Unable to compile (even with version controlled conda py37 environment)

[iamnicogomez]

Hi philippdre,

I am am on OSX 10.15.5 with Conda and python3.7 (with all the recommended package versions set by conda virtual environment) running into compiling problems. As you will see, I first thought this was a cflags problem so i gathered the necessary cflags and added them to the gcc call. I have also tried simply using "-I/Users/nicog/opt/miniconda3/envs/py37/include" to no avail. I have also tried using g++. No luck. Do you or does anyone know the nature of this problem?

Thanks, Nico

(base) claude:~ nicog$ conda activate py37

(py37) claude:~ nicog$ /Users/nicog/opt/miniconda3/envs/py37/bin/python3.7m-config --cflags -I/Users/nicog/opt/miniconda3/envs/py37/include/python3.7m -I/Users/nicog/opt/miniconda3/envs/py37/include/python3.7m -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/nicog/opt/miniconda3/envs/py37/include -arch x86_64 -I/Users/nicog/opt/miniconda3/envs/py37/include -arch x86_64

(py37) claude:~ nicog$ cd omniCLIP/stat

(py37) claude:stat nicog$ set -e

(py37) claude:stat nicog$ cython viterbi.pyx -3

(py37) claude:stat nicog$ gcc -shared -pthread -fPIC -fwrapv -O2 -Wall -fno-strict-aliasing -I/Users/nicog/opt/miniconda3/envs/py37/include/python3.7m -I/Users/nicog/opt/miniconda3/envs/py37/include/python3.7m -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/nicog/opt/miniconda3/envs/py37/include -arch x86_64 -I/Users/nicog/opt/miniconda3/envs/py37/include -arch x86_64 -o viterbi.so viterbi.c

In file included from /Users/nicog/opt/miniconda3/envs/py37/include/python3.7m/numpy/ndarraytypes.h:1822, from /Users/nicog/opt/miniconda3/envs/py37/include/python3.7m/numpy/ndarrayobject.h:12, from /Users/nicog/opt/miniconda3/envs/py37/include/python3.7m/numpy/arrayobject.h:4, from viterbi.c:598: /Users/nicog/opt/miniconda3/envs/py37/include/python3.7m/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] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~ viterbi.c: In function ‘pyx_pf_7viterbi_viterbi’: viterbi.c:2907:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2907 | for (pyx_t_11 = 0; pyx_t_11 < pyx_t_10; pyx_t_11+=1) { | ^ viterbi.c:2941:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2941 | for (pyx_t_11 = 0; pyx_t_11 < pyx_t_10; pyx_t_11+=1) { | ^ viterbi.c:2953:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2953 | for (pyx_t_20 = 0; pyx_t_20 < pyx_t_19; pyx_t_20+=1) { | ^ viterbi.c:2993:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2993 | for (pyx_t_28 = 1; pyx_t_28 < pyx_t_27; pyx_t_28+=1) { | ^ viterbi.c:3125:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3125 | for (pyx_t_11 = 1; pyx_t_11 < pyx_t_10; pyx_t_11+=1) { | ^ Undefined symbols for architecture x86_64: "_PyBaseObject_Type", referenced from: _pyx_tp_newEnum in ccG8pfXU.o Pyx_PyErrGivenExceptionMatches.part.0 in ccG8pfXU.o Pyx_ValidateAndInit_memviewslice.constprop.0 in ccG8pfXU.o _pyx_memoryview_copy_object_from_slice in ccG8pfXU.o _pyx_memoryview_get_slice_frommemoryview in ccG8pfXU.o pyx_memoryview_is_slice in ccG8pfXU.o _pyxpwpyx_MemviewEnum_1__reduce_cython in ccG8pfXU.o ... "_PyBuffer_Release", referenced from: _pyx_tp_dealloc_memoryview in ccG8pfXU.o PyxGetBufferAndValidate.constprop.0 in ccG8pfXU.o pyx_pf_7viterbi_viterbi.isra.0 in ccG8pfXU.o "_PyBytes_FromString", referenced from: _pyx_memoryview_assign_item_from_object in ccG8pfXU.o ___pyx_memoryview_copy_newcontig in ccG8pfXU.o pyx_memoryview_convert_item_to_object in ccG8pfXU.o "_PyBytes_FromStringAndSize", referenced from: _pyx_memoryview_convert_item_to_object in ccG8pfXU.o _pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyBytesType", referenced from: pyx_memoryview_assign_item_from_object in ccG8pfXU.o _pyx_tp_new_array in ccG8pfXU.o "_PyCFunctionNewEx", referenced from: pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyCFunction_Type", referenced from: ___Pyx_PyObjectCall2Args in ccG8pfXU.o pyx_memoryview_repr_ in ccG8pfXU.o pyx_memoryview_err_dim in ccG8pfXU.o _pyx_memoryview_assign_item_from_object in ccG8pfXU.o _pyx_unpickle_Enumset_state in ccG8pfXU.o ___pyx_pw_15View_dot_MemoryView_1pyx_unpickle_Enum in ccG8pfXU.o _pyx_memoryview_err in ccG8pfXU.o ... 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"_PyObjectGetAttrString", referenced from: Pyx_ImportType in ccG8pfXU.o _Pyx_copy_spec_tomodule in ccG8pfXU.o pyx_pymod_create in ccG8pfXU.o "_PyObject_GetBuffer", referenced from: _Pyx_GetBufferAndValidate.constprop.0 in ccG8pfXU.o pyx_memoryview_cinit__.constprop.0 in ccG8pfXU.o "_PyObjectGetItem", referenced from: Pyx_PyObject_GetIndex in ccG8pfXU.o _pyx_unpickle_Enumsetstate in ccG8pfXU.o pyx_memoryview_convert_item_to_object in ccG8pfXU.o "_PyObject_GetIter", referenced from: _pyx_memoryview_get_item_pointer in ccG8pfXU.o unellipsify in ccG8pfXU.o _pyx_memview_slice in ccG8pfXU.o "_PyObject_Hash", referenced from: _pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyObject_IsTrue", referenced from: ___pyx_arraygetbuffer in ccG8pfXU.o pyx_memoryview_cinit_.constprop.0 in ccG8pfXU.o pyx_mp_ass_subscript_memoryview in ccG8pfXU.o _pyx_memviewslice in ccG8pfXU.o pyx_memoryview_getitem_ in ccG8pfXU.o pyx_tp_new_array in ccG8pfXU.o "_PyObject_Malloc", referenced from: _pyx_tp_new_array in ccG8pfXU.o "_PyObject_Not", referenced from: _Pyx_AddTraceback in ccG8pfXU.o "_PyObjectRichCompare", referenced from: pyx_arraygetbuffer in ccG8pfXU.o pyx_tp_new_array in ccG8pfXU.o "_PyObject_RichCompareBool", referenced from: _Pyx_setup_reduce_is_named in ccG8pfXU.o "_PyObjectSetAttr", referenced from: Pyx_AddTraceback in ccG8pfXU.o _pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyObject_SetAttrString", referenced from: _pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyObjectSetItem", referenced from: pyx_mp_ass_subscript_array in ccG8pfXU.o "_PyObject_Size", referenced from: __unellipsify in ccG8pfXU.o "_PySequenceTuple", referenced from: pyx_memoryview_assign_item_from_object in ccG8pfXU.o "_PySlice_New", referenced from: _pyx_pymod_exec_viterbi in ccG8pfXU.o "_PySlice_Type", referenced from: unellipsify in ccG8pfXU.o "_PyThreadState_Get", referenced from: _Pyx_PyObjectCall in ccG8pfXU.o Pyx_PyFunction_FastCallDict.constprop.0 in ccG8pfXU.o _PyxPyObjectCallOneArg in ccG8pfXU.o Pyx_PyObjectCall2Args in ccG8pfXU.o pyx_memoryview_new in ccG8pfXU.o _pyx_pw_pyx_memoryviewslice_3setstate_cython in ccG8pfXU.o _pyx_pw_pyx_memoryviewslice_1reduce_cython in ccG8pfXU.o ... "_PyThread_allocate_lock", referenced from: _pyx_memoryviewcinit.constprop.0 in ccG8pfXU.o pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyThread_free_lock", referenced from: _pyx_tp_dealloc_memoryview in ccG8pfXU.o "_PyTraceBack_Here", referenced from: _Pyx_AddTraceback in ccG8pfXU.o "_PyTupleNew", referenced from: Pyx_Raise.constprop.0 in ccG8pfXU.o _PyxPyObject_CallOneArg in ccG8pfXU.o ___Pyx_PyObjectCall2Args in ccG8pfXU.o pyx_memoryview_new in ccG8pfXU.o _pyx_memoryviewfromslice in ccG8pfXU.o pyx_memoryview_str_ in ccG8pfXU.o pyx_memoryview_repr__ in ccG8pfXU.o ... "_PyTuplePack", referenced from: pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyTuple_Type", referenced from: _Pyx_PyObjectGetIndex in ccG8pfXU.o pyx_memoryview_assign_item_from_object in ccG8pfXU.o _pyx_pw_15View_dot_MemoryView_1pyx_unpickle_Enum in ccG8pfXU.o _pyx_pw_pyx_MemviewEnum_3setstate_cython in ccG8pfXU.o _pyx_memoryview_convert_item_to_object in ccG8pfXU.o _pyx_memoryview_get_item_pointer in ccG8pfXU.o unellipsify in ccG8pfXU.o ... "_PyTypeModified", referenced from: Pyx_setup_reduce in ccG8pfXU.o _pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyType_Ready", referenced from: _pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyUnicodeAsUnicode", referenced from: Pyx_ParseOptionalKeywords.constprop.0 in ccG8pfXU.o "_PyUnicode_Compare", referenced from: _Pyx_ParseOptionalKeywords.constprop.0 in ccG8pfXU.o "_PyUnicodeDecode", referenced from: pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyUnicode_DecodeASCII", referenced from: _pyx_memoryview_errdim in ccG8pfXU.o pyx_memoryviewerr in ccG8pfXU.o pyx_memoryview_copy_new_contig in ccG8pfXU.o "_PyUnicode_Format", referenced from: _pyx_memoryviewstr in ccG8pfXU.o pyx_memoryview_repr_ in ccG8pfXU.o pyx_memoryview_err_dim in ccG8pfXU.o _pyx_pw_15View_dot_MemoryView_1pyx_unpickle_Enum in ccG8pfXU.o _pyx_memoryview_copy_contents in ccG8pfXU.o _pyx_memoryview_get_item_pointer in ccG8pfXU.o unellipsify in ccG8pfXU.o ... "_PyUnicodeFromFormat", referenced from: Pyx_AddTraceback in ccG8pfXU.o "_PyUnicode_FromString", referenced from: _Pyx_AddTraceback in ccG8pfXU.o "_PyUnicode_FromStringAndSize", referenced from: _pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyUnicodeFromUnicode", referenced from: pyx_memoryview_err_dim in ccG8pfXU.o ___pyx_memoryviewerr in ccG8pfXU.o pyx_memoryview_copy_new_contig in ccG8pfXU.o "_PyUnicode_InternFromString", referenced from: _pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyUnicode_Type", referenced from: _pyx_array_getbuffer in ccG8pfXU.o unellipsify in ccG8pfXU.o _pyx_tp_new_array in ccG8pfXU.o "_Py_FatalError", referenced from: _pyx_fatalerror.constprop.0 in ccG8pfXU.o "_Py_GetVersion", referenced from: _pyx_pymod_exec_viterbi in ccG8pfXU.o "_PyOptimizeFlag", referenced from: pyx_memview_slice in ccG8pfXU.o "__PyDict_GetItemKnownHash", referenced from: PyxGetModuleGlobalName in ccG8pfXU.o _PyxAddTraceback in ccG8pfXU.o pyx_MemviewEnuminit in ccG8pfXU.o pyx_pw_15View_dot_MemoryView_1pyx_unpickle_Enum in ccG8pfXU.o _pyxmemoryviewcinit_.constprop.0 in ccG8pfXU.o pyx_pw_7viterbi_1viterbi in ccG8pfXU.o _pyx_tp_new_array in ccG8pfXU.o ... "PyList_Extend", referenced from: unellipsify in ccG8pfXU.o "PyObject_GetDictPtr", referenced from: _Pyx_AddTraceback in ccG8pfXU.o "PyThreadState_UncheckedGet", referenced from: _Pyx_PyFunctionFastCallNoKw in ccG8pfXU.o Pyx_AddTraceback in ccG8pfXU.o _pyx_memoryview_setitem_slice_assign_scalar in ccG8pfXU.o _pyx_memoryview_isslice in ccG8pfXU.o pyx_pw_pyx_MemviewEnum_1reduce_cython in ccG8pfXU.o _pyx_memoryview_convert_item_to_object in ccG8pfXU.o ___pyx_pf_7viterbi_viterbi.isra.0 in ccG8pfXU.o ... "PyType_Lookup", referenced from: _Pyx_setup_reduce in ccG8pfXU.o "PyUnicodeReady", referenced from: pyx_arraygetbuffer in ccG8pfXU.o pyx_tp_new_array in ccG8pfXU.o "PyCheckRecursionLimit", referenced from: Pyx_PyObject_Call in ccG8pfXU.o _Pyx_PyFunctionFastCallDict.constprop.0 in ccG8pfXU.o PyxPyObjectCallOneArg in ccG8pfXU.o Pyx_PyObject_Call2Args in ccG8pfXU.o _pyx_memoryviewnew in ccG8pfXU.o pyx_pw_pyx_memoryviewslice_3__setstate_cython in ccG8pfXU.o _pyx_pw_pyx_memoryviewslice_1reduce_cython in ccG8pfXU.o ... "PyCheckRecursiveCall", referenced from: Pyx_PyObject_Call in ccG8pfXU.o _Pyx_PyFunctionFastCallDict.constprop.0 in ccG8pfXU.o PyxPyObjectCallOneArg in ccG8pfXU.o Pyx_PyObject_Call2Args in ccG8pfXU.o _pyx_memoryviewnew in ccG8pfXU.o pyx_pw_pyx_memoryviewslice_3__setstate_cython in ccG8pfXU.o _pyx_pw_pyx_memoryviewslice_1reduce_cython in ccG8pfXU.o ... "PyFalseStruct", referenced from: Pyx_AddTraceback in ccG8pfXU.o _pyx_memoryviewnew in ccG8pfXU.o pyx_memoryview_fromslice in ccG8pfXU.o _pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_fcontig in ccG8pfXU.o pyx_memoryview_pyx_pf_15View_dot_MemoryView_10memoryview_16is_ccontig in ccG8pfXU.o pyx_array_get_memview in ccG8pfXU.o _pyx_array_getbuffer in ccG8pfXU.o ... "PyNoneStruct", referenced from: pyx_tp_clear_Enum in ccG8pfXU.o _pyx_tp_clearmemoryview in ccG8pfXU.o pyx_tp_new_Enum in ccG8pfXU.o _pyx_tp_deallocmemoryview in ccG8pfXU.o pyx_tp_clear_memoryviewslice in ccG8pfXU.o pyx_tp_deallocmemoryviewslice in ccG8pfXU.o _pyxgetproppyx_memoryview_size in ccG8pfXU.o ... "PyTrueStruct", referenced from: Pyx_AddTraceback in ccG8pfXU.o ___pyx_memoryviewnew in ccG8pfXU.o pyx_memoryview_fromslice in ccG8pfXU.o _pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_fcontig in ccG8pfXU.o pyx_memoryview_pyx_pf_15View_dot_MemoryView_10memoryview_16is_ccontig in ccG8pfXU.o pyx_array_get_memview in ccG8pfXU.o ___pyx_array_getbuffer in ccG8pfXU.o ... ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status

[algaebrown]

I experience similar problems with compile. But not sure if it is the same problem

1. The way to find correct path to replace -I in the gcc line is: python -c "import sysconfig; print(sysconfig.get_path('include'))" returns /home/hsher/miniconda3/envs/omniCLIP/include/python3.7m (will be different for yours)

2. I then experience fatal error: numpy/arrayobject.h: No such file or directory I solve by finding where numpy include is: python -c "import numpy; print(numpy.get_include())" which returns /home/hsher/.local/lib/python3.7/site-packages/numpy/core/include (will be different for yours)

and create softlink: mypython=/home/hsher/miniconda3/envs/omniCLIP/include/python3.7m mynumpy=/home/hsher/.local/lib/python3.7/site-packages/numpy/core/include/numpy remember the last numpy cd $mypython ln -s $mynumpy numpy

hope this is helpful to any struggling people!

[philippdre]

Dear Nico,

did the suggestion of algaebrown solve your problem?

Best, Philipp