Hi!
I have been coding a C-program which will read data from the
netCDF format (a commonly used file format in the geophysical research
community: see Unidata's URL for explanation:
http://www.unidata.ucar.edu/packages/netcdf/), and have got to the point
where I don't know what the error message mean. The C-program is called
nc2r.c.
When compiling the code, I get a number of warnings, but these are the
same warnings that I get when I compile a corresponding code that runs
on its own (i.e. doesn't use the R-libraries)
cc -shared -lc -o nc2r.so nc2r.c -I/home/matlab6/extern/include
-I/usr/include -I/usr/lib/R/include -I/home/kareb/local/include
-L/usr/lib/gcc-lib/i386-linux/2.95.2 /usr/lib/libnetcdf.a -lg2c -lm
nc2r.c: In function `ncread':
nc2r.c:259: warning: assignment makes integer from pointer without a
cast
nc2r.c:260: warning: assignment makes integer from pointer without a
cast
nc2r.c:261: warning: assignment makes integer from pointer without a
cast
nc2r.c:262: warning: assignment makes integer from pointer without a
cast
nc2r.c:263: warning: assignment makes integer from pointer without a
cast
nc2r.c: In function `nc2r':
nc2r.c:310: warning: assignment from incompatible pointer type
nc2r.c:311: warning: assignment from incompatible pointer type
nc2r.c:312: warning: assignment from incompatible pointer type
nc2r.c:325: warning: assignment from incompatible pointer type
nc2r.c:330: warning: assignment from incompatible pointer type
nc2r.c:335: warning: assignment from incompatible pointer type
nc2r.c:340: warning: assignment from incompatible pointer type
nc2r.c:345: warning: assignment from incompatible pointer type
The code is compiled, and I start R:
R : Copyright 1999, The R Development Core Team
Version 0.90.1 (December 15, 1999)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type "?license" or "?licence" for distribution details.
R is a collaborative project with many contributors.
Type "?contributors" for a list.
Type "demo()" for some demos, "help()" for on-line help, or
"help.start()" for a HTML browser interface to help.
Type "q()" to quit R.
> dyn.load(paste("nc2r", .Platform$dynlib.ext, sep=""))
Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to
load shared library "/home/kareb/netcdf/nc2r.so":
/home/kareb/netcdf/nc2r.so: undefined symbol: __dso_handle
The symbol "__dso_handle" I presume is defined in Rinternals.h or some
R-routines, or am I wrong? Are my R-path set incorrectly? Why does R say
that it cannot load nc2r.so, when this file is in the local directory?
There were some clashes between definitions in R.h and Rinternals.h, so
I did not include R.h.
Also, is ther any way of returning more than one object from the C-call
(ie. the data field, longitude vector, latitude vector, time vector, and
the missing value)
Yours sincerely Rasmus Benestad
-----------------------------------------------------------------------
The main part of the code looks like:
SEXP nc2r(char **fname, char **vname){
int ncread();
int status,i,j,k,nx,ny,nt;
long int ptrs[5]; /* array of pointers holding locations */
/* returned by malloc in ncread */
double ofs, scl; /* offset and scaling
factors */
double *ptr;
SEXP field, dim, dimnames, lon, lat, tim, missing;
printf("ncfile= %s, vname=%s\n",fname,vname);
printf("\nfield->%x\nlon -> %x\nlat -> %x\ntim -> %x\nmissing
->
%x\n",
field,lon,lat,tim,missing);
/* Call the function dealing with the netCDF data */
/* The data is placed in memeory */
status=ncread(fname, vname, &nx, &ny, &nt, &ptrs, &scl,
&ofs);
/* Allocate space for pointers */
/* Use PROTECT to ensure R doesn't mess with the data */
PROTECT(field = allocVector(REALSXP,nx*ny*nt));
PROTECT(lon = allocVector(REALSXP,nx));
PROTECT(lat = allocVector(REALSXP,ny));
PROTECT(tim = allocVector(REALSXP,nt));
PROTECT(missing= allocVector(REALSXP,1));
PROTECT(dim= allocVector(INTSXP,3));
/* Set the dimensions */
/* Index oredring: i=0:nx-1, j=0:ny-1 -> i + nx * j */
/* See Writing R extensions manual p. 26 */
INTEGER(dim)[0]=nx;
INTEGER(dim)[1]=ny;
INTEGER(dim)[2]=nt;
setAttrib(field, R_DimSymbol, dim);
PROTECT(dimnames = allocVector(VECSXP, 3));
VECTOR(dimnames)[0]="Lon";
VECTOR(dimnames)[1]="Lat";
VECTOR(dimnames)[2]="Time";
setAttrib(field, R_DimNamesSymbol, dimnames);
printf("\nfield->%x\nlon -> %x\nlat -> %x\ntim -> %x\nmissing
->
%x\n",
field,lon,lat,tim,missing);
printf("The dimensions are (nx x ny x nt): %d x %d x %d
\n",nx,ny,nt);
printf("\nCopy into R-objects\n");
/* Copy the data to the R-objects */
ptr=&ptrs[0];
for (i=0;i<nx*ny*nt;i++) {
REAL(field)[i] = *(ptr+i) * scl + ofs;
}
ptr=&ptrs[1];
for (i=0;i<nx;i++) {
REAL(lon)[i] = *(ptr+i);
}
ptr=&ptrs[2];
for (j=0;j<ny;j++) {
REAL(lat)[j] = *(ptr+j);
}
ptr=&ptrs[3];
for (k=0;k<nt;k++) {
REAL(tim)[k] = *(ptr+k);
}
ptr=&ptrs[4];
REAL(missing)[1]=*ptr;
printf("\nFinished successfully!\n");
/* Garbage collecting */
UNPROTECT(7);
return(field);
}
--
______________________________________________________________________________
Rasmus E. Benestad, D.Phil, GradInstP, The Norwegian Meteorological Institute
rasmus.benestad at dnmi.no
http://home.enitel.no/benestad/rasmus.html
phone: (+47) 22 96 31 70 mobile: (+47) 99 45 04 16 fax: (+47) 22 96 30 50
______________________________________________________________________________
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