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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 Kevin ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar _______________________________________________ OpenBabel-Devel mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-devel Openbabel Install
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