MacOS Sierra 10.12 (16A323) with 2.4.0 of OpenBabel and Java 1.8.0_60
On Wed, Oct 5, 2016 at 11:30 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> 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/H
>>> ome/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
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>>> >>>> > _______________________________________________
>>> >>>> > OpenBabel-discuss mailing list
>>> >>>> > OpenBabel-discuss@lists.sourceforge.net
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>>> >>>> >
>>> >>>
>>> >>>
>>> >
>>>
>>
>>
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