To get things to work in Python, I have to set some dlopen flags as follows:
sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL) The following discussion hints at something similar for R: http://www.mail-archive.com/r-help@r-project.org/msg143108.html. - Noel On 25 March 2013 20:30, Kevin Horan <kho...@globalrecordings.net> wrote: > Thanks, but swig did not help. > > > 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 #this is the correct result > 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. > > Kevin > > On 03/21/2013 05:51 AM, Noel O'Boyle wrote: >> This isn't exactly answering your question, but have you considered >> creating the R Swig wrapper. This may just simply work out of the box >> (or indeed not!) with little effort. >> >> - Noel >> >> On 20 March 2013 16:13, Kevin Horan<kevinho...@globalrecordings.net> wrote: >>> 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 >>> OpenBabel-Devel@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > ------------------------------------------------------------------------------ > Own the Future-Intel® Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. > Compete for recognition, cash, and the chance to get your game > on Steam. $5K grand prize plus 10 genre and skill prizes. > Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel ------------------------------------------------------------------------------ Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
