[Jepp-users] JEPP gets confused with multiple installed python interpreters (?)
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[Jepp-users] JEPP gets confused with multiple installed python interpreters (?)
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From: Florian J. <ju...@mp...> - 2014-05-16 09:52:18
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Hello Jeppers,
I would like to use JEP in order to access a very rich, third party python library.
(This library wraps opengm, a huge C++ based optimization library... details maybe not so important...)
I installed the opengm python module in one of 3 python environments I (unfortunately) need to have on my machine.
(I am sitting on a 10.9 OSX, having the native python, the macports 2.7 python, and a third one I've built all myself from source...)
I am sorry that already the preamble to my problem is so complex... :(
I have also built JEPP form source, but I run into a problem that really puzzles me... I come to point soon... ;)
Ok, here we go with a swquence of commands I type in:
jug@myers-mac-7:~/Dropbox/WorkingData/Repositories/GIT/jep$ which jep
jug@myers-mac-7:~/Dropbox/WorkingData/Repositories/GIT/jep$ which python
/Users/jug/local/ilastik/bin/python
jug@myers-mac-7:~/Dropbox/WorkingData/Repositories/GIT/jep$ python setup.py clean
running clean
removing build
removing build/lib.macosx-10.9-x86_64-2.7
removing build/scripts-2.7
removing build/temp.macosx-10.9-x86_64-2.7
removing build/bdist.macosx-10.9-x86_64
jug@myers-mac-7:~/Dropbox/WorkingData/Repositories/GIT/jep$ python setup.py install
running install
running build
running build_java
/System/Library/Frameworks/JavaVM.framework/Commands/javac -deprecation -d build/java -classpath src/ src/jep/ClassList.java src/jep/InvocationHandler.java src/jep/Jep.java src/jep/JepException.java src/jep/JepScriptEngine.java src/jep/JepScriptEngineFactory.java src/jep/Proxy.java src/jep/Run.java src/jep/Test.java src/jep/Util.java src/jep/python/PyClass.java src/jep/python/PyModule.java src/jep/python/PyObject.java
running build_javah
/System/Library/Frameworks/JavaVM.framework/Commands/javah -classpath build/java -o build/include/jep.h jep.Jep
/System/Library/Frameworks/JavaVM.framework/Commands/javah -classpath build/java -o build/include/jep_object.h jep.python.PyObject
/System/Library/Frameworks/JavaVM.framework/Commands/javah -classpath build/java -o build/include/invocationhandler.h jep.InvocationHandler
running build_jar
copying src/jep/classlist_6.txt to build/java/jep/classlist_6.txt
copying src/jep/classlist_7.txt to build/java/jep/classlist_7.txt
/System/Library/Frameworks/JavaVM.framework/Commands/jar -cfe build/java/jep.jar jep.Run -C build/java/ jep
running build_py
creating build/lib.macosx-10.9-x86_64-2.7
creating build/lib.macosx-10.9-x86_64-2.7/jep
copying jep/__init__.py -> build/lib.macosx-10.9-x86_64-2.7/jep
copying jep/console.py -> build/lib.macosx-10.9-x86_64-2.7/jep
copying jep/hook.py -> build/lib.macosx-10.9-x86_64-2.7/jep
copying jep/jdbc.py -> build/lib.macosx-10.9-x86_64-2.7/jep
copying jep/version.py -> build/lib.macosx-10.9-x86_64-2.7/jep
running build_ext
building 'jep' extension
creating build/temp.macosx-10.9-x86_64-2.7
creating build/temp.macosx-10.9-x86_64-2.7/src
creating build/temp.macosx-10.9-x86_64-2.7/src/jep
creating build/temp.macosx-10.9-x86_64-2.7/src/jep/python
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future -DPACKAGE=jep -DUSE_DEALLOC=1 -DVERSION="3.2.0" -I/System/Library/Frameworks/JavaVM.framework/Headers -Isrc/jep -Ibuild/include -I/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/jep/invocationhandler.c -o build/temp.macosx-10.9-x86_64-2.7/src/jep/invocationhandler.o
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future -DPACKAGE=jep -DUSE_DEALLOC=1 -DVERSION="3.2.0" -I/System/Library/Frameworks/JavaVM.framework/Headers -Isrc/jep -Ibuild/include -I/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/jep/jep.c -o build/temp.macosx-10.9-x86_64-2.7/src/jep/jep.o
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future -DPACKAGE=jep -DUSE_DEALLOC=1 -DVERSION="3.2.0" -I/System/Library/Frameworks/JavaVM.framework/Headers -Isrc/jep -Ibuild/include -I/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/jep/pyembed.c -o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyembed.o
src/jep/pyembed.c:336:5: warning: 'JNI_GetCreatedJavaVMs' is deprecated [-Wdeprecated-declarations]
JNI_GetCreatedJavaVMs(&jvm, 1, NULL);
^
/System/Library/Frameworks/JavaVM.framework/Headers/jni.h:1940:1: note: 'JNI_GetCreatedJavaVMs' declared here
JNI_GetCreatedJavaVMs(JavaVM **, jsize, jsize *);
^
src/jep/pyembed.c:1525:10: warning: implicit declaration of function 'PyMarshal_ReadLongFromFile' is invalid in C99 [-Wimplicit-function-declaration]
magic = PyMarshal_ReadLongFromFile(fp);
^
src/jep/pyembed.c:1532:30: warning: implicit declaration of function 'PyMarshal_ReadLastObjectFromFile' is invalid in C99 [-Wimplicit-function-declaration]
v = (PyObject *) (intptr_t) PyMarshal_ReadLastObjectFromFile(fp);
^
3 warnings generated.
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future -DPACKAGE=jep -DUSE_DEALLOC=1 -DVERSION="3.2.0" -I/System/Library/Frameworks/JavaVM.framework/Headers -Isrc/jep -Ibuild/include -I/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/jep/pyjarray.c -o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyjarray.o
src/jep/pyjarray.c:1298:49: warning: variable 'self' is uninitialized when used within its own initialization [-Wuninitialized]
PyJarray_Object *self = (PyJarray_Object *) self;
~~~~ ^~~~
src/jep/pyjarray.c:1583:5: warning: incompatible pointer types initializing 'ssizeobjargproc' (aka 'int (*)(PyObject *, Py_ssize_t, PyObject *)') with an expression of
type 'intobjargproc' (aka 'int (*)(PyObject *, int, PyObject *)') [-Wincompatible-pointer-types]
(intobjargproc) pyjarray_setitem, /* sq_ass_item */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/jep/pyjarray.c:1584:5: warning: incompatible pointer types initializing 'ssizessizeobjargproc' (aka 'int (*)(PyObject *, Py_ssize_t, Py_ssize_t, PyObject *)') with
an expression of type 'intintobjargproc' (aka 'int (*)(PyObject *, int, int, PyObject *)') [-Wincompatible-pointer-types]
(intintobjargproc) 0, /* sq_ass_slice */
^~~~~~~~~~~~~~~~~~~~
src/jep/pyjarray.c:1714:5: warning: incompatible pointer types initializing 'lenfunc' (aka 'Py_ssize_t (*)(PyObject *)') with an expression of type 'inquiry'
(aka 'int (*)(PyObject *)') [-Wincompatible-pointer-types]
(inquiry) pyjarrayiter_len, /* sq_length */
^~~~~~~~~~~~~~~~~~~~~~~~~~
4 warnings generated.
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future -DPACKAGE=jep -DUSE_DEALLOC=1 -DVERSION="3.2.0" -I/System/Library/Frameworks/JavaVM.framework/Headers -Isrc/jep -Ibuild/include -I/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/jep/pyjclass.c -o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyjclass.o
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future -DPACKAGE=jep -DUSE_DEALLOC=1 -DVERSION="3.2.0" -I/System/Library/Frameworks/JavaVM.framework/Headers -Isrc/jep -Ibuild/include -I/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/jep/pyjfield.c -o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyjfield.o
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future -DPACKAGE=jep -DUSE_DEALLOC=1 -DVERSION="3.2.0" -I/System/Library/Frameworks/JavaVM.framework/Headers -Isrc/jep -Ibuild/include -I/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/jep/pyjmethod.c -o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyjmethod.o
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future -DPACKAGE=jep -DUSE_DEALLOC=1 -DVERSION="3.2.0" -I/System/Library/Frameworks/JavaVM.framework/Headers -Isrc/jep -Ibuild/include -I/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/jep/pyjobject.c -o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyjobject.o
src/jep/pyjobject.c:796:5: warning: incompatible pointer types initializing 'richcmpfunc' (aka 'PyObject *(*)(PyObject *, PyObject *, int)') with an expression of type
'PyObject *(PyJobject_Object *, PyObject *, int)' [-Wincompatible-pointer-types]
pyjobject_richcompare, /* tp_richcompare */
^~~~~~~~~~~~~~~~~~~~~
1 warning generated.
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future -DPACKAGE=jep -DUSE_DEALLOC=1 -DVERSION="3.2.0" -I/System/Library/Frameworks/JavaVM.framework/Headers -Isrc/jep -Ibuild/include -I/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/jep/util.c -o build/temp.macosx-10.9-x86_64-2.7/src/jep/util.o
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future -DPACKAGE=jep -DUSE_DEALLOC=1 -DVERSION="3.2.0" -I/System/Library/Frameworks/JavaVM.framework/Headers -Isrc/jep -Ibuild/include -I/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/jep/python/jep_object.c -o build/temp.macosx-10.9-x86_64-2.7/src/jep/python/jep_object.o
gcc -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/jug/local/ilastik/lib -L/Users/jug/local/ilastik/lib -stdlib=libstdc++ -Wno-error=unused-command-line-argument-hard-error-in-future -L/opt/local/lib -O3 -march=core2 -mtune=native -ffast-math -Wno-error=unused-command-line-argument-hard-error-in-future build/temp.macosx-10.9-x86_64-2.7/src/jep/invocationhandler.o build/temp.macosx-10.9-x86_64-2.7/src/jep/jep.o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyembed.o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyjarray.o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyjclass.o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyjfield.o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyjmethod.o build/temp.macosx-10.9-x86_64-2.7/src/jep/pyjobject.o build/temp.macosx-10.9-x86_64-2.7/src/jep/util.o build/temp.macosx-10.9-x86_64-2.7/src/jep/python/jep_object.o -lpython2.7 -ldl -o build/lib.macosx-10.9-x86_64-2.7/jep.so -framework JavaVM -framework CoreFoundation -u _PyMac_Error
clang: warning: unknown argument: '-framework JavaVM' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
clang: warning: unknown argument: '-framework CoreFoundation -u _PyMac_Error' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
clang: warning: argument unused during compilation: '-framework JavaVM'
clang: warning: argument unused during compilation: '-framework CoreFoundation -u _PyMac_Error'
running build_scripts
creating build/scripts-2.7
copying and adjusting src/scripts/jep -> build/scripts-2.7
changing mode of build/scripts-2.7/jep from 644 to 755
running install_lib
copying build/lib.macosx-10.9-x86_64-2.7/jep.so -> /Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
running install_scripts
copying build/scripts-2.7/jep -> /Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/bin
changing mode of /Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/bin/jep to 755
running install_data
copying build/java/jep.jar -> /Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/lib/jep
ln -sf /Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/jep.so /Library/Java/Extensions/libjep.jnilib
running install_egg_info
Removing /Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/jep-3.2.0-py2.7.egg-info
Writing /Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/jep-3.2.0-py2.7.egg-info
jug@myers-mac-7:~/Dropbox/WorkingData/Repositories/GIT/jep$ python
Python 2.7.3 (default, Mar 28 2014, 10:46:03)
[GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.38)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> quit()
jug@myers-mac-7:~/Dropbox/WorkingData/Repositories/GIT/jep$ which jep
/Users/jug/local/ilastik/Frameworks/Python.framework/Versions/2.7/bin/jep
jug@myers-mac-7:~/Dropbox/WorkingData/Repositories/GIT/jep$ jep
>>> import sys; print(sys.version)
2.7.6 (default, Nov 18 2013, 15:12:51)
[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.2.79)]
>>> quit()
So what's the problem?
Starting JEPP via 'jep' gives me a DIFFERENT python then 'python' would. (See the last couple of lines...)
If you are still with me... plese HELP!
Thanks a lot,
Florian
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MPI of Molecular Cell Biology and Genetics
Group: Gene Myers
Pfotenhauer Strasse 108
01307 Dresden
Germany
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