Windows installation fails

[larandvit]

Hello,

I'm trying to install javabridge on Windows and it fails.

Environment Windows 7 jdk1.8.0_131 (32 bit) Visual Studio 2015 C++ compiler Python 3.6.3 (32 bit)

Try to install it in different ways 1)pip install javabridge 2)python setup.py install 3) set MSSdk=1 set DISTUTILS_USE_SDK=1 pip install javabridge

I receive the same result

building java2cpython library creating build\temp.win32-3.6\Release\java

C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-Ic:\program files (x86)\python36-32\Include" -Ijava "-IC:\Program Files (x86)\Java\jdk1.8.0_131\include" "-IC:\Program Files (x86)\Java\jdk1.8.0_131\include\win32" "-Ic:\program files (x86)\python36-32\include" "-Ic:\program files (x86)\python36-32\include" "-IC:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.6.1\include\um" "-IC:\Program Files (x86)\Windows Kits\8.1\include\shared" "-IC:\Program Files (x86)\Windows Kits\8.1\include\um" "-IC:\Program Files (x86)\Windows Kits\8.1\include\winrt" /Tcjava/org_cellprofiler_javabridge_CPython.c /Fobuild\temp.win32-3.6\Release\java/org_cellprofiler_javabridge_CPython.obj

org_cellprofiler_javabridge_CPython.c
java/org_cellprofiler_javabridge_CPython.c(69): error C2373: 'JNI_OnLoad': redefinition; different type modifiers
C:\Program Files (x86)\Java\jdk1.8.0_131\include\jni.h(1945): note: see declaration of 'JNI_OnLoad'

The last two lines tell the reason.

Can you please fix it or suggest a workaround?

Vitaly.

[LeeKamentsky]

Hi Vitaly, It looks like you are using a 32-bit version of Python. I'm not sure if I can replicate that environment any longer (but I'll try tonight). Is it possible for you to use a 64-bit toolchain? I'm not sure if that will solve the problem, though.

--Lee

[larandvit]

Thank you, Lee, for quick response.

32 bit Python installation is default one for Windows. I'm not sure if there is an option to install 64 bit one. I had more issues before but after matching 32 bit for all related tools (tool chain), I almost could build it.

Vitaly.

[larandvit]

Hi Lee,

I've managed to compile javabridge as 32 bit but when I run it it generates run-time.

I've changed the code in org_cellprofiler_javabridge_CPython.c

original code: jint JNI_OnLoad(JavaVM *vm, void *reserved) new code: JNIEXPORT jint JNICALL JNI_OnLoad(JavaVM *vm, void *reserved)

Also, I've found another issue with access to Windows registry. The code below produces run-time in locate.py

kjava = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE, java_key_path)
kjdk = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE, jdk_key_path)

I suspect the reason is that even I run the build in command line with option as an administrator, the building process doesn't have access to the Windows registry.

I've just run SET commands for JAVA_HOME and JAVA_SDK in command line to bypass registry call.

The successful message after installing the build is

Installed c:\program files (x86)\python36-32\lib\site-packages\javabridge-1.0.15-py3.6-win32.egg Processing dependencies for javabridge==1.0.15 Searching for numpy==1.13.3 Best match: numpy 1.13.3 Adding numpy 1.13.3 to easy-install.pth file

Using c:\program files (x86)\python36-32\lib\site-packages Finished processing dependencies for javabridge==1.0.15

The code what I run to test javabridge

import os
import javabridge

javabridge.start_vm(run_headless=True)

try:
    print(javabridge.run_script('java.lang.String.format("Hello, %s!", greetee);',
                                dict(greetee='world')))
finally:
    javabridge.kill_vm()

The error message is

_Traceback (most recent call last): File "...\test.py", line 2, in import javabridge File "C:\Program Files (x86)\Python36-32\lib\site-packages\javabridge-1.0.15-py3.6-win32.egg\javabridge__init__.py", line 38, in from .jutil import start_vm, kill_vm, vm, activate_awt, deactivate_awt File "C:\Program Files (x86)\Python36-32\lib\site-packages\javabridge-1.0.15-py3.6-win32.egg\javabridge\jutil.py", line 157, in import javabridge._javabridge as javabridge ImportError: DLL load failed: %1 is not a valid Win32 application.

My next step is to try it with Python 64 bit.

Can you provide with your thoughts or suggestions?

Vitaly.

[LeeKamentsky]

Regarding the registry errors, if I remember correctly, there are separate keys that allow access to the 32-bit registry values (see https://msdn.microsoft.com/en-us/library/windows/desktop/ms724072(v=vs.85).aspx for a discussion). It may be that the values are in the 64-bit registry and not the 32-bit and that "KEY_WOW64_64KEY" needs to be at the base of the registry key path. Again, I'd have to test to see if this is true. The work-around is to set JAVA_HOME and JAVA_SDK to bypass - you've done the right thing there.

The next error message gives me a good clue as to what's going wrong. C:\Program Files (x86)\Python36-32\lib\site-packages\javabridge-1.0.15-py3.6-win32.egg is the path to a zip file containing the Python files needed to run Javabridge. _javabridge.dll is unlikely to be in there and would be inaccessible if it were. The setup script should be marked with an indication that it's not safe to make a zipfile egg and that's missing which is my fault.

Could you patch setup.py for me here: https://github.com/LeeKamentsky/python-javabridge/blob/master/setup.py#L394 passing the argument, zip_safe=False and try again? If that works, I'd really appreciate you forking the project and submitting a pull request with both your changes to org_cellprofiler_javabridge_CPython.c and to setup.py. I can modify them myself if that's difficult for you, but a little easier for me to get a patch from you than to do it myself.

[larandvit]

Hi Lee,

As per your instruction, I've added code below to setup.py file. It's still generating the same error message.

    cmdclass={'build_ext': build_ext},
    zip_safe=False)

The message after successful build is

removing 'build\bdist.win32\egg' (and everything under it) Processing javabridge-1.0.15-py3.6-win32.egg creating c:\program files (x86)\python36-32\lib\site-packages\javabridge-1.0.15-py3.6-win32.egg Extracting javabridge-1.0.15-py3.6-win32.egg to c:\program files (x86)\python36-32\lib\site-packages Adding javabridge 1.0.15 to easy-install.pth file

Installed c:\program files (x86)\python36-32\lib\site-packages\javabridge-1.0.15-py3.6-win32.egg Processing dependencies for javabridge==1.0.15 Searching for numpy==1.13.3 Best match: numpy 1.13.3 Adding numpy 1.13.3 to easy-install.pth file

Using c:\program files (x86)\python36-32\lib\site-packages Finished processing dependencies for javabridge==1.0.15

I can see extracted javabridge-1.0.15-py3.6-win32.egg file in C:\Program Files (x86)\Python36-32\Lib\site-packages\javabridge-1.0.15-py3.6-win32.egg folder. There are two sub folders: EGG-INFO and javabridge.

What would you suggest as next steps?

Thanks.

Vitaly.

[LeeKamentsky]

I would try the 64-bit version unless you want to continue debugging.

In the javabridge folder, is there a file named _javabridge.dll? You might try running the 32-bit dependency walker on it to see if it's a valid .dll and to check its dependencies: http://www.dependencywalker.com/

[larandvit]

Hi Lee,

I don't see _javabridge.dll file. Please review a list of file installed. I can provide with zipped file as well.

I would like to continue the debugging of 32 bit installation. I'm confident we can make it work,

 Directory of C:\Program Files (x86)\Python36-32\Lib\site-packages\javabridge-1.0.15-py3.6-win32.egg

01/11/2017  08:29 PM    <DIR>          .
01/11/2017  08:29 PM    <DIR>          ..
01/11/2017  08:29 PM    <DIR>          EGG-INFO
01/11/2017  08:34 PM    <DIR>          javabridge
               0 File(s)              0 bytes

 Directory of C:\Program Files (x86)\Python36-32\Lib\site-packages\javabridge-1.0.15-py3.6-win32.egg\EGG-INFO

01/11/2017  08:29 PM    <DIR>          .
01/11/2017  08:29 PM    <DIR>          ..
01/11/2017  08:29 PM                 1 dependency_links.txt
01/11/2017  08:29 PM                73 entry_points.txt
01/11/2017  08:29 PM                73 native_libs.txt
01/11/2017  08:29 PM                 2 not-zip-safe
01/11/2017  08:29 PM               885 PKG-INFO
01/11/2017  08:29 PM                 6 requires.txt
01/11/2017  08:29 PM             1,295 SOURCES.txt
01/11/2017  08:29 PM                11 top_level.txt
               8 File(s)          2,346 bytes

 Directory of C:\Program Files (x86)\Python36-32\Lib\site-packages\javabridge-1.0.15-py3.6-win32.egg\javabridge

01/11/2017  08:34 PM    <DIR>          .
01/11/2017  08:34 PM    <DIR>          ..
01/11/2017  08:32 PM    <DIR>          jars
01/11/2017  08:29 PM            80,230 jutil.py
01/11/2017  08:29 PM             9,284 locate.py
01/11/2017  08:29 PM             3,496 noseplugin.py
01/11/2017  08:29 PM    <DIR>          tests
01/11/2017  08:29 PM            20,193 wrappers.py
01/11/2017  08:29 PM           232,448 _javabridge.cp36-win32.pyd
01/11/2017  08:29 PM               306 _javabridge.py
01/11/2017  08:29 PM                23 _version.py
01/11/2017  08:29 PM             2,984 __init__.py
01/11/2017  08:29 PM    <DIR>          __pycache__
               8 File(s)        348,964 bytes

 Directory of C:\Program Files (x86)\Python36-32\Lib\site-packages\javabridge-1.0.15-py3.6-win32.egg\javabridge\jars

01/11/2017  08:32 PM    <DIR>          .
01/11/2017  08:32 PM    <DIR>          ..
01/11/2017  08:29 PM             4,112 cpython.jar
01/11/2017  08:29 PM            14,336 java2cpython.dll
01/11/2017  08:29 PM         1,134,765 rhino-1.7R4.jar
01/11/2017  08:29 PM             1,830 runnablequeue.jar
01/11/2017  08:29 PM               989 test.jar
               5 File(s)      1,156,032 bytes

 Directory of C:\Program Files (x86)\Python36-32\Lib\site-packages\javabridge-1.0.15-py3.6-win32.egg\javabridge\tests

01/11/2017  08:29 PM    <DIR>          .
01/11/2017  08:29 PM    <DIR>          ..
01/11/2017  08:29 PM             2,516 test_cpython.py
01/11/2017  08:29 PM            22,400 test_javabridge.py
01/11/2017  08:29 PM            28,692 test_jutil.py
01/11/2017  08:29 PM             5,984 test_wrappers.py
01/11/2017  08:29 PM                 0 __init__.py
01/11/2017  08:29 PM    <DIR>          __pycache__
               5 File(s)         59,592 bytes

 Directory of C:\Program Files (x86)\Python36-32\Lib\site-packages\javabridge-1.0.15-py3.6-win32.egg\javabridge\tests\__pycache__

01/11/2017  08:29 PM    <DIR>          .
01/11/2017  08:29 PM    <DIR>          ..
01/11/2017  08:29 PM             2,889 test_cpython.cpython-36.pyc
01/11/2017  08:29 PM            23,492 test_javabridge.cpython-36.pyc
01/11/2017  08:29 PM            31,832 test_jutil.cpython-36.pyc
01/11/2017  08:29 PM             9,268 test_wrappers.cpython-36.pyc
01/11/2017  08:29 PM               198 __init__.cpython-36.pyc
               5 File(s)         67,679 bytes

 Directory of C:\Program Files (x86)\Python36-32\Lib\site-packages\javabridge-1.0.15-py3.6-win32.egg\javabridge\__pycache__

01/11/2017  08:29 PM    <DIR>          .
01/11/2017  08:29 PM    <DIR>          ..
01/11/2017  08:29 PM            70,685 jutil.cpython-36.pyc
01/11/2017  08:29 PM             6,472 locate.cpython-36.pyc
01/11/2017  08:29 PM             3,896 noseplugin.cpython-36.pyc
01/11/2017  08:29 PM            18,310 wrappers.cpython-36.pyc
01/11/2017  08:29 PM               503 _javabridge.cpython-36.pyc
01/11/2017  08:29 PM               214 _version.cpython-36.pyc
01/11/2017  08:29 PM             2,905 __init__.cpython-36.pyc
               7 File(s)        102,985 bytes

     Total Files Listed:
              38 File(s)      1,737,598 bytes
              20 Dir(s)  53,061,943,296 bytes free

[LeeKamentsky]

OK - I'm sorry, it was _javabridge.pyd I was looking for. I see you've got _javabridge.cp36-win32.pyd. I think I might have to try and replicate this on my Windows machine this weekend. You might try running the dependency walker on _javabridge.cp36-win32.pyd and maybe that will provide some clue.

[larandvit]

Hi Lee,

I tried 64 bit Python and javabridge. It works just perfect as expected: pip install javabridge. I'll try Linux as well.

Thanks.

Vitaly.

[larandvit]

Hi Lee,

javabridge works on CentOS 7.4 with Python 3.4. I spent some time to figure out all dependencies. • sudo yum install epel-release • sudo yum install python34 • sudo yum install python34-setuptools • sudo easy_install-3.4 pip • sudo yum install python34-devel • sudo yum install java-1.8.0-openjdk-devel • sudo pip install numpy • sudo pip install javabridge

Thanks.

Vitaly.

[altendky]

I believe that both these pull requests relate to this issue: https://github.com/LeeKamentsky/python-javabridge/pull/133 (merged, helps to find Java 1.8+), https://github.com/LeeKamentsky/python-javabridge/pull/135 (not merged, helps with Windows x86/32-bit installs)