Thanks a lot Matt,
Just if someone like to see how I called a C function from R with files as
argumets.
For simplicity, this example is copying the content of input file into
output file
-----------------------------------------
My main program is :
source("parse.R")
parseGBest('gbest40.seq', 'gbest40.out'); // .seq is input file, .out is
output file
---------------------------------------
I wrote a wrapper function (parse.R) as follows:
dyn.load("parse.so");
parseGBest= function(infile, outfile)
{
# Do some whatever you like here
.C("parse", infile, outfile)
}
--------------------------------------
parse.c File looks like follows:
#include<R.h>
#include <stdio.h>
#include <stdlib.h>
#include<string.h>
void adel(char **infile, char **outfile)
{
char line[81];
FILE *fr, *of;
if (!(fr = fopen(*infile, "r")))
{
fprintf(stdout, "Error while opening input file\n");
return ;
}
if (!(of = fopen(*outfile, "w")))
{
fprintf(stdout, "Error while opening output file\n");
return ;
}
while(fgets(line, 81, fr) != NULL)
{
fputs(line, of);
}
fclose(fr);
fclose(of);
}
--------------------------------------
Thats it!!!!!!!!!!!!!
I saved almost a week in parsing all those genbank est files(almost 413
files).
Thanks R&C interface team.
--Fahim
On Wed, Jul 14, 2010 at 10:18 AM, Matt Shotwell <[email protected]> wrote:
> 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
>
>
--
Fahim Mohammad
Bioinforformatics Lab
University of Louisville
Louisville, KY, USA
Ph: +1-502-409-1167
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