stub of each file.
> Help appreciated.
> Thanks
> 
> ---------------------------------------
> My function call would be:
> source("parse.R")
> parseGBest('./gbest/inFile.seq',   './gbest/outFile.out');
> ---------------------------------------
> I wrote a wrapper function (parse.R) as follows:
> 
> dyn.load("parse.so");
> parseGBest = function(inFile, outFile)
> {
> .C( "parse" , inFile , outFile);
> }
> 
> How to write receive the filenames in function( , ) above. and how to call
> .C
> 
> ----------------------------------------
> parse.c file is as below:  How to receive the argument in funcion and how
to
> make it compatible with my argv[ ].
> 
> 
> void parse( int argc, char *argv[] )  //This is working as standalone C
> program. How to receive
>                                                   // the above files so
that
> it become compatible with my argv[ ]
>     {
> 
>     FILE *fr, *of;
>     char line[81];
> 
> 
>  if ( *argc == 3 )*/
>         {
>         if ( ( fr = fopen( argv[0], "r" )) == NULL )
>             {
>             puts( "Can't open input file.\n" );
>             exit( 0 );
>             }
>         if ( ( of = fopen( argv[1], "w" )) == NULL )
>             {
>             puts( "Output file not given.\n" );
>             }
>       }
>    else
>         {printf("wrong usage: Try Agay!!! correct usage is:= 
functionName
> inputfileToParse outFileToWriteInto\n");
>        }
>     while(fgets(line, 81, fr) != NULL)
> 
> --
> ---
> --
> }
> 
> 
> 
> Thanks again
> Fahim
> 
-- 
Matthew S. Shotwell
Graduate Student
Division of Biostatistics and Epidemiology
Medical University of South Carolina
http://biostatmatt.com