What exact OS and version are you using?
On 5 Oct 2016 10:47 p.m., "Jason Ott" <jott...@ucr.edu> wrote:
> 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
>> >>>> >
>> >>>> >
>> >>>> > ------------------------------------------------------------
>> ------------------
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>> >>>> >
>> >>>
>> >>>
>> >
>>
>
>
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