I posted this in openbabel-devel but didn't get much help, so hopefully
someone here can help. I don't think its too openbabel specific.
I would like to make use of open babel from within the R language.
Initially I just need to do some format conversions, but may expand the
usage to other parts of OpenBabel as well. I am familiar with embedding
C/C++ code in R, but I'm having some trouble with the plugin mechanism
of OpenBabel in this case. The problem is that the formats are not
available when I run the OpenBabel code from within R. So, for example,
if I search for the SDF format like so:
OBFormat *format = conv.FindFormat("SDF");
I always get back a 0 value. The same chunk of code executed outside of
R, as a normal stand-alone program, works fine. So does anyone know how
I can ensure that the formats get loaded? Thanks.
One other thing to mention, someone might suggest linking against a
static version of openbabel which includes all the plugins. I would like
to avoid that if possible since this needs to work in an R package that
will be distributed across platforms, so it would be hard to ask people
to compile a special, static, version of openbabel just to compile this
R package. Since it needs to work on windows, mac and linux, it would be
nice if I can make use of any existing installed shared obenbabel
libraries. If it turns out it can't be done, then I'll go down that
path. Thanks.
Here is an example of the problem:
test program (obtest2.cc):
#include <iostream>
#include <openbabel/obconversion.h>
#include <R.h>
#include <Rinternals.h>
extern "C" { SEXP test(); }
int main(){
test();
}
SEXP test()
{
OpenBabel::OBConversion conv;
OpenBabel::OBFormat *format = conv.FindFormat("SDF"); //
search for SDF format
std::cout<<"format: "<<format<<std::endl;
// print out
search result, either 0 or an address
return R_NilValue;
}
compile:
g++ -I/usr/include/openbabel-2.0 -I/usr/share/R/include -fpic -c
obtest2.cc -o obtest2.o
g++ -o obtest2 obtest2.o -fpic -lopenbabel
-lR # Executable
g++ -shared -o libobtest2.so obtest2.o -fpic -lopenbabel -lR # R
library
Run executable:
$ ./obtest2
format: 0x7f1858275d20 #found some result, this is what I expect
Run in R:
R>dyn.load("libobtest2.so")
R>.Call("test")
format: 0 # the format was not found, so 0 was
returned
NULL
After some more experimentation, I have discovered I can get it to work
in the following way, but I think it is a bit impractical. If I compile
the shared library as:
g++ -shared -o libobtest2.so obtest2.o -fpic
/usr/lib/openbabel/2.2.3/mdlformat.so -lopenbabel -lR
so the name of one of the plugins is specified. Then, in R I run:
R>dyn.load("/usr/lib/openbabel/2.2.3/mdlformat.so")
R>dyn.load("libobtest2.so")
R>.Call("test")
format: 0x7fe114c96d20
NULL
So then it works. But this requires that I know the full path to every
plugin when the code is compiled and when the library is loaded. Is
there a practical way to do this, say, if this were part of an R
package? I have also tried compiling the shared library as before,
without the plugin, and then just loading the plugin with dyn.load but
this does not work. It seems like it should though, does anyone know why
it doesn't? Conversely, if you compile with the plugin specified, but
don't load it with dyn.load it seg faults.
The way it works normally in OpenBabel is that each plugin is its
own shared library and then they get loaded at run time with the dlopen
function (on linux at least). I have verified that this code is still
being executed when called from within R, but it doesn't work for some
reason.
Also, swig does not help.
Thanks.
Kevin