Java bindings for openbabel 2.4.0

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Java bindings for openbabel 2.4.0

Jason Ott
Hello all!

I have been trying all day to build the java bindings for open babel.  I have:
  1. installed through mac ports,
  2. 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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Re: Java bindings for openbabel 2.4.0

David Hall
I believe swig is needed for creating java (and python) bindings and it says swig was not found

-David

On Oct 4, 2016, at 8:10 PM, Jason Ott <[hidden email]> wrote:

Hello all!

I have been trying all day to build the java bindings for open babel.  I have:
  1. installed through mac ports,
  2. 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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Re: Java bindings for openbabel 2.4.0

Noel O'Boyle
Administrator
In reply to this post by Jason Ott
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 <[hidden email]> 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: Java bindings for openbabel 2.4.0

Jason Ott
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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>


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Re: Java bindings for openbabel 2.4.0

Geoff Hutchison
In reply to this post by Noel O'Boyle
My fault - I'll issue a 2.4.1 shortly (i.e., either today or tomorrow, US time).

Thanks,
-Geoff
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Re: Java bindings for openbabel 2.4.0

Noel O'Boyle
Administrator
In reply to this post by Jason Ott

This part is covered in the docs at least. You are missing eigen.


On 5 Oct 2016 6:02 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>


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Re: Java bindings for openbabel 2.4.0

Jason Ott

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" <[hidden email]> wrote:

This part is covered in the docs at least. You are missing eigen.


On 5 Oct 2016 6:02 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>


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Re: Java bindings for openbabel 2.4.0

Noel O'Boyle
Administrator
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 <[hidden email]> 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" <[hidden email]> wrote:
>>
>> This part is covered in the docs at least. You are missing eigen.
>>
>>
>> On 5 Oct 2016 6:02 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]>
>>> 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 <[hidden email]> 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
>>>> > [hidden email]
>>>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>> >
>>>
>>>
>

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Re: Java bindings for openbabel 2.4.0

Jason Ott
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 <[hidden email]> 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 <[hidden email]> 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" <[hidden email]> wrote:
>>
>> This part is covered in the docs at least. You are missing eigen.
>>
>>
>> On 5 Oct 2016 6:02 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]>
>>> 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 <[hidden email]> 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
>>>> > [hidden email]
>>>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>> >
>>>
>>>
>


------------------------------------------------------------------------------
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Re: Java bindings for openbabel 2.4.0

Noel O'Boyle
Administrator

What exact OS and version are you using?


On 5 Oct 2016 10:47 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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" <[hidden email]> wrote:
>>
>> This part is covered in the docs at least. You are missing eigen.
>>
>>
>> On 5 Oct 2016 6:02 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]>
>>> 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 <[hidden email]> 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
>>>> > [hidden email]
>>>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>> >
>>>
>>>
>


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Re: Java bindings for openbabel 2.4.0

Jason Ott
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 <[hidden email]> wrote:

What exact OS and version are you using?


On 5 Oct 2016 10:47 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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" <[hidden email]> wrote:
>>
>> This part is covered in the docs at least. You are missing eigen.
>>
>>
>> On 5 Oct 2016 6:02 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]>
>>> 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 <[hidden email]> 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
>>>> > [hidden email]
>>>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>> >
>>>
>>>
>



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Re: Java bindings for openbabel 2.4.0

Jason Ott
Here is the simple code I wrote to test loading the library:
public static void runOpenBabel() {
logger.info(System.getProperty("java.library.path"));
try {
//System.load("~/Applications/openbabel/lib/libopenbabel_java.jnilib");
System.loadLibrary("openbabel_java");
logger.debug("Successfully loaded the openbabel lib");
} catch(UnsatisfiedLinkError e) {
logger.fatal("cannot load jni lib");
} }
The path ends up being: ~Applications/openbabel/lib

What I do is I add to the java.library.path variable: -Djava.library.path=/path/to/openbabel/lib/   => which translates to above

And the above code will throw the following error:
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x0000000110c55761, pid=64236, tid=7171
#
# JRE version: Java(TM) SE Runtime Environment (8.0_60-b27) (build 1.8.0_60-b27)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.60-b23 mixed mode bsd-amd64 compressed oops)
# Problematic frame:
# C  [libawt_lwawt.dylib+0x44761]  JNI_OnLoad+0x91
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /Users/jason/Projects/IntelliJ/ChemTrails/hs_err_pid64236.log
#
# If you would like to submit a bug report, please visit:
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

Process finished with exit code 134

Upon running CMake, make, make install for openbabel there were no reported errors.



On Thu, Oct 6, 2016 at 10:06 AM, Jason Ott <[hidden email]> wrote:
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 <[hidden email]> wrote:

What exact OS and version are you using?


On 5 Oct 2016 10:47 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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" <[hidden email]> wrote:
>>
>> This part is covered in the docs at least. You are missing eigen.
>>
>>
>> On 5 Oct 2016 6:02 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]>
>>> 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 <[hidden email]> 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
>>>> > [hidden email]
>>>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>> >
>>>
>>>
>




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Re: Java bindings for openbabel 2.4.0

Noel O'Boyle
Administrator
Sorry for the silence but I don't have access to a Mac to help beyond
this. What I would have done to try to debug is to play around with
the LD_LIBRARY_PATH and LD_PRELOAD variables (or their Mac
equivalents), and also build debug versions of Open Babel and run the
Java from gdb or valgrind to find the exact point of failure in our
code, or take a look at the core dump mentioned in your email. Also it
can be worth trying the Oracle supplied Java instead of the Mac one
(if there is a difference).

- Noel

On 6 October 2016 at 18:52, Jason Ott <[hidden email]> wrote:

> Here is the simple code I wrote to test loading the library:
>
> public static void runOpenBabel() {
>    logger.info(System.getProperty("java.library.path"));
>    try {
>
> //System.load("~/Applications/openbabel/lib/libopenbabel_java.jnilib");
>       System.loadLibrary("openbabel_java");
>       logger.debug("Successfully loaded the openbabel lib");
>    } catch(UnsatisfiedLinkError e) {
>       logger.fatal("cannot load jni lib");
>    }
> }
>
> The path ends up being: ~Applications/openbabel/lib
>
> What I do is I add to the java.library.path variable:
> -Djava.library.path=/path/to/openbabel/lib/   => which translates to above
>
> And the above code will throw the following error:
>
> #
> # A fatal error has been detected by the Java Runtime Environment:
> #
> #  SIGSEGV (0xb) at pc=0x0000000110c55761, pid=64236, tid=7171
> #
> # JRE version: Java(TM) SE Runtime Environment (8.0_60-b27) (build
> 1.8.0_60-b27)
> # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.60-b23 mixed mode bsd-amd64
> compressed oops)
> # Problematic frame:
> # C  [libawt_lwawt.dylib+0x44761]  JNI_OnLoad+0x91
> #
> # Failed to write core dump. Core dumps have been disabled. To enable core
> dumping, try "ulimit -c unlimited" before starting Java again
> #
> # An error report file with more information is saved as:
> # /Users/jason/Projects/IntelliJ/ChemTrails/hs_err_pid64236.log
> #
> # If you would like to submit a bug report, please visit:
> #   http://bugreport.java.com/bugreport/crash.jsp
> # The crash happened outside the Java Virtual Machine in native code.
> # See problematic frame for where to report the bug.
> #
>
> Process finished with exit code 134
>
> Upon running CMake, make, make install for openbabel there were no reported
> errors.
>
>
>
>
> On Thu, Oct 6, 2016 at 10:06 AM, Jason Ott <[hidden email]> wrote:
>>
>> 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 <[hidden email]>
>> wrote:
>>>
>>> What exact OS and version are you using?
>>>
>>>
>>> On 5 Oct 2016 10:47 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]>
>>>> 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 <[hidden email]> 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" <[hidden email]> wrote:
>>>>> >>
>>>>> >> This part is covered in the docs at least. You are missing eigen.
>>>>> >>
>>>>> >>
>>>>> >> On 5 Oct 2016 6:02 p.m., "Jason Ott" <[hidden email]> 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 <[hidden email]>
>>>>> >>> 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 <[hidden email]> 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
>>>>> >>>> > [hidden email]
>>>>> >>>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>> >>>> >
>>>>> >>>
>>>>> >>>
>>>>> >
>>>>
>>>>
>>
>

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