GMatch4py
GMatch4py copied to clipboard
Published
20 hours ago •
Jacobe2169
Jacobe2169
warning: libstdc++ is deprecated; move to libc++ with a minimum deployment target of OS X 10.9 [-Wdeprecated]
Hi, When I executed this command sudo python3 setup.py install, I encountered the following error.
veradeMacBook-Pro:GMatch4py vera$ sudo python3 setup.py install
Password:
gmatch4py/kernels/weisfeiler_lehman.pyx: cannot find cimported module '..base'
gmatch4py/vertex_ranking.pyx: cannot find cimported module '.base'
gmatch4py/vertex_edge_overlap.pyx: cannot find cimported module '.base'
gmatch4py/mcs.pyx: cannot find cimported module '.base'
gmatch4py/bag_of_cliques.pyx: cannot find cimported module '.base'
gmatch4py/bon.pyx: cannot find cimported module '.base'
gmatch4py/jaccard.pyx: cannot find cimported module '.base'
gmatch4py/ged/graph_edit_dist.pyx: cannot find cimported module '.abstract_graph_edit_dist'
gmatch4py/ged/graph_edit_dist.pyx: cannot find cimported module '..base'
gmatch4py/ged/graph_edit_dist.pxd: cannot find cimported module '.abstract_graph_edit_dist'
gmatch4py/ged/bipartite_graph_matching_2.pyx: cannot find cimported module '..base'
gmatch4py/ged/greedy_edit_distance.pyx: cannot find cimported module '.graph_edit_dist'
gmatch4py/ged/hausdorff_edit_distance.pyx: cannot find cimported module '..base'
gmatch4py/ged/abstract_graph_edit_dist.pyx: cannot find cimported module '..base'
gmatch4py/ged/abstract_graph_edit_dist.pxd: cannot find cimported module '..base'
/anaconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long_description_content_type'
warnings.warn(msg)
/anaconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'setup_requires'
warnings.warn(msg)
/anaconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'install_requires'
warnings.warn(msg)
running install
running build
running build_py
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/gmatch4py
copying gmatch4py/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/gmatch4py
creating build/lib.macosx-10.7-x86_64-3.7/gmatch4py/helpers
copying gmatch4py/helpers/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/gmatch4py/helpers
running build_ext
building 'gmatch4py.kernels.random_walk_kernel' extension
creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/gmatch4py
creating build/temp.macosx-10.7-x86_64-3.7/gmatch4py/kernels
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -I/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/anaconda3/include/python3.7m -c gmatch4py/kernels/random_walk_kernel.cpp -o build/temp.macosx-10.7-x86_64-3.7/gmatch4py/kernels/random_walk_kernel.o
warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the
libc++ standard library instead [-Wstdlibcxx-not-found]
1 warning generated.
creating build/lib.macosx-10.7-x86_64-3.7/gmatch4py/kernels
g++ -bundle -undefined dynamic_lookup -L/anaconda3/lib -arch x86_64 -L/anaconda3/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.7-x86_64-3.7/gmatch4py/kernels/random_walk_kernel.o -o build/lib.macosx-10.7-x86_64-3.7/gmatch4py/kernels/random_walk_kernel.cpython-37m-darwin.so
clang: warning: libstdc++ is deprecated; move to libc++ with a minimum deployment target of OS X 10.9 [-Wdeprecated]
ld: library not found for -lstdc++
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'g++' failed with exit status 1
My env is in anaconda python3.6, Mac 10.14(Mojave)
Hi @verazuo, did you install Xcode Command Line Tools (xcode select --install) ?
I tried to find some solutions to fix this bug and tried many ways. And this command successfully makes GMatch4py installed in my Mac which inspired from here
sudo CFLAGS=-stdlib=libc++ python3 setup.py install
But I don't think this is a good solution, As there are many warnings generated. Hope can hear a better solution from you. Thanks a lot.
(py36) veradeMacBook-Pro:GMatch4py vera$ sudo CFLAGS=-stdlib=libc++ python3 setup.py install
/anaconda3/envs/py36/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type'
warnings.warn(msg)
/anaconda3/envs/py36/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'setup_requires'
warnings.warn(msg)
/anaconda3/envs/py36/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'install_requires'
warnings.warn(msg)
running install
running build
running build_py
running build_ext
building 'gmatch4py.kernels.weisfeiler_lehman' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/kernels/weisfeiler_lehman.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels/weisfeiler_lehman.o
In file included from gmatch4py/kernels/weisfeiler_lehman.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels/weisfeiler_lehman.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/weisfeiler_lehman.cpython-36m-darwin.so
building 'gmatch4py.kernels.shortest_path_kernel' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/kernels/shortest_path_kernel.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels/shortest_path_kernel.o
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels/shortest_path_kernel.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/shortest_path_kernel.cpython-36m-darwin.so
building 'gmatch4py.vertex_ranking' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/vertex_ranking.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/vertex_ranking.o
In file included from gmatch4py/vertex_ranking.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/vertex_ranking.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/vertex_ranking.cpython-36m-darwin.so
building 'gmatch4py.vertex_edge_overlap' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/vertex_edge_overlap.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/vertex_edge_overlap.o
In file included from gmatch4py/vertex_edge_overlap.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/vertex_edge_overlap.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/vertex_edge_overlap.cpython-36m-darwin.so
building 'gmatch4py.deltacon' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/deltacon.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/deltacon.o
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/deltacon.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/deltacon.cpython-36m-darwin.so
building 'gmatch4py.base' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/base.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/base.o
In file included from gmatch4py/base.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/base.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/base.cpython-36m-darwin.so
building 'gmatch4py.mcs' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/mcs.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/mcs.o
In file included from gmatch4py/mcs.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/mcs.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/mcs.cpython-36m-darwin.so
building 'gmatch4py.bag_of_cliques' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/bag_of_cliques.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/bag_of_cliques.o
In file included from gmatch4py/bag_of_cliques.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/bag_of_cliques.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/bag_of_cliques.cpython-36m-darwin.so
building 'gmatch4py.bon' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/bon.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/bon.o
In file included from gmatch4py/bon.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/bon.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/bon.cpython-36m-darwin.so
building 'gmatch4py.alg_types' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/alg_types.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/alg_types.o
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/alg_types.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/alg_types.cpython-36m-darwin.so
building 'gmatch4py.helpers.reader' extension
creating build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/helpers/reader.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/reader.o
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/reader.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/reader.cpython-36m-darwin.so
building 'gmatch4py.helpers.compute_similarity_matrix' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/helpers/compute_similarity_matrix.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/compute_similarity_matrix.o
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/compute_similarity_matrix.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/compute_similarity_matrix.cpython-36m-darwin.so
building 'gmatch4py.helpers.generate_config' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/helpers/generate_config.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/generate_config.o
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/generate_config.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/generate_config.cpython-36m-darwin.so
building 'gmatch4py.jaccard' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/jaccard.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/jaccard.o
In file included from gmatch4py/jaccard.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/jaccard.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/jaccard.cpython-36m-darwin.so
building 'gmatch4py.ged.graph_edit_dist' extension
creating build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/ged/graph_edit_dist.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/graph_edit_dist.o
In file included from gmatch4py/ged/graph_edit_dist.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
creating build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/graph_edit_dist.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/graph_edit_dist.cpython-36m-darwin.so
building 'gmatch4py.ged.bipartite_graph_matching_2' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/ged/bipartite_graph_matching_2.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/bipartite_graph_matching_2.o
In file included from gmatch4py/ged/bipartite_graph_matching_2.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/bipartite_graph_matching_2.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/bipartite_graph_matching_2.cpython-36m-darwin.so
building 'gmatch4py.ged.greedy_edit_distance' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/ged/greedy_edit_distance.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/greedy_edit_distance.o
In file included from gmatch4py/ged/greedy_edit_distance.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/greedy_edit_distance.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/greedy_edit_distance.cpython-36m-darwin.so
building 'gmatch4py.ged.hausdorff_edit_distance' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/ged/hausdorff_edit_distance.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/hausdorff_edit_distance.o
In file included from gmatch4py/ged/hausdorff_edit_distance.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/hausdorff_edit_distance.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/hausdorff_edit_distance.cpython-36m-darwin.so
building 'gmatch4py.ged.abstract_graph_edit_dist' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/ged/abstract_graph_edit_dist.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/abstract_graph_edit_dist.o
In file included from gmatch4py/ged/abstract_graph_edit_dist.cpp:647:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:
/anaconda3/envs/py36/lib/python3.6/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 " \
^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/abstract_graph_edit_dist.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/abstract_graph_edit_dist.cpython-36m-darwin.so
running install_lib
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/bag_of_cliques.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py
creating /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/kernels
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/shortest_path_kernel.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/kernels
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/random_walk_kernel.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/kernels
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/weisfeiler_lehman.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/kernels
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/mcs.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/bon.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/base.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/deltacon.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/alg_types.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/jaccard.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/vertex_edge_overlap.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py
creating /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/__init__.py -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/reader.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/generate_config.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/compute_similarity_matrix.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/vertex_ranking.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py
creating /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/greedy_edit_distance.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/abstract_graph_edit_dist.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/graph_edit_dist.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/bipartite_graph_matching_2.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/hausdorff_edit_distance.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged
byte-compiling /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/__init__.py to __init__.cpython-36.pyc
byte-compiling /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers/__init__.py to __init__.cpython-36.pyc
running install_egg_info
Writing /anaconda3/envs/py36/lib/python3.6/site-packages/GMatch4py-0.2.2-py3.6.egg-info
Then input python
(py36) veradeMacBook-Pro:GMatch4py vera$ python
Python 3.6.7 |Anaconda, Inc.| (default, Oct 23 2018, 14:01:38)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import GMatch4py
>>> exit()
For the compilation warning, don't worry about it 😄 it should not affect the module! However, for the CFLAG parameter, it is weird! Did you try to install the Xcode Command Line tools? Normally, it should contain add stdlibc++ to your system.
Hi @verazuo, did you install Xcode Command Line Tools (
xcode select --install) ?
I guess I didn't install Xcode Command Line Tools in my computer.
(py36) veradeMacBook-Pro:GMatch4py vera$ xcode select --install
-bash: xcode: command not found
Should I install it?
oops x) I gave you the wrong command !
This one should work : xcode-select --install
Oh then I guess I have installed it
(py36) veradeMacBook-Pro:GMatch4py vera$ xcode-select --install
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
Hummm.... From what I found, it seems that the last update of mac OS is responsible : https://github.com/pandas-dev/pandas/issues/23424#issuecomment-434497519
Maybe it can be fixed using this solution : https://github.com/pandas-dev/pandas/issues/23424#issuecomment-435612148
hi @Jacobe2169 , sorry for bothering you again. I meet another problem with GMatch4py. When I run this command
import GMatch4py as gm
ged=gm.GraphEditDistance(1,1,1,1)
There is a error throw out:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
AttributeError: module 'GMatch4py' has no attribute 'GraphEditDistance'
Do you have any idea about it ? Thx
I fixed it.
I think the bug might be caused by the package path and the installation environment.
When gmatch4py is installed, the code import gmatch4py as gm will still points to the GMatch4py-master directory but not /site-packages/gmatch4py directory
Actually, you need to make sure below steps has been executed.
- Download code from this github repository
- cd into it
-
sudo CFLAGS=-stdlib=libc++ python3 setup.py install - delete the code from this github repository
- clear the trash
- restart the terminal
Then things will be ok.
Below is the entire possible installation process.
I reinstall GMatch4py in my conda base environment by this command. ( Before I install GMatch4py in my conda py36 environment )
veradeMacBook-Pro:GMatch4py$ sudo CFLAGS=-stdlib=libc++ python3 setup.py install
The warning is similar to this one.
I noticed that gmatch4py is copied to anaconda envs.
copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/greedy_edit_distance.cpython-36m-darwin.so -> /anaconda3/lib/python3.7/site-packages/gmatch4py/ged
And when I try to import gmatch4py, it tells me
veradeMacBook-Pro:GMatch4py vera$ python
Python 3.6.7 |Anaconda, Inc.| (default, Oct 23 2018, 14:01:38)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import gmatch4py as gm
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/vera/Downloads/GMatch4py/gmatch4py/__init__.py", line 4, in <module>
from .ged.graph_edit_dist import *
ModuleNotFoundError: No module named 'gmatch4py.ged.graph_edit_dist'
I guess maybe when I import gmatch4py, it automatically points to /GMatch4py/. So I delete all code of ./GMatch4py/ (code downloaded from this github repository), and keep code in /anaconda3/lib/python3.7/site-packages/gmatch4py.
Clear the trash (Otherwise the code import gmatch4py will still be led to the /.trash/GMatch4py/ directory)
Try to import it again, I get this.
>>> import gmatch4py as gm
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/__init__.py", line 4, in <module>
from .ged.graph_edit_dist import *
ModuleNotFoundError: No module named 'gmatch4py.ged.graph_edit_dist'
I have no idea about this situation, so I restart the terminal. Then everything is OK.
veradeMacBook-Pro:~ vera$ python
Python 3.7.0 (default, Jun 28 2018, 07:39:16)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import networkx as nx
>>> import gmatch4py as gm
>>> g1=nx.complete_bipartite_graph(5,4)
>>> g2=nx.complete_bipartite_graph(6,4)
>>> ged=gm.GraphEditDistance(1,1,1,1) # all edit costs are equal to 1
>>> result=ged.compare([g1,g2],None)
>>> print(result)
[[ 0. 14.]
[10. 0.]]
>>>
I also tried the above operation in conda py36 environment and successfully installed gmatch4py.
Hi @verazuo, Thanks for the detailed post! 😄
I'll add the CFLAGS=-stdlib=libc++ for Mojave users in the readme!
The import issue Basically, Gmatch4Py used Cython, a C/Python binding module which decrease the execution time of the algorithms. To use "Cythonized" module, one must go through a compilation process. Since the installation process includes the compilation, Gmatch4py source code can be used as it is. So when you're importing the module from the git directory, it's using the non-compiled format, hence Python can't interpret it. I will add a section in the readme file on this issue 😄
The trash clearing and the term restarting operations I'm wondering, between the directory deletion and the new import did you close the python terminal? If not, it is weird that restarting the terminal resolve the issue... or maybe anaconda is acting weird.
I personally use Python basic installation and official package manager pip but it's nice to know it's work also on Anaconda configurations.
Again thanks a lot for your feedback!
I pushed a modification of the setup.py in the last version: https://github.com/Jacobe2169/GMatch4py/commit/4cea92b063b684b7d54ead25b33cc52e1f454228
Can you check if it's working without the CFLAG ?
Sure, I create a new conda envs named test.
And download this github repository after your modification. But the code seems didn't work at my test envs.
(test) veradeMacBook-Pro:GMatch4py-master vera$ sudo python3 setup.py install
Compiling gmatch4py/kernels/random_walk_kernel.pyx because it changed.
Compiling gmatch4py/kernels/weisfeiler_lehman.pyx because it changed.
Compiling gmatch4py/kernels/shortest_path_kernel.pyx because it changed.
Compiling gmatch4py/vertex_ranking.pyx because it changed.
Compiling gmatch4py/vertex_edge_overlap.pyx because it changed.
Compiling gmatch4py/deltacon.pyx because it changed.
Compiling gmatch4py/base.pyx because it changed.
Compiling gmatch4py/mcs.pyx because it changed.
Compiling gmatch4py/bag_of_cliques.pyx because it changed.
Compiling gmatch4py/bon.pyx because it changed.
Compiling gmatch4py/alg_types.pyx because it changed.
Compiling gmatch4py/helpers/reader.pyx because it changed.
Compiling gmatch4py/helpers/compute_similarity_matrix.pyx because it changed.
Compiling gmatch4py/helpers/generate_config.pyx because it changed.
Compiling gmatch4py/jaccard.pyx because it changed.
Compiling gmatch4py/ged/graph_edit_dist.pyx because it changed.
Compiling gmatch4py/ged/bipartite_graph_matching_2.pyx because it changed.
Compiling gmatch4py/ged/greedy_edit_distance.pyx because it changed.
Compiling gmatch4py/ged/hausdorff_edit_distance.pyx because it changed.
Compiling gmatch4py/ged/abstract_graph_edit_dist.pyx because it changed.
[ 1/20] Cythonizing gmatch4py/alg_types.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/alg_types.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[ 2/20] Cythonizing gmatch4py/bag_of_cliques.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/bag_of_cliques.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[ 3/20] Cythonizing gmatch4py/base.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: ./gmatch4py/base.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
[ 4/20] Cythonizing gmatch4py/bon.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/bon.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[ 5/20] Cythonizing gmatch4py/deltacon.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/deltacon.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[ 6/20] Cythonizing gmatch4py/ged/abstract_graph_edit_dist.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: ./gmatch4py/ged/abstract_graph_edit_dist.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
[ 7/20] Cythonizing gmatch4py/ged/bipartite_graph_matching_2.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/ged/bipartite_graph_matching_2.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[ 8/20] Cythonizing gmatch4py/ged/graph_edit_dist.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: ./gmatch4py/ged/graph_edit_dist.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
[ 9/20] Cythonizing gmatch4py/ged/greedy_edit_distance.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/ged/greedy_edit_distance.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[10/20] Cythonizing gmatch4py/ged/hausdorff_edit_distance.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/ged/hausdorff_edit_distance.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[11/20] Cythonizing gmatch4py/helpers/compute_similarity_matrix.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/helpers/compute_similarity_matrix.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[12/20] Cythonizing gmatch4py/helpers/generate_config.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/helpers/generate_config.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[13/20] Cythonizing gmatch4py/helpers/reader.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/helpers/reader.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[14/20] Cythonizing gmatch4py/jaccard.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/jaccard.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[15/20] Cythonizing gmatch4py/kernels/random_walk_kernel.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/kernels/random_walk_kernel.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[16/20] Cythonizing gmatch4py/kernels/shortest_path_kernel.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/kernels/shortest_path_kernel.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[17/20] Cythonizing gmatch4py/kernels/weisfeiler_lehman.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/kernels/weisfeiler_lehman.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[18/20] Cythonizing gmatch4py/mcs.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/mcs.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[19/20] Cythonizing gmatch4py/vertex_edge_overlap.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/vertex_edge_overlap.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
[20/20] Cythonizing gmatch4py/vertex_ranking.pyx
/anaconda3/envs/test/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/vera/Downloads/GMatch4py-master/gmatch4py/vertex_ranking.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/anaconda3/envs/test/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type'
warnings.warn(msg)
/anaconda3/envs/test/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'setup_requires'
warnings.warn(msg)
/anaconda3/envs/test/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'install_requires'
warnings.warn(msg)
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.6
creating build/lib.macosx-10.7-x86_64-3.6/gmatch4py
copying gmatch4py/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/gmatch4py
creating build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers
copying gmatch4py/helpers/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers
running build_ext
building 'gmatch4py.kernels.random_walk_kernel' extension
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/gmatch4py
creating build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/envs/test/include -arch x86_64 -I/anaconda3/envs/test/include -arch x86_64 -I/anaconda3/envs/test/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/test/include/python3.6m -c gmatch4py/kernels/random_walk_kernel.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels/random_walk_kernel.o -stdlib=libc++
creating build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/test/lib -arch x86_64 -L/anaconda3/envs/test/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels/random_walk_kernel.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/random_walk_kernel.cpython-36m-darwin.so
clang: warning: libstdc++ is deprecated; move to libc++ with a minimum deployment target of OS X 10.9 [-Wdeprecated]
ld: library not found for -lstdc++
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'g++' failed with exit status 1
The error log is as the same as before.
And for the part of the trash clearing and the term restarting operations, I cannot remember the detail, but I guess I didn't close the python terminal. So maybe you are right.
I tried to find some solutions to fix this bug and tried many ways. And this command successfully makes GMatch4py installed in my Mac which inspired from here
sudo CFLAGS=-stdlib=libc++ python3 setup.py installBut I don't think this is a good solution, As there are many warnings generated. Hope can hear a better solution from you. Thanks a lot.
(py36) veradeMacBook-Pro:GMatch4py vera$ sudo CFLAGS=-stdlib=libc++ python3 setup.py install /anaconda3/envs/py36/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type' warnings.warn(msg) /anaconda3/envs/py36/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'setup_requires' warnings.warn(msg) /anaconda3/envs/py36/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py running build_ext building 'gmatch4py.kernels.weisfeiler_lehman' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/kernels/weisfeiler_lehman.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels/weisfeiler_lehman.o In file included from gmatch4py/kernels/weisfeiler_lehman.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels/weisfeiler_lehman.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/weisfeiler_lehman.cpython-36m-darwin.so building 'gmatch4py.kernels.shortest_path_kernel' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/kernels/shortest_path_kernel.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels/shortest_path_kernel.o g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/kernels/shortest_path_kernel.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/shortest_path_kernel.cpython-36m-darwin.so building 'gmatch4py.vertex_ranking' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/vertex_ranking.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/vertex_ranking.o In file included from gmatch4py/vertex_ranking.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/vertex_ranking.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/vertex_ranking.cpython-36m-darwin.so building 'gmatch4py.vertex_edge_overlap' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/vertex_edge_overlap.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/vertex_edge_overlap.o In file included from gmatch4py/vertex_edge_overlap.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/vertex_edge_overlap.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/vertex_edge_overlap.cpython-36m-darwin.so building 'gmatch4py.deltacon' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/deltacon.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/deltacon.o g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/deltacon.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/deltacon.cpython-36m-darwin.so building 'gmatch4py.base' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/base.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/base.o In file included from gmatch4py/base.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/base.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/base.cpython-36m-darwin.so building 'gmatch4py.mcs' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/mcs.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/mcs.o In file included from gmatch4py/mcs.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/mcs.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/mcs.cpython-36m-darwin.so building 'gmatch4py.bag_of_cliques' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/bag_of_cliques.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/bag_of_cliques.o In file included from gmatch4py/bag_of_cliques.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/bag_of_cliques.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/bag_of_cliques.cpython-36m-darwin.so building 'gmatch4py.bon' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/bon.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/bon.o In file included from gmatch4py/bon.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/bon.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/bon.cpython-36m-darwin.so building 'gmatch4py.alg_types' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/alg_types.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/alg_types.o g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/alg_types.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/alg_types.cpython-36m-darwin.so building 'gmatch4py.helpers.reader' extension creating build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/helpers/reader.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/reader.o g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/reader.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/reader.cpython-36m-darwin.so building 'gmatch4py.helpers.compute_similarity_matrix' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/helpers/compute_similarity_matrix.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/compute_similarity_matrix.o g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/compute_similarity_matrix.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/compute_similarity_matrix.cpython-36m-darwin.so building 'gmatch4py.helpers.generate_config' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/helpers/generate_config.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/generate_config.o g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/helpers/generate_config.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/generate_config.cpython-36m-darwin.so building 'gmatch4py.jaccard' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/jaccard.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/jaccard.o In file included from gmatch4py/jaccard.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/jaccard.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/jaccard.cpython-36m-darwin.so building 'gmatch4py.ged.graph_edit_dist' extension creating build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/ged/graph_edit_dist.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/graph_edit_dist.o In file included from gmatch4py/ged/graph_edit_dist.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. creating build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/graph_edit_dist.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/graph_edit_dist.cpython-36m-darwin.so building 'gmatch4py.ged.bipartite_graph_matching_2' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/ged/bipartite_graph_matching_2.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/bipartite_graph_matching_2.o In file included from gmatch4py/ged/bipartite_graph_matching_2.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/bipartite_graph_matching_2.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/bipartite_graph_matching_2.cpython-36m-darwin.so building 'gmatch4py.ged.greedy_edit_distance' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/ged/greedy_edit_distance.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/greedy_edit_distance.o In file included from gmatch4py/ged/greedy_edit_distance.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/greedy_edit_distance.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/greedy_edit_distance.cpython-36m-darwin.so building 'gmatch4py.ged.hausdorff_edit_distance' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/ged/hausdorff_edit_distance.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/hausdorff_edit_distance.o In file included from gmatch4py/ged/hausdorff_edit_distance.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/hausdorff_edit_distance.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/hausdorff_edit_distance.cpython-36m-darwin.so building 'gmatch4py.ged.abstract_graph_edit_dist' extension gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/py36/include/python3.6m -c gmatch4py/ged/abstract_graph_edit_dist.cpp -o build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/abstract_graph_edit_dist.o In file included from gmatch4py/ged/abstract_graph_edit_dist.cpp:647: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823: /anaconda3/envs/py36/lib/python3.6/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 " \ ^ 1 warning generated. g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/py36/lib -arch x86_64 -L/anaconda3/envs/py36/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/gmatch4py/ged/abstract_graph_edit_dist.o -o build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/abstract_graph_edit_dist.cpython-36m-darwin.so running install_lib copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/bag_of_cliques.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py creating /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/kernels copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/shortest_path_kernel.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/kernels copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/random_walk_kernel.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/kernels copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/kernels/weisfeiler_lehman.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/kernels copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/mcs.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/bon.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/base.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/deltacon.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/alg_types.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/jaccard.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/vertex_edge_overlap.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py creating /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/__init__.py -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/reader.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/generate_config.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/helpers/compute_similarity_matrix.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/vertex_ranking.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py creating /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/greedy_edit_distance.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/abstract_graph_edit_dist.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/graph_edit_dist.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/bipartite_graph_matching_2.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged copying build/lib.macosx-10.7-x86_64-3.6/gmatch4py/ged/hausdorff_edit_distance.cpython-36m-darwin.so -> /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/ged byte-compiling /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/__init__.py to __init__.cpython-36.pyc byte-compiling /anaconda3/envs/py36/lib/python3.6/site-packages/gmatch4py/helpers/__init__.py to __init__.cpython-36.pyc running install_egg_info Writing /anaconda3/envs/py36/lib/python3.6/site-packages/GMatch4py-0.2.2-py3.6.egg-infoThen input
python(py36) veradeMacBook-Pro:GMatch4py vera$ python Python 3.6.7 |Anaconda, Inc.| (default, Oct 23 2018, 14:01:38) [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import GMatch4py >>> exit()
works for me!
