Java bindings undefined symbol: _ZTVN9OpenBabel30OBMinimizingRMSDConformerScoreE

[kmvinoth]

• [*] I believe this to be a bug with Open Babel
• This is a feature request

Environment Information

Open Babel version: 2.4.0
Operating system and version: Ubuntu 16.04

Actual Behavior

I am using openbabel in my java application(app). I want to distribute my application as jar file(app.jar). My jar file library contains openbabel.jar and other jar files required for the application to run in the lib directory.

I complied java bindings for openbabel using the command

sudo cmake /home/vin/openbabel2.4 
-DCMAKE_INSTALL_PREFIX=~/Tools 
-DCMAKE_BUILD_TYPE=DEBUG  
-DJAVA_BINDINGS=ON 
-DEIGEN3_INCLUDE_DIR=/home/vin/Eigen3 
-DSWIG_EXECUTABLE=/usr/bin/swig 
-DRUN_SWIG=ON
sudo make

The compilation went well and took the libopenbabel_java.so and libopenbabel.so from the build directory and packed it along with my application in the directory (app/rescources) and specified the path to the app/resources directory in the source code (system.load("/home/vin/app/resources/libopenbabel_java.so")) of my application for performing an openbabel task.

When I run my application jar file (app.jar) and perform an openbabel task (generate conformers) I am getting the below error

Exception in thread "AWT-EventQueue-0" java.lang.UnsatisfiedLinkError: /home/praktikant/OPAS_ALPHA_1.0/resources/libopenbabel_java.so: /home/praktikant/OPAS_ALPHA_1.0/resources/libopenbabel_java.so: undefined symbol: _ZTVN9OpenBabel30OBMinimizingRMSDConformerScoreE

I am not sure that it is a bug in openbabel or am I missing something in the java bindings compilation? I have attached the CMakeCache.txt
CMakeCache.txt

I also looked into the Java bindings trouble #1102 in the issues, it is some what close but not exactly the same. Thank you for your time.

[baoilleach]

Using "sudo" for anything except the installation step is a mistake. It can lead to all sorts of problems that I am not going to debug.

If you start over, avoid sudo, and send us the command-line, the CMakeCache.txt and output of make, we can take it from there. I note in passing that the CMakeCache.txt that you appended does not correspond to the command-line above (e.g. different PATHs).

[ghutchis]

Please try this with the latest build (3.1) - open a new issue if you still have a problem. I'm going to mark this closed.