Does a linux build produce a java jar file that can be used in matlab?

[chrisdembia]

In #17, @aymanhab asked if a Linux build produces a jar file that can be used in Matlab. I'm creating a new issue to investigate this.

[chrisdembia]

The jar builds successfully. I have tried using the .jar in MATLAB but have been unsuccessful so far. I will continue trying tomorrow.

1. The JavaCompile target produces the .jar in the build directory, but is the resulting jar installed into the installation dir?
2. The .class files are installed into the installation dir when running make install after having run make JavaCompile. I assume this is desired behavior. The .class files and the .java files are in the same directory.
3. The JavaCompile target was not built for me when I ran make. I had to explicitly run make JavaCompile. Is this the desired behavior?

[chrisdembia]

Currently the jar does not work in Matlab. First, it's because the org-opensim-modeling.jar used the complete paths to the class files (on my computer, the paths inside the jar were something like home.fitze.repos.opensim.opensim-core.....src.org.opensim.modeling).

So I changed the working dir of the JavaCompile custom command to ${CMAKE_BUILD..}/OpenSim/Wrapping/Java/src.

Then I got:

>> import org.opensim.modeling.*
>> Model()
Warning: A Java exception occurred trying to load the org/opensim/modeling/Model
class:
Java exception occurred:
java.lang.UnsupportedClassVersionError: org/opensim/modeling/Model : Unsupported
major.minor version 51.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(Unknown Source)
    at java.security.SecureClassLoader.defineClass(Unknown Source)
    at java.net.URLClassLoader.defineClass(Unknown Source)
    at java.net.URLClassLoader.access$000(Unknown Source)
    at java.net.URLClassLoader$1.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClassInternal(Unknown Source)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Unknown Source)
    at
    com.mathworks.jmi.OpaqueJavaInterface.findClass(OpaqueJavaInterface.java:470) 

Do you know what this means?

[aymanhab]

This's likely an issue with the Java version used to compile the jar file
is different from the one used by MATLAB (likely compiling with JDK 1.7
while Matlab is on 1.6)

On Thu, Jun 26, 2014 at 9:55 AM, Christopher Dembia <
notifications@github.com> wrote:

Currently the jar does not work in Matlab. First, it's because the
org-opensim-modeling.jar used the complete paths to the class files (on my
computer, the paths inside the jar were something like
home.fitze.repos.opensim.opensim-core.....src.org.opensim.modeling).

So I changed the working dir of the JavaCompile custom command to
${CMAKE_BUILD..}/OpenSim/Wrapping/Java/src.

Then I got:

import org.opensim.modeling.*
Model()
Warning: A Java exception occurred trying to load the org/opensim/modeling/Model
class:
Java exception occurred:
java.lang.UnsupportedClassVersionError: org/opensim/modeling/Model : Unsupported
major.minor version 51.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(Unknown Source)
at java.security.SecureClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.access$000(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClassInternal(Unknown Source)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
at
com.mathworks.jmi.OpaqueJavaInterface.findClass(OpaqueJavaInterface.java:470)

Do you know what this means?

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#40 (comment)
.

[chrisdembia]

I think that is what it is. I followed these instructions http://www.mathworks.com/matlabcentral/answers/103056-how-do-i-change-the-java-virtual-machine-jvm-that-matlab-is-using-for-mac-os to make MATLAB use my JRE 1.7, and that worked, but now I'm dealing with other linking issues.

[chrisdembia]

A better option would be to specify the -source command to the java compiler. I tried this though and it didn't work.

[chrisdembia]

I had to take these two additional steps:

1. Set my LD_LIBRARY_PATH to the correct directory containing osimJavaJNI.so
2. Update my MATLAB's libgfortran with sudo ln -sf /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0 /usr/local/MATLAB/R2013a/sys/os/glnxa64/libgfortran.so.3. See http://stackoverflow.com/questions/9628273/libgfortran-version-gfortran-1-4-not-found.

The other thing we need to do is ensure we build for 1.6; we can either tell the user to use 1.6 or we can try to ensure this using command line arguments (which might not be sufficient).

[aymanhab]

So, what versionof Java does the latest Matlab come with? Does it use
Sun/Oracle or openjdk on linux?

On Thu, Jun 26, 2014 at 10:15 AM, Christopher Dembia <
notifications@github.com> wrote:

I had to take these two additional steps:

1. Set my LD_LIBRARY_PATH to the correct directory containing
   osimJavaJNI.so
2. Update my MATLAB's libgfortran with sudo ln -sf
   /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
   /usr/local/MATLAB/R2013a/sys/os/glnxa64/libgfortran.so.3. See
   http://stackoverflow.com/questions/9628273/libgfortran-version-gfortran-1-4-not-found
   .

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#40 (comment)
.

[aymanhab]

Chris, did you submit your cmake file change? I'd like to have that change and to add the dependency so that JavaCompile compiles the jar file and install it with standard install so we can move on to the next step of building the GUI.

[chrisdembia]

See java-jar branch, PR #65. I suppose you can either work off that branch, or merge that PR and create a new PR.