shogunPYTHON_wrap.cxx.o error when install shogun

[hmzhangBio]

I follow the install manual to compile shogun manually. I installed it in miniconda env. The following steps were taken

shogun_6.1.3 was downloaded

cd shogun-shogun_6.1.3 mkdir build cd build

cmake -DCMAKE_INSTALL_PREFIX=/data12/hongmei/software/shogun/ -DPYTHON_INCLUDE_DIR=/data12/hongmei/miniconda3/include/python3.6m -DPYTHON_LIBRARY=/data12/hongmei/miniconda3/lib/libpython3.6m.so -DPYTHON_EXECUTABLE=/data12/hongmei/miniconda3/bin/python3 -DINTERFACE_PYTHON=ON ..

make

Then, the 'shogunPYTHON_wrap.cxx.o' failed error info showed up. The following is the output of make

[ 0%] Built target ShogunVersionProtobuf [ 1%] Generating version header [ 1%] Built target version [ 1%] Built target class_list [ 2%] Built target rxcpp [ 2%] Built target ChunksProtobuf [ 2%] Built target HeadersProtobuf [ 68%] Built target libshogun [ 68%] Built target shogun [ 68%] copying SWIG files [ 68%] Built target interface_python_src [ 68%] Built target python_doxy2swig [ 68%] Building CXX object src/interfaces/python/CMakeFiles/_interface_python.dir/shogunPYTHON_wrap.cxx.o src/interfaces/python/CMakeFiles/_interface_python.dir/build.make:93: recipe for target 'src/interfaces/python/CMakeFiles/_interface_python.dir/shogunPYTHON_wrap.cxx.o' failed CMakeFiles/Makefile2:866: recipe for target 'src/interfaces/python/CMakeFiles/_interface_python.dir/all' failed Makefile:171: recipe for target 'all' failed

I don't know how to fix it. Could you please give me a help? Thanks

[gf712]

Is that the complete output? Are there no compiler errors when building shogunPYTHON_wrap.cxx.o?

[hmzhangBio]

Thanks for the reply!

Here are the whole output.

[ 0%] Built target ShogunVersionProtobuf [ 1%] Generating version header [ 1%] Built target version [ 1%] Built target class_list [ 2%] Built target rxcpp [ 2%] Built target ChunksProtobuf [ 2%] Built target HeadersProtobuf [ 68%] Built target libshogun [ 68%] Built target shogun [ 68%] copying SWIG files [ 68%] Built target interface_python_src [ 68%] Built target python_doxy2swig [ 68%] Building CXX object src/interfaces/python/CMakeFiles/_interface_python.dir/shogunPYTHON_wrap.cxx.o In file included from /data12/hongmei/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /data12/hongmei/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /data12/hongmei/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:6469: /data12/hongmei/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

warning "Using deprecated NumPy API, disable it with " \

^ cc1plus: warning: unrecognized command line option ‘-Wno-c++11-narrowing’ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:648061:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:648349:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:648637:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:648925:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:649213:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:649501:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:650077:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:650365:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:650653:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:701917:1: error: invalid conversion from ‘PyObject ()(PyObject, PyObject, bool) {aka _object ()(_object, _object, bool)}’ to ‘binaryfunc {aka _object ()(_object, _object)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:702403:1: error: invalid conversion from ‘PyObject ()(PyObject, PyObject, bool) {aka _object ()(_object, _object, bool)}’ to ‘binaryfunc {aka _object ()(_object, _object)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:702889:1: error: invalid conversion from ‘PyObject ()(PyObject, PyObject, bool) {aka _object ()(_object, _object, bool)}’ to ‘binaryfunc {aka _object ()(_object, _object)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:703375:1: error: invalid conversion from ‘PyObject ()(PyObject, PyObject, bool) {aka _object ()(_object, _object, bool)}’ to ‘binaryfunc {aka _object ()(_object, _object)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:703861:1: error: invalid conversion from ‘PyObject ()(PyObject, PyObject, bool) {aka _object ()(_object, _object, bool)}’ to ‘binaryfunc {aka _object ()(_object, _object)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:704347:1: error: invalid conversion from ‘PyObject ()(PyObject, PyObject, bool) {aka _object ()(_object, _object, bool)}’ to ‘binaryfunc {aka _object ()(_object, _object)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:704833:1: error: invalid conversion from ‘PyObject ()(PyObject, PyObject, bool) {aka _object ()(_object, _object, bool)}’ to ‘binaryfunc {aka _object ()(_object, _object)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:705319:1: error: invalid conversion from ‘PyObject ()(PyObject, PyObject, bool) {aka _object ()(_object, _object, bool)}’ to ‘binaryfunc {aka _object ()(_object, _object)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:705805:1: error: invalid conversion from ‘PyObject ()(PyObject, PyObject, bool) {aka _object ()(_object, _object, bool)}’ to ‘binaryfunc {aka _object ()(_object, _object)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:714314:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:714594:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:715227:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:715462:1: error: invalid conversion from ‘PyObject ()(PyObject, Py_ssize_t, bool) {aka _object ()(_object, long int, bool)}’ to ‘ssizeargfunc {aka _object ()(_object, long int)}’ [-fpermissive] }; ^ /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:765189:1: error: invalid conversion from ‘PyObject ()(PyObject, PyObject, bool) {aka _object ()(_object, _object, bool)}’ to ‘binaryfunc {aka _object ()(_object, _object*)}’ [-fpermissive] }; ^ cc1plus: warning: unrecognized command line option ‘-Wno-c++11-narrowing’ src/interfaces/python/CMakeFiles/_interface_python.dir/build.make:93: recipe for target 'src/interfaces/python/CMakeFiles/_interface_python.dir/shogunPYTHON_wrap.cxx.o' failed make[2]: [src/interfaces/python/CMakeFiles/_interface_python.dir/shogunPYTHON_wrap.cxx.o] Error 1 CMakeFiles/Makefile2:866: recipe for target 'src/interfaces/python/CMakeFiles/_interface_python.dir/all' failed make[1]: [src/interfaces/python/CMakeFiles/_interface_python.dir/all] Error 2 Makefile:171: recipe for target 'all' failed make: *** [all] Error 2

Thanks.

[gf712]

It seems like you have added flags to the compiler using environment variables? Which compiler are you using? What is the output of echo $CPPFLAGS?

[hmzhangBio]

Thanks a lot for the help.

I used gcc 5.4.0 and cmake 3.17.5 to do the compiling. I got nothing for echo $CPPFLAGS.

The errors were changed after installing swig to system. Please see below.

[ 67%] Generating shogun_doxygen.i [ 67%] Built target python_doxy2swig [ 67%] Linking CXX shared module _shogun.so CMakeFiles/_interface_python.dir/shogunPYTHON_wrap.cxx.o: In function shogun_CSGObject___getstate__(shogun::CSGObject*)': /data12/hongmei/software/shogun-shogun_6.1.3/build/src/interfaces/python/shogunPYTHON_wrap.cxx:9561: warning: the use oftmpnam' is dangerous, better use mkstemp' [ 67%] Built target _interface_python [ 67%] Linking CXX executable kernel_machine_train_locked ../../../src/shogun/libshogun.so.18.0: undefined reference tocurl_easy_setopt@CURL_OPENSSL_3' ../../../src/shogun/libshogun.so.18.0: undefined reference to curl_easy_cleanup@CURL_OPENSSL_3' ../../../src/shogun/libshogun.so.18.0: undefined reference tocurl_easy_init@CURL_OPENSSL_3' ../../../src/shogun/libshogun.so.18.0: undefined reference to `curl_easy_perform@CURL_OPENSSL_3' collect2: error: ld returned 1 exit status examples/undocumented/libshogun/CMakeFiles/kernel_machine_train_locked.dir/build.make:112: recipe for target 'examples/undocumented/libshogun/kernel_machine_train_locked' failed make[2]: [examples/undocumented/libshogun/kernel_machine_train_locked] Error 1 CMakeFiles/Makefile2:887: recipe for target 'examples/undocumented/libshogun/CMakeFiles/kernel_machine_train_locked.dir/all' failed make[1]: [examples/undocumented/libshogun/CMakeFiles/kernel_machine_train_locked.dir/all] Error 2 Makefile:171: recipe for target 'all' failed make: *** [all] Error 2

Any idea to fix this? Thanks

[jonpsy]

+1 to this, the main build python interface failed on mine as well

/home/psykik/Documents/shogun/build/src/interfaces/python/shogunPYTHON_wrap.cxx: At global scope:
/home/psykik/Documents/shogun/build/src/interfaces/python/shogunPYTHON_wrap.cxx:425231:1: error: invalid conversion from ‘int (*)(PyObject*, FILE*, int)’ {aka ‘int (*)(_object*, _IO_FILE*, int)’} to ‘Py_ssize_t’ {aka ‘long int’} [-fpermissive]
 };

Using ccache compiler develop build

[hmzhangBio]

@gf712, thanks for your patience to answer my questions. I was wondering could you please give me some suggestions to above errors? Thanks in advance!

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale[bot]]

This issue is now being closed due to a lack of activity. Feel free to reopen it.