Installation in Anaconda Environment (Mac OS X)

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Emma Hoppe

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Jul 3, 2014, 2:13:44 PM7/3/14
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I'm new to Python (and really coding in general), but I've started learning because need to use it to automate some machine learning tasks in Weka. I've installed Anaconda and have changed the path in a file (whichever one was instructed) so that new packages for Python are installed in its folder. I'm getting an invalid syntax error when I try and install the python-weka-wrapper. Does anyone have any ideas? 

pip install -U https://github.com/chrisspen/weka/tarball/master

Downloading/unpacking https://github.com/chrisspen/weka/tarball/master

  Downloading master (unknown size): 77kB downloaded

  Running setup.py (path:/var/folders/gk/q20cw4xd3mz08prsjgsl3syh0000gn/T/pip-f8fmaxvd-build/setup.py) egg_info for package from https://github.com/chrisspen/weka/tarball/master

    Traceback (most recent call last):

      File "<string>", line 17, in <module>

      File "/var/folders/gk/q20cw4xd3mz08prsjgsl3syh0000gn/T/pip-f8fmaxvd-build/setup.py", line 6, in <module>

        from weka import classifiers as weka

      File "/private/var/folders/gk/q20cw4xd3mz08prsjgsl3syh0000gn/T/pip-f8fmaxvd-build/weka/classifiers.py", line 122

        exec '%s = _func' % _proper_name

                        ^

    SyntaxError: invalid syntax

    Complete output from command python setup.py egg_info:

    Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/var/folders/gk/q20cw4xd3mz08prsjgsl3syh0000gn/T/pip-f8fmaxvd-build/setup.py", line 6, in <module>

    from weka import classifiers as weka

  File "/private/var/folders/gk/q20cw4xd3mz08prsjgsl3syh0000gn/T/pip-f8fmaxvd-build/weka/classifiers.py", line 122

    exec '%s = _func' % _proper_name

                    ^

SyntaxError: invalid syntax

----------------------------------------

Cleaning up...

Command python setup.py egg_info failed with error code 1 in /var/folders/gk/q20cw4xd3mz08prsjgsl3syh0000gn/T/pip-f8fmaxvd-build

Storing debug log for failure in /Users/emmahoppe/.pip/pip.log

emma-hoppes-mbp:~ emmahoppe$ 



Many thanks!

Christopher Beckham

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Jul 3, 2014, 6:11:35 PM7/3/14
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Hmm, that seems like a completely different Weka wrapper to the one this mailing list is based on (https://github.com/fracpete/python-weka-wrapper which you may also be interested in trying out).

I'll try install that wrapper though when I get back home and see what happens. Just from looking at the error  I'm a bit unsure as to why its occuring.

Cheers


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Christopher Beckham

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Jul 3, 2014, 10:52:19 PM7/3/14
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It seems to work for me (on my Windows machine however). What version of Python are you using? (On your terminal, run: python --version)

I'm running 2.7.3.

Emma

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Jul 7, 2014, 5:04:19 AM7/7/14
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Thanks so much for trying it out. I do apologize for earlier; I was trying out both wrappers to see if I could get one to work, and uploaded the wrong readout. 
I'm running anaconda: Python 3.4.1 :: Anaconda 2.0.1 (x86_64). 
Here's what I get when I try and install javabridge (that's the right one, correct?):

Last login: Mon Jul  7 04:50:22 on ttys000

emma-hoppes-mbp:~ emmahoppe$ pip install javabridge

Downloading/unpacking javabridge

  Downloading javabridge-1.0.3.tar.gz (1.2MB): 1.2MB downloaded

  Running setup.py (path:/private/var/folders/gk/q20cw4xd3mz08prsjgsl3syh0000gn/T/pip_build_emmahoppe/javabridge/setup.py) egg_info for package javabridge

    Traceback (most recent call last):

      File "<string>", line 17, in <module>

      File "/private/var/folders/gk/q20cw4xd3mz08prsjgsl3syh0000gn/T/pip_build_emmahoppe/javabridge/setup.py", line 45

        print ' '.join(cmd)

                ^

    SyntaxError: invalid syntax

    Complete output from command python setup.py egg_info:

    Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/private/var/folders/gk/q20cw4xd3mz08prsjgsl3syh0000gn/T/pip_build_emmahoppe/javabridge/setup.py", line 45

    print ' '.join(cmd)

            ^

SyntaxError: invalid syntax


----------------------------------------

Cleaning up...

Command python setup.py egg_info failed with error code 1 in /private/var/folders/gk/q20cw4xd3mz08prsjgsl3syh0000gn/T/pip_build_emmahoppe/javabridge

Storing debug log for failure in /Users/emmahoppe/.pip/pip.log














Does that mean that there's something wrong with pip? Have you used conda before? Do you think I could use conda to install it instead of pip if that's the problem? Or is there a way to manually load the program(s) into the packages folder of Anaconda? All current pacakges (numpy, pandas, etc.) have bin, info, and lib as their subfolders. Could I configure the package manually to be accessible to my IDE in the conda environment. 
Thank you so so much for your help!!!!



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Christopher Beckham

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Jul 7, 2014, 6:00:21 AM7/7/14
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Hi Emma,

I think it's related to your version of Python. There are two commonly used versions of Python, 2.7 and 3.4, which are (in a way) quite different from each other. So I would not expect Python 2.7 code to run on 3.4, and vice versa. I strongly believe both errors you have posted are related to the version, and that everything else is probably ok. 

I have not used Anaconda in a while (it's not currently on my machine), but I saw this on the Anaconda website:

"Easily switch between Python 2.6, 2.7, 3.3, 3.4, and experiment with multiple versions of libraries, using our conda package manager and its great support for virtual environments"

This implies that you're able to switch the Python version from within Anaconda. So maybe there's some way to change the version? If you're unable to figure that one out, you can download a Python 2.7 64-bit Mac OS-X installer on the Anaconda download page.

Cheers


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Emma

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Jul 7, 2014, 4:15:50 PM7/7/14
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Hmm. Now I get the following. Any suggestions? I have no clue what it all means...







(python2)emma-hoppes-mbp:~ emmahoppe$ sudo pip install javabridge

Password:

Downloading/unpacking javabridge

  Downloading javabridge-1.0.3.tar.gz (1.2MB): 1.2MB downloaded

  Running setup.py (path:/private/tmp/pip_build_root/javabridge/setup.py) egg_info for package javabridge

    Using jdk_home = Doesn't matter

    

Requirement already satisfied (use --upgrade to upgrade): numpy in /anaconda/envs/python2/lib/python2.7/site-packages (from javabridge)

Installing collected packages: javabridge

  Running setup.py install for javabridge

    Using jdk_home = Doesn't matter

    building 'javabridge._javabridge' extension

    gcc -fno-strict-aliasing -I//anaconda/envs/python2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I//anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include -I/System/Library/Frameworks/JavaVM.framework/Headers -I//anaconda/envs/python2/include/python2.7 -c _javabridge.c -o build/temp.macosx-10.5-x86_64-2.7/_javabridge.o

    In file included from _javabridge.c:346:

    In file included from //anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:

    In file included from //anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:

    In file included from //anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761:

    //anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "          "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

    #warning "Using deprecated NumPy API, disable it by " \

     ^

    _javabridge.c:2289:20: warning: 'JNI_GetDefaultJavaVMInitArgs' is deprecated [-Wdeprecated-declarations]

      __pyx_v_result = JNI_GetDefaultJavaVMInitArgs(((void *)(&__pyx_v_args)));

                       ^

    /System/Library/Frameworks/JavaVM.framework/Headers/jni.h:1934:1: note: 'JNI_GetDefaultJavaVMInitArgs' declared here

    JNI_GetDefaultJavaVMInitArgs(void *args);

    ^

    _javabridge.c:4350:37: warning: 'JNI_CreateJavaVM' is deprecated [-Wdeprecated-declarations]

      __pyx_t_3 = __Pyx_PyInt_From_jint(JNI_CreateJavaVM((&__pyx_v_self->vm), ((void **)(&__pyx_v_env)), (&__pyx_v_args))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

                                        ^

    /System/Library/Frameworks/JavaVM.framework/Headers/jni.h:1937:1: note: 'JNI_CreateJavaVM' declared here

    JNI_CreateJavaVM(JavaVM **pvm, void **penv, void *args);

    ^

    In file included from _javabridge.c:347:

    In file included from //anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:327:

    //anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: unused function '_import_umath' [-Wunused-function]

    _import_umath(void)

    ^

    _javabridge.c:26737:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function]

    static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {

                                   ^

    _javabridge.c:411:29: warning: unused function '__Pyx_Py_UNICODE_strlen' [-Wunused-function]

    static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)

                                ^

    _javabridge.c:23734:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function]

    static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,

                                   ^

    _javabridge.c:23748:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function]

    static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,

                                   ^

    _javabridge.c:23842:26: warning: unused function '__Pyx_PyUnicode_Equals' [-Wunused-function]

    static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {

                             ^

    _javabridge.c:26112:48: warning: unused function '__pyx_t_float_complex_from_parts' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {

                                                   ^

    _javabridge.c:26122:30: warning: unused function '__Pyx_c_eqf' [-Wunused-function]

        static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {

                                 ^

    _javabridge.c:26125:48: warning: unused function '__Pyx_c_sumf' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {

                                                   ^

    _javabridge.c:26131:48: warning: unused function '__Pyx_c_difff' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {

                                                   ^

    _javabridge.c:26143:48: warning: unused function '__Pyx_c_quotf' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {

                                                   ^

    _javabridge.c:26150:48: warning: unused function '__Pyx_c_negf' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {

                                                   ^

    _javabridge.c:26156:30: warning: unused function '__Pyx_c_is_zerof' [-Wunused-function]

        static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {

                                 ^

    _javabridge.c:26159:48: warning: unused function '__Pyx_c_conjf' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {

                                                   ^

    _javabridge.c:26173:52: warning: unused function '__Pyx_c_powf' [-Wunused-function]

            static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {

                                                       ^

    _javabridge.c:26232:49: warning: unused function '__pyx_t_double_complex_from_parts' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {

                                                    ^

    _javabridge.c:26242:30: warning: unused function '__Pyx_c_eq' [-Wunused-function]

        static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {

                                 ^

    _javabridge.c:26245:49: warning: unused function '__Pyx_c_sum' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {

                                                    ^

    _javabridge.c:26251:49: warning: unused function '__Pyx_c_diff' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {

                                                    ^

    _javabridge.c:26263:49: warning: unused function '__Pyx_c_quot' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {

                                                    ^

    _javabridge.c:26270:49: warning: unused function '__Pyx_c_neg' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {

                                                    ^

    _javabridge.c:26276:30: warning: unused function '__Pyx_c_is_zero' [-Wunused-function]

        static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {

                                 ^

    _javabridge.c:26279:49: warning: unused function '__Pyx_c_conj' [-Wunused-function]

        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {

                                                    ^

    _javabridge.c:26293:53: warning: unused function '__Pyx_c_pow' [-Wunused-function]

            static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {

                                                        ^

    _javabridge.c:26346:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration]

    static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {

                              ^

    _javabridge.c:20881:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew1' [-Wunused-function]

    static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) {

                                   ^

    _javabridge.c:20931:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew2' [-Wunused-function]

    static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyObject *__pyx_v_b) {

                                   ^

    _javabridge.c:20981:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew3' [-Wunused-function]

    static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) {

                                   ^

    _javabridge.c:21031:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew4' [-Wunused-function]

    static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d) {

                                   ^

    _javabridge.c:21081:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew5' [-Wunused-function]

    static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d, PyObject *__pyx_v_e) {

                                   ^

    _javabridge.c:21835:27: warning: unused function '__pyx_f_5numpy_set_array_base' [-Wunused-function]

    static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_arr, PyObject *__pyx_v_base) {

                              ^

    _javabridge.c:21923:32: warning: unused function '__pyx_f_5numpy_get_array_base' [-Wunused-function]

    static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__pyx_v_arr) {

                                   ^

    35 warnings generated.

    gcc -fno-strict-aliasing -I//anaconda/envs/python2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I//anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include -I/System/Library/Frameworks/JavaVM.framework/Headers -I//anaconda/envs/python2/include/python2.7 -c _javabridge_mac.c -o build/temp.macosx-10.5-x86_64-2.7/_javabridge_mac.o

    _javabridge_mac.c:1295:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function]

    static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {

                               ^

    _javabridge_mac.c:1292:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function]

    static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {

                                   ^

    _javabridge_mac.c:406:29: warning: unused function '__Pyx_Py_UNICODE_strlen' [-Wunused-function]

    static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)

                                ^

    _javabridge_mac.c:1359:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function]

    static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {

                             ^

    _javabridge_mac.c:1414:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function]

    static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {

                                    ^

    _javabridge_mac.c:1443:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function]

    static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {

                                    ^

    _javabridge_mac.c:839:32: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function]

    static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {

                                   ^

    _javabridge_mac.c:886:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration]

    static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {

                              ^

    _javabridge_mac.c:986:26: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration]

    static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {

                             ^

    9 warnings generated.

    gcc -fno-strict-aliasing -I//anaconda/envs/python2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I//anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include -I/System/Library/Frameworks/JavaVM.framework/Headers -I//anaconda/envs/python2/include/python2.7 -c mac_javabridge_utils.c -o build/temp.macosx-10.5-x86_64-2.7/mac_javabridge_utils.o

    clang: error: no such file or directory: 'mac_javabridge_utils.c'

    clang: error: no input files

    error: command 'gcc' failed with exit status 1

    Complete output from command //anaconda/envs/python2/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/javabridge/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-TQdiPJ-record/install-record.txt --single-version-externally-managed --compile:

    Using jdk_home = Doesn't matter


running install


running build


running build_py


creating build


creating build/lib.macosx-10.5-x86_64-2.7


creating build/lib.macosx-10.5-x86_64-2.7/javabridge


copying javabridge/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/javabridge


copying javabridge/_version.py -> build/lib.macosx-10.5-x86_64-2.7/javabridge


copying javabridge/jutil.py -> build/lib.macosx-10.5-x86_64-2.7/javabridge


copying javabridge/locate.py -> build/lib.macosx-10.5-x86_64-2.7/javabridge


copying javabridge/noseplugin.py -> build/lib.macosx-10.5-x86_64-2.7/javabridge


copying javabridge/wrappers.py -> build/lib.macosx-10.5-x86_64-2.7/javabridge


creating build/lib.macosx-10.5-x86_64-2.7/javabridge/jars


copying javabridge/jars/rhino-1.7R4.jar -> build/lib.macosx-10.5-x86_64-2.7/javabridge/jars


copying javabridge/jars/runnablequeue.jar -> build/lib.macosx-10.5-x86_64-2.7/javabridge/jars


copying javabridge/jars/test.jar -> build/lib.macosx-10.5-x86_64-2.7/javabridge/jars


running build_ext


running build_java


building 'javabridge._javabridge' extension


creating build/temp.macosx-10.5-x86_64-2.7


gcc -fno-strict-aliasing -I//anaconda/envs/python2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I//anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include -I/System/Library/Frameworks/JavaVM.framework/Headers -I//anaconda/envs/python2/include/python2.7 -c _javabridge.c -o build/temp.macosx-10.5-x86_64-2.7/_javabridge.o


In file included from _javabridge.c:346:


In file included from //anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:


In file included from //anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:


In file included from //anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761:


//anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "          "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]


#warning "Using deprecated NumPy API, disable it by " \


 ^


_javabridge.c:2289:20: warning: 'JNI_GetDefaultJavaVMInitArgs' is deprecated [-Wdeprecated-declarations]


  __pyx_v_result = JNI_GetDefaultJavaVMInitArgs(((void *)(&__pyx_v_args)));


                   ^


/System/Library/Frameworks/JavaVM.framework/Headers/jni.h:1934:1: note: 'JNI_GetDefaultJavaVMInitArgs' declared here


JNI_GetDefaultJavaVMInitArgs(void *args);


^


_javabridge.c:4350:37: warning: 'JNI_CreateJavaVM' is deprecated [-Wdeprecated-declarations]


  __pyx_t_3 = __Pyx_PyInt_From_jint(JNI_CreateJavaVM((&__pyx_v_self->vm), ((void **)(&__pyx_v_env)), (&__pyx_v_args))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}


                                    ^


/System/Library/Frameworks/JavaVM.framework/Headers/jni.h:1937:1: note: 'JNI_CreateJavaVM' declared here


JNI_CreateJavaVM(JavaVM **pvm, void **penv, void *args);


^


In file included from _javabridge.c:347:


In file included from //anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:327:


//anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: unused function '_import_umath' [-Wunused-function]


_import_umath(void)


^


_javabridge.c:26737:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function]


static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {


                               ^


_javabridge.c:411:29: warning: unused function '__Pyx_Py_UNICODE_strlen' [-Wunused-function]


static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)


                            ^


_javabridge.c:23734:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function]


static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,


                               ^


_javabridge.c:23748:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function]


static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,


                               ^


_javabridge.c:23842:26: warning: unused function '__Pyx_PyUnicode_Equals' [-Wunused-function]


static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {


                         ^


_javabridge.c:26112:48: warning: unused function '__pyx_t_float_complex_from_parts' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {


                                               ^


_javabridge.c:26122:30: warning: unused function '__Pyx_c_eqf' [-Wunused-function]


    static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {


                             ^


_javabridge.c:26125:48: warning: unused function '__Pyx_c_sumf' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {


                                               ^


_javabridge.c:26131:48: warning: unused function '__Pyx_c_difff' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {


                                               ^


_javabridge.c:26143:48: warning: unused function '__Pyx_c_quotf' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {


                                               ^


_javabridge.c:26150:48: warning: unused function '__Pyx_c_negf' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {


                                               ^


_javabridge.c:26156:30: warning: unused function '__Pyx_c_is_zerof' [-Wunused-function]


    static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {


                             ^


_javabridge.c:26159:48: warning: unused function '__Pyx_c_conjf' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {


                                               ^


_javabridge.c:26173:52: warning: unused function '__Pyx_c_powf' [-Wunused-function]


        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {


                                                   ^


_javabridge.c:26232:49: warning: unused function '__pyx_t_double_complex_from_parts' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {


                                                ^


_javabridge.c:26242:30: warning: unused function '__Pyx_c_eq' [-Wunused-function]


    static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {


                             ^


_javabridge.c:26245:49: warning: unused function '__Pyx_c_sum' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {


                                                ^


_javabridge.c:26251:49: warning: unused function '__Pyx_c_diff' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {


                                                ^


_javabridge.c:26263:49: warning: unused function '__Pyx_c_quot' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {


                                                ^


_javabridge.c:26270:49: warning: unused function '__Pyx_c_neg' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {


                                                ^


_javabridge.c:26276:30: warning: unused function '__Pyx_c_is_zero' [-Wunused-function]


    static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {


                             ^


_javabridge.c:26279:49: warning: unused function '__Pyx_c_conj' [-Wunused-function]


    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {


                                                ^


_javabridge.c:26293:53: warning: unused function '__Pyx_c_pow' [-Wunused-function]


        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {


                                                    ^


_javabridge.c:26346:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration]


static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {

                          ^

_javabridge.c:20881:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew1' [-Wunused-function]

static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) {

                               ^

_javabridge.c:20931:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew2' [-Wunused-function]

static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyObject *__pyx_v_b) {

                               ^

_javabridge.c:20981:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew3' [-Wunused-function]


static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) {


                               ^


_javabridge.c:21031:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew4' [-Wunused-function]


static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d) {


                               ^


_javabridge.c:21081:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew5' [-Wunused-function]


static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d, PyObject *__pyx_v_e) {

                               ^

_javabridge.c:21835:27: warning: unused function '__pyx_f_5numpy_set_array_base' [-Wunused-function]


static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_arr, PyObject *__pyx_v_base) {

                          ^

_javabridge.c:21923:32: warning: unused function '__pyx_f_5numpy_get_array_base' [-Wunused-function]

static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__pyx_v_arr) {

                               ^

35 warnings generated.

gcc -fno-strict-aliasing -I//anaconda/envs/python2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I//anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include -I/System/Library/Frameworks/JavaVM.framework/Headers -I//anaconda/envs/python2/include/python2.7 -c _javabridge_mac.c -o build/temp.macosx-10.5-x86_64-2.7/_javabridge_mac.o

_javabridge_mac.c:1295:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function]

static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {

                           ^

_javabridge_mac.c:1292:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function]


static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {

                               ^

_javabridge_mac.c:406:29: warning: unused function '__Pyx_Py_UNICODE_strlen' [-Wunused-function]

static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)

                            ^

_javabridge_mac.c:1359:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function]

static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {

                         ^

_javabridge_mac.c:1414:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function]

static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {

                                ^

_javabridge_mac.c:1443:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function]

static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {

                                ^

_javabridge_mac.c:839:32: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function]

static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {

                               ^

_javabridge_mac.c:886:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration]

static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {

                          ^

_javabridge_mac.c:986:26: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration]

static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {

                         ^

9 warnings generated.

gcc -fno-strict-aliasing -I//anaconda/envs/python2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I//anaconda/envs/python2/lib/python2.7/site-packages/numpy/core/include -I/System/Library/Frameworks/JavaVM.framework/Headers -I//anaconda/envs/python2/include/python2.7 -c mac_javabridge_utils.c -o build/temp.macosx-10.5-x86_64-2.7/mac_javabridge_utils.o

clang: error: no such file or directory: 'mac_javabridge_utils.c'

clang: error: no input files

error: command 'gcc' failed with exit status 1

----------------------------------------

Cleaning up...

Command //anaconda/envs/python2/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/javabridge/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-TQdiPJ-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/tmp/pip_build_root/javabridge

Storing debug log for failure in /Users/emmahoppe/.pip/pip.log

To view this discussion on the web visit https://groups.google.com/d/msgid/python-weka-wrapper/CAB9m2mirLEoUS9VS8oKx0wSMgoaZo2d9Ft-hjJL961N%2BJkRo1A%40mail.gmail.com.

Christopher Beckham

unread,
Jul 7, 2014, 4:48:03 PM7/7/14
to python-we...@googlegroups.com
Oddly enough, it's saying a particular file is missing in the javabridge. I'd download the latest version from Github:


Download the zip file, extract it somewhere, cd into the directory and run:

sudo python setup.py install

See what happens then.

Cheers


To view this discussion on the web visit https://groups.google.com/d/msgid/python-weka-wrapper/CAH54sMpQCK9pbeNKdCgG2CuzMLztBY0h3Td%2B%3D7C_BFZsXRWsUQ%40mail.gmail.com.
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