Re: [Open Babel] Java bindings for openbabel 2.4.0

[Noel O'B. <bao...@gm...>]

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 <jo...@uc...> 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" <bao...@gm...> wrote:
>>
>> This part is covered in the docs at least. You are missing eigen.
>>
>>
>> On 5 Oct 2016 6:02 p.m., "Jason Ott" <jo...@uc...> 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 <bao...@gm...>
>>> 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 <jo...@uc...> 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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>>>> >
>>>
>>>
>