The bindings get built just fine. I the both the jar and jnilib files are
created. The problem that arises is when I try to run openbabel within my
java application. I implement the tutorial and I get:
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x000000011e879761, pid=62346, tid=6915
...
Process finished with exit code 134
The jar is in the classpath and the jni is loaded using: either
System.load("/path/to/jnilib"); or System.loadLibrary("openbabel_java");
where I add the jnilib to the class.path environment variable. I assume
I'm doing this part correctly. But I could be mistaken.
Thanks,
Jason
On Wed, Oct 5, 2016 at 1:07 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Sorry - missed that. It's best to ignore that README as you shouldn't
> need to run g++ yourself. The bindings are built when you run "make &&
> make install". Just make sure that CMake finds Eigen at the configure
> step.
>
> If it still doesn't work please provide your CMakeCache.txt, and the
> output of "VERBOSE=1 make", and maybe we can see where things are
> going wrong.
>
> - Noel
>
> On 5 October 2016 at 19:01, Jason Ott <jott...@ucr.edu> wrote:
> > I have eigen3 installed. If you look at my gcc install command. I had to
> > add a path for it. It's there and functional.
> >
> >
> > On Oct 5, 2016 10:55, "Noel O'Boyle" <baoille...@gmail.com> wrote:
> >>
> >> This part is covered in the docs at least. You are missing eigen.
> >>
> >>
> >> On 5 Oct 2016 6:02 p.m., "Jason Ott" <jott...@ucr.edu> wrote:
> >>>
> >>> That worked like a charm! Thanks. So now I have been trying to
> include
> >>> said java bindings in my project...
> >>>
> >>> I added the openbabel.jar file to my classpath. So I can import and
> all
> >>> classes are resolved and looking good! However, when I try running the
> >>> basic program from the tutorial my System.loadLibrary("openbabel_
> java")
> >>> throws a segfault from native up to my java.
> >>>
> >>> I tried to follow the readme in the /scripts/java/ directory, but I
> >>> cannot get the very first compilation step to work. But I noticed that
> >>> under [install_path]/lib/ there is both the openbabel.jar and
> >>> libopenbabel_java.jnilib, which should be enough to get the thing
> working.
> >>>
> >>> When I follow that readme in /scripts/java/ I get the following error:
> >>>
> >>> openbabel-java.cpp:9941:25: error: no member named 'DiverseConfGen' in
> >>> 'OpenBabel::OBForceField'
> >>>
> >>> result = (int)(arg1)->DiverseConfGen(arg2,arg3,arg4,arg5); jresult =
> >>> (jint)result; return jresult; }
> >>>
> >>> ~~~~~~ ^
> >>>
> >>> openbabel-java.cpp:9946:25: error: no member named 'DiverseConfGen' in
> >>> 'OpenBabel::OBForceField'
> >>>
> >>> result = (int)(arg1)->DiverseConfGen(arg2,arg3,arg4); jresult =
> >>> (jint)result; return jresult; }
> >>>
> >>> ~~~~~~ ^
> >>>
> >>> openbabel-java.cpp:9950:54: error: no member named 'DiverseConfGen' in
> >>> 'OpenBabel::OBForceField'
> >>>
> >>> arg3 = (unsigned int)jarg3; result =
> >>> (int)(arg1)->DiverseConfGen(arg2,arg3); jresult = (jint)result;
> return
> >>> jresult; }
> >>>
> >>> ~~~~~~ ^
> >>>
> >>> openbabel-java.cpp:9954:25: error: no member named 'DiverseConfGen' in
> >>> 'OpenBabel::OBForceField'
> >>>
> >>> result = (int)(arg1)->DiverseConfGen(arg2); jresult = (jint)result;
> >>> return jresult; }
> >>>
> >>> ~~~~~~ ^
> >>>
> >>> 4 errors generated.
> >>>
> >>>
> >>> I compile with the following command: g++ -c -fpic openbabel-java.cpp
> -I
> >>> ../../include/ -I
> >>> /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/include/
> -I
> >>> /Library/Java/JavaVirtualMachines/jdk1.8.0_
> 60.jdk/Contents/Home/include/darwin/
> >>> -I /opt/local/include/eigen3/
> >>>
> >>>
> >>> Any support would be appreciated. Thanks.
> >>>
> >>>
> >>> On Wed, Oct 5, 2016 at 6:48 AM, Noel O'Boyle <baoille...@gmail.com>
> >>> wrote:
> >>>>
> >>>> Ah -- looks like we missed something in the release. The Swig bindings
> >>>> should have been included. As it is, you will need to install swig,
> >>>> and specify -DSWIG_EXECUTABLE=whatever.
> >>>>
> >>>> - Noel
> >>>>
> >>>> On 5 October 2016 at 01:10, Jason Ott <jott...@ucr.edu> wrote:
> >>>> > Hello all!
> >>>> >
> >>>> > I have been trying all day to build the java bindings for open
> babel.
> >>>> > I
> >>>> > have:
> >>>> >
> >>>> > installed through mac ports,
> >>>> > downloaded source and compiled using the following flags:
> >>>> >
> >>>> > -DCMAKE_INSTALL_PREFIX=~/Applications/openbabel -DJAVA_BINDINGS=ON
> >>>> > -DBUILD_GUI=OFF
> >>>> >
> >>>> > I am running MacOS Sierra. No special configs or anything. The
> java
> >>>> > bindings are never generated in the
> >>>> > openbabel-openbabel-2.4.0/scripts/java/
> >>>> > folder or anywhere in the installation location.
> >>>> >
> >>>> > When I do the "cmake ./
> >>>> > -DCMAKE_INSTALL_PREFIX=~/Applications/openbabel
> >>>> > -DJAVA_BINDINGS=ON -DBUILD_GUI=OFF" I get the following output:
> >>>> >
> >>>> > -- Using included inchi library.
> >>>> > -- Could NOT find wxWidgets (missing: wxWidgets_LIBRARIES
> >>>> > wxWidgets_INCLUDE_DIRS)
> >>>> > -- Checking available shared pointer...
> >>>> > -- Use std::shared_ptr in memory
> >>>> > -- Cairo found. PNG output will be supported.
> >>>> > -- GUI will not be built
> >>>> > -- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR)
> >>>> > -- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR)
> (Required
> >>>> > is at
> >>>> > least version "2.0")
> >>>> > -- SWIG 2.0 NOT found
> >>>> > -- Configuring done
> >>>> > -- Generating done
> >>>> > -- Build files have been written to:
> >>>> > /Users/jason/Desktop/openbabel-openbabel-2-4-0
> >>>> >
> >>>> > So that tells me that that java AND python bindings should exist
> >>>> > *somewhere*
> >>>> > but they don't.
> >>>> >
> >>>> > Thanks,
> >>>> >
> >>>> > Jason
> >>>> >
> >>>> >
> >>>> > ------------------------------------------------------------
> ------------------
> >>>> > Check out the vibrant tech community on one of the world's most
> >>>> > engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> >>>> > _______________________________________________
> >>>> > OpenBabel-discuss mailing list
> >>>> > OpenBabel-discuss@lists.sourceforge.net
> >>>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >>>> >
> >>>
> >>>
> >
>
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