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scikit learn not able to install on jetson tx2 using pip #12707

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edwinjose900 opened this issue Dec 1, 2018 · 11 comments

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@edwinjose900
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@edwinjose900 edwinjose900 commented Dec 1, 2018

error: Command "aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/nvidia/.local/lib/python3.5/site-packages/numpy/core/include -I/home/nvidia/.local/lib/python3.5/site-packages/numpy/core/include -I/usr/include/python3.5m -c sklearn/neighbors/quad_tree.c -o build/temp.linux-aarch64-3.5/sklearn/neighbors/quad_tree.o -MMD -MF build/temp.linux-aarch64-3.5/sklearn/neighbors/quad_tree.o.d" failed with exit status 1

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@amueller amueller commented Dec 1, 2018

Can you please give the full traceback? That's an ARM and you're running linux?

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@ogrisel ogrisel commented Dec 4, 2018

Also please give the cython and gcc version.

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@ogrisel ogrisel commented Dec 4, 2018

At some point we might want to find a way to setup some CI to test sklearn on ARM.

We could use amd64 infra to run the build and or tests in an emulated ARM debian chroot:

https://www.tomaz.me/2013/12/02/running-travis-ci-tests-on-arm.html

But I am afraid that even it we manage to get cross-compiling working, running the sklearn tests would be too slow when emulated.

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@edwinjose900 edwinjose900 commented Dec 4, 2018

Can you please give the full traceback? That's an ARM and you're running linux?

its on jetson tx2

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@rytrose rytrose commented Dec 4, 2018

I'm having the same issue. Jetson TX2, aarch64, Ubuntu 16.04, gcc version 5.4.0 20160609, Cython version 0.28.5. Traceback:

Compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    creating build/temp.linux-aarch64-3.6/sklearn/__check_build
    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/__check_build/_check_build.c
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/__check_build/_check_build.o -Lbuild/temp.linux-aarch64-3.6 -o build/lib.linux-aarch64-3.6/sklearn/__check_build/_check_build.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.cluster._dbscan_inner' extension
    compiling C++ sources
    C compiler: aarch64-linux-gnu-g++ -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    creating build/temp.linux-aarch64-3.6/sklearn/cluster
    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-g++: sklearn/cluster/_dbscan_inner.cpp
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/cluster/_dbscan_inner.cpp:271:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/cluster/_dbscan_inner.cpp:271:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
     _import_array(void)
     ^
    aarch64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/cluster/_dbscan_inner.o -Lbuild/temp.linux-aarch64-3.6 -o build/lib.linux-aarch64-3.6/sklearn/cluster/_dbscan_inner.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.cluster._hierarchical' extension
    compiling C++ sources
    C compiler: aarch64-linux-gnu-g++ -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-g++: sklearn/cluster/_hierarchical.cpp
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/cluster/_hierarchical.cpp:269:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    aarch64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/cluster/_hierarchical.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/cluster/_hierarchical.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.cluster._k_means_elkan' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/cluster/_k_means_elkan.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/cluster/_k_means_elkan.c:259:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/cluster/_k_means_elkan.c:259:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
     _import_array(void)
     ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/cluster/_k_means_elkan.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/cluster/_k_means_elkan.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.cluster._k_means' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-DHAVE_CBLAS -DATLAS_INFO="\"3.10.2\"" -Isklearn/src/cblas -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/atlas -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/cluster/_k_means.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/cluster/_k_means.c:281:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    sklearn/cluster/_k_means.c: In function ‘__pyx_fuse_0__pyx_f_7sklearn_7cluster_8_k_means__assign_labels_array’:
    sklearn/cluster/_k_means.c:3271:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_v_dot = cblas_sdot;
                   ^
    sklearn/cluster/_k_means.c: In function ‘__pyx_fuse_1__pyx_f_7sklearn_7cluster_8_k_means__assign_labels_array’:
    sklearn/cluster/_k_means.c:4062:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_v_dot = cblas_ddot;
                   ^
    sklearn/cluster/_k_means.c: In function ‘__pyx_fuse_0__pyx_f_7sklearn_7cluster_8_k_means__assign_labels_csr’:
    sklearn/cluster/_k_means.c:5556:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_v_dot = cblas_sdot;
                   ^
    sklearn/cluster/_k_means.c: In function ‘__pyx_fuse_1__pyx_f_7sklearn_7cluster_8_k_means__assign_labels_csr’:
    sklearn/cluster/_k_means.c:6412:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_v_dot = cblas_ddot;
                   ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/cluster/_k_means.o -L/usr/lib/atlas-base -Lbuild/temp.linux-aarch64-3.6 -lf77blas -lcblas -latlas -lf77blas -lcblas -lm -o build/lib.linux-aarch64-3.6/sklearn/cluster/_k_means.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.datasets._svmlight_format' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    creating build/temp.linux-aarch64-3.6/sklearn/datasets
    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/datasets/_svmlight_format.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/datasets/_svmlight_format.c:257:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/datasets/_svmlight_format.o -Lbuild/temp.linux-aarch64-3.6 -o build/lib.linux-aarch64-3.6/sklearn/datasets/_svmlight_format.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.decomposition._online_lda' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    creating build/temp.linux-aarch64-3.6/sklearn/decomposition
    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/decomposition/_online_lda.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/decomposition/_online_lda.c:260:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/decomposition/_online_lda.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/decomposition/_online_lda.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.decomposition.cdnmf_fast' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/decomposition/cdnmf_fast.c
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/decomposition/cdnmf_fast.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/decomposition/cdnmf_fast.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.ensemble._gradient_boosting' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    creating build/temp.linux-aarch64-3.6/sklearn/ensemble
    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/ensemble/_gradient_boosting.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/ensemble/_gradient_boosting.c:256:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/ensemble/_gradient_boosting.o -Lbuild/temp.linux-aarch64-3.6 -o build/lib.linux-aarch64-3.6/sklearn/ensemble/_gradient_boosting.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.feature_extraction._hashing' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    creating build/temp.linux-aarch64-3.6/sklearn/feature_extraction
    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/feature_extraction/_hashing.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/feature_extraction/_hashing.c:260:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/feature_extraction/_hashing.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/feature_extraction/_hashing.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.manifold._utils' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    creating build/temp.linux-aarch64-3.6/sklearn/manifold
    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    extra options: '-O3'
    aarch64-linux-gnu-gcc: sklearn/manifold/_utils.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/manifold/_utils.c:264:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/manifold/_utils.c:264:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
     _import_array(void)
     ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/manifold/_utils.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/manifold/_utils.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.manifold._barnes_hut_tsne' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-DHAVE_CBLAS -DATLAS_INFO="\"3.10.2\"" -Isklearn/src/cblas -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/atlas -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    extra options: '-O4'
    aarch64-linux-gnu-gcc: sklearn/manifold/_barnes_hut_tsne.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/manifold/_barnes_hut_tsne.c:280:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    sklearn/manifold/_barnes_hut_tsne.c: In function ‘__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negative’:
    sklearn/manifold/_barnes_hut_tsne.c:2913:9: warning: variable ‘__pyx_v_force’ set but not used [-Wunused-but-set-variable]
       float __pyx_v_force[3];
             ^
    sklearn/manifold/_barnes_hut_tsne.c:2912:9: warning: variable ‘__pyx_v_iQ’ set but not used [-Wunused-but-set-variable]
       float __pyx_v_iQ[1];
             ^
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/manifold/_barnes_hut_tsne.c:280:
    sklearn/manifold/_barnes_hut_tsne.c: At top level:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
     _import_array(void)
     ^
    sklearn/manifold/_barnes_hut_tsne.c: In function ‘__pyx_pw_7sklearn_8manifold_16_barnes_hut_tsne_1gradient’:
    sklearn/manifold/_barnes_hut_tsne.c:3346:74: warning: ‘__pyx_v_neg_force[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           (__pyx_v_neg_f[((__pyx_v_i * __pyx_v_n_dimensions) + __pyx_v_ax)]) = (__pyx_v_neg_force[__pyx_v_ax]);
                                                                              ^
    sklearn/manifold/_barnes_hut_tsne.c:2914:9: note: ‘__pyx_v_neg_force[2]’ was declared here
       float __pyx_v_neg_force[3];
             ^
    sklearn/manifold/_barnes_hut_tsne.c:3346:74: warning: ‘__pyx_v_neg_force[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           (__pyx_v_neg_f[((__pyx_v_i * __pyx_v_n_dimensions) + __pyx_v_ax)]) = (__pyx_v_neg_force[__pyx_v_ax]);
                                                                              ^
    sklearn/manifold/_barnes_hut_tsne.c:2914:9: note: ‘__pyx_v_neg_force[1]’ was declared here
       float __pyx_v_neg_force[3];
             ^
    sklearn/manifold/_barnes_hut_tsne.c:3346:74: warning: ‘__pyx_v_neg_force[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           (__pyx_v_neg_f[((__pyx_v_i * __pyx_v_n_dimensions) + __pyx_v_ax)]) = (__pyx_v_neg_force[__pyx_v_ax]);
                                                                              ^
    sklearn/manifold/_barnes_hut_tsne.c:2914:9: note: ‘__pyx_v_neg_force[0]’ was declared here
       float __pyx_v_neg_force[3];
             ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/manifold/_barnes_hut_tsne.o -L/usr/lib/atlas-base -Lbuild/temp.linux-aarch64-3.6 -lf77blas -lcblas -latlas -lf77blas -lcblas -o build/lib.linux-aarch64-3.6/sklearn/manifold/_barnes_hut_tsne.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.metrics.cluster.expected_mutual_info_fast' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    creating build/temp.linux-aarch64-3.6/sklearn/metrics
    creating build/temp.linux-aarch64-3.6/sklearn/metrics/cluster
    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/metrics/cluster/expected_mutual_info_fast.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/metrics/cluster/expected_mutual_info_fast.c:260:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/metrics/cluster/expected_mutual_info_fast.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/metrics/cluster/expected_mutual_info_fast.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.metrics.pairwise_fast' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-DHAVE_CBLAS -DATLAS_INFO="\"3.10.2\"" -Isklearn/src/cblas -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/atlas -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/metrics/pairwise_fast.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/metrics/pairwise_fast.c:280:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/metrics/pairwise_fast.o -L/usr/lib/atlas-base -Lbuild/temp.linux-aarch64-3.6 -lf77blas -lcblas -latlas -lf77blas -lcblas -lm -o build/lib.linux-aarch64-3.6/sklearn/metrics/pairwise_fast.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.neighbors.ball_tree' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    creating build/temp.linux-aarch64-3.6/sklearn/neighbors
    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/neighbors/ball_tree.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/neighbors/ball_tree.c:259:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    sklearn/neighbors/ball_tree.c: In function ‘__pyx_f_7sklearn_9neighbors_9ball_tree_10BinaryTree__kde_single_depthfirst’:
    sklearn/neighbors/ball_tree.c:19804:63: warning: ‘__pyx_v_sample_weight’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             __pyx_t_12 = PyFloat_FromDouble((__pyx_v_sample_weight[(__pyx_v_idx_array[__pyx_v_i])])); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                                   ^
    sklearn/neighbors/ball_tree.c: In function ‘__pyx_f_7sklearn_9neighbors_9ball_tree_10BinaryTree__kde_single_breadthfirst’:
    sklearn/neighbors/ball_tree.c:22425:52: warning: ‘__pyx_v_sample_weight’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         __pyx_v_N = (__pyx_v_N + (__pyx_v_sample_weight[(__pyx_v_idx_array[__pyx_v_i])]));
                                                        ^
    sklearn/neighbors/ball_tree.c:18621:50: note: ‘__pyx_v_sample_weight’ was declared here
       __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_sample_weight;
                                                      ^
    sklearn/neighbors/ball_tree.c: In function ‘__pyx_f_7sklearn_9neighbors_9ball_tree_10BinaryTree__recursive_build’:
    sklearn/neighbors/ball_tree.c:22766:82: warning: ‘__pyx_v_sample_weight’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           __pyx_v_sum_weight_node = (__pyx_v_sum_weight_node + (__pyx_v_sample_weight[(__pyx_v_idx_array[__pyx_v_i])]));
                                                                                      ^
    sklearn/neighbors/ball_tree.c:22588:50: note: ‘__pyx_v_sample_weight’ was declared here
       __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_sample_weight;
                                                      ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/neighbors/ball_tree.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/neighbors/ball_tree.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.neighbors.kd_tree' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/neighbors/kd_tree.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/neighbors/kd_tree.c:259:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    sklearn/neighbors/kd_tree.c: In function ‘__pyx_f_7sklearn_9neighbors_7kd_tree_10BinaryTree__kde_single_breadthfirst’:
    sklearn/neighbors/kd_tree.c:22396:52: warning: ‘__pyx_v_sample_weight’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         __pyx_v_N = (__pyx_v_N + (__pyx_v_sample_weight[(__pyx_v_idx_array[__pyx_v_i])]));
                                                        ^
    sklearn/neighbors/kd_tree.c:18592:50: note: ‘__pyx_v_sample_weight’ was declared here
       __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_sample_weight;
                                                      ^
    sklearn/neighbors/kd_tree.c: In function ‘__pyx_f_7sklearn_9neighbors_7kd_tree_10BinaryTree__kde_single_depthfirst’:
    sklearn/neighbors/kd_tree.c:19775:63: warning: ‘__pyx_v_sample_weight’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             __pyx_t_12 = PyFloat_FromDouble((__pyx_v_sample_weight[(__pyx_v_idx_array[__pyx_v_i])])); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                                   ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/neighbors/kd_tree.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/neighbors/kd_tree.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.neighbors.dist_metrics' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/neighbors/dist_metrics.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/neighbors/dist_metrics.c:260:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    sklearn/neighbors/dist_metrics.c: In function ‘__pyx_f_7sklearn_9neighbors_12dist_metrics_18SEuclideanDistance_dist’:
    sklearn/neighbors/dist_metrics.c:6383:85: warning: passing argument 1 of ‘__pyx_f_7sklearn_9neighbors_12dist_metrics_18SEuclideanDistance_rdist’ from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_t_1 = __pyx_f_7sklearn_9neighbors_12dist_metrics_18SEuclideanDistance_rdist(((struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == -1.0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                                                         ^
    sklearn/neighbors/dist_metrics.c:6182:54: note: expected ‘struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_SEuclideanDistance *’ but argument is of type ‘struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_DistanceMetric *’
     static __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t __pyx_f_7sklearn_9neighbors_12dist_metrics_18SEuclideanDistance_rdist(struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_SEuclideanDistance *__pyx_v_self, __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_x1, __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_x2, __pyx_t_7sklearn_9neighbors_8typedefs_ITYPE_t __pyx_v_size) {
                                                          ^
    sklearn/neighbors/dist_metrics.c: In function ‘__pyx_f_7sklearn_9neighbors_12dist_metrics_17MinkowskiDistance_dist’:
    sklearn/neighbors/dist_metrics.c:7173:84: warning: passing argument 1 of ‘__pyx_f_7sklearn_9neighbors_12dist_metrics_17MinkowskiDistance_rdist’ from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_t_1 = __pyx_f_7sklearn_9neighbors_12dist_metrics_17MinkowskiDistance_rdist(((struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == -1.0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                                                        ^
    sklearn/neighbors/dist_metrics.c:7091:54: note: expected ‘struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_MinkowskiDistance *’ but argument is of type ‘struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_DistanceMetric *’
     static __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t __pyx_f_7sklearn_9neighbors_12dist_metrics_17MinkowskiDistance_rdist(struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_MinkowskiDistance *__pyx_v_self, __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_x1, __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_x2, __pyx_t_7sklearn_9neighbors_8typedefs_ITYPE_t __pyx_v_size) {
                                                          ^
    sklearn/neighbors/dist_metrics.c: In function ‘__pyx_f_7sklearn_9neighbors_12dist_metrics_18WMinkowskiDistance_dist’:
    sklearn/neighbors/dist_metrics.c:7873:85: warning: passing argument 1 of ‘__pyx_f_7sklearn_9neighbors_12dist_metrics_18WMinkowskiDistance_rdist’ from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_t_1 = __pyx_f_7sklearn_9neighbors_12dist_metrics_18WMinkowskiDistance_rdist(((struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == -1.0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                                                         ^
    sklearn/neighbors/dist_metrics.c:7682:54: note: expected ‘struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_WMinkowskiDistance *’ but argument is of type ‘struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_DistanceMetric *’
     static __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t __pyx_f_7sklearn_9neighbors_12dist_metrics_18WMinkowskiDistance_rdist(struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_WMinkowskiDistance *__pyx_v_self, __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_x1, __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_x2, __pyx_t_7sklearn_9neighbors_8typedefs_ITYPE_t __pyx_v_size) {
                                                          ^
    sklearn/neighbors/dist_metrics.c: In function ‘__pyx_f_7sklearn_9neighbors_12dist_metrics_19MahalanobisDistance_dist’:
    sklearn/neighbors/dist_metrics.c:8731:86: warning: passing argument 1 of ‘__pyx_f_7sklearn_9neighbors_12dist_metrics_19MahalanobisDistance_rdist’ from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_t_1 = __pyx_f_7sklearn_9neighbors_12dist_metrics_19MahalanobisDistance_rdist(((struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == -1.0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                                                          ^
    sklearn/neighbors/dist_metrics.c:8485:54: note: expected ‘struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_MahalanobisDistance *’ but argument is of type ‘struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_DistanceMetric *’
     static __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t __pyx_f_7sklearn_9neighbors_12dist_metrics_19MahalanobisDistance_rdist(struct __pyx_obj_7sklearn_9neighbors_12dist_metrics_MahalanobisDistance *__pyx_v_self, __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_x1, __pyx_t_7sklearn_9neighbors_8typedefs_DTYPE_t *__pyx_v_x2, __pyx_t_7sklearn_9neighbors_8typedefs_ITYPE_t __pyx_v_size) {
                                                          ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/neighbors/dist_metrics.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/neighbors/dist_metrics.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.neighbors.typedefs' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/neighbors/typedefs.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/neighbors/typedefs.c:259:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/neighbors/typedefs.c:259:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
     _import_array(void)
     ^
    aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/sklearn/neighbors/typedefs.o -Lbuild/temp.linux-aarch64-3.6 -lm -o build/lib.linux-aarch64-3.6/sklearn/neighbors/typedefs.cpython-36m-aarch64-linux-gnu.so
    building 'sklearn.neighbors.quad_tree' extension
    compiling C sources
    C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    aarch64-linux-gnu-gcc: sklearn/neighbors/quad_tree.c
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/neighbors/quad_tree.c:259:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    sklearn/neighbors/quad_tree.c: In function ‘__pyx_f_7sklearn_9neighbors_9quad_tree_9_QuadTree_insert_point’:
    sklearn/neighbors/quad_tree.c:3582:14: error: format not a string literal and no format arguments [-Werror=format-security]
           printf(__pyx_k_QuadTree_found_a_duplicate);
                  ^
    sklearn/neighbors/quad_tree.c: In function ‘__pyx_f_7sklearn_9neighbors_9quad_tree_9_QuadTree__get_cell_ndarray’:
    sklearn/neighbors/quad_tree.c:6643:36: warning: passing argument 1 of ‘(PyObject * (*)(PyTypeObject *, PyArray_Descr *, int,  npy_intp *, npy_intp *, void *, int,  PyObject *))*(PyArray_API + 752u)’ from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_t_2 = PyArray_NewFromDescr(((PyObject *)__pyx_ptype_5numpy_ndarray), ((PyArray_Descr *)__pyx_t_1), 1, __pyx_v_shape, __pyx_v_strides, ((void *)__pyx_v_self->cells), NPY_DEFAULT, Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                        ^
    sklearn/neighbors/quad_tree.c:6643:36: note: expected ‘PyTypeObject * {aka struct _typeobject *}’ but argument is of type ‘PyObject * {aka struct _object *}’
    cc1: some warnings being treated as errors
    In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from sklearn/neighbors/quad_tree.c:259:
    /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    sklearn/neighbors/quad_tree.c: In function ‘__pyx_f_7sklearn_9neighbors_9quad_tree_9_QuadTree_insert_point’:
    sklearn/neighbors/quad_tree.c:3582:14: error: format not a string literal and no format arguments [-Werror=format-security]
           printf(__pyx_k_QuadTree_found_a_duplicate);
                  ^
    sklearn/neighbors/quad_tree.c: In function ‘__pyx_f_7sklearn_9neighbors_9quad_tree_9_QuadTree__get_cell_ndarray’:
    sklearn/neighbors/quad_tree.c:6643:36: warning: passing argument 1 of ‘(PyObject * (*)(PyTypeObject *, PyArray_Descr *, int,  npy_intp *, npy_intp *, void *, int,  PyObject *))*(PyArray_API + 752u)’ from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_t_2 = PyArray_NewFromDescr(((PyObject *)__pyx_ptype_5numpy_ndarray), ((PyArray_Descr *)__pyx_t_1), 1, __pyx_v_shape, __pyx_v_strides, ((void *)__pyx_v_self->cells), NPY_DEFAULT, Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                        ^
    sklearn/neighbors/quad_tree.c:6643:36: note: expected ‘PyTypeObject * {aka struct _typeobject *}’ but argument is of type ‘PyObject * {aka struct _object *}’
    cc1: some warnings being treated as errors
    error: Command "aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c sklearn/neighbors/quad_tree.c -o build/temp.linux-aarch64-3.6/sklearn/neighbors/quad_tree.o -MMD -MF build/temp.linux-aarch64-3.6/sklearn/neighbors/quad_tree.o.d" failed with exit status 1

    ----------------------------------------
Command "/usr/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-vsoinjd0/scikit-learn/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-o1ri7r_w/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-vsoinjd0/scikit-learn/
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@amueller amueller commented Dec 8, 2018

Seems like a cython issue possibly? Can you try to update cython?

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@amueller amueller commented Dec 8, 2018

@rytrose are you installing using pip? That could be an issue with us shipping with old Cython code in sdist, see #12671

@rytrose can you try

pip install https://github.com/scikit-learn/scikit-learn/archive/0.20.1.tar.gz
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@rytrose rytrose commented Dec 10, 2018

Yes! Some combination of updating cython to 0.29.1 and installing sk-learn 0.20.1 from your tar worked. Sorry I didn't isolate them to see which, but I thank you for your help, @amueller !

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@amueller amueller commented Dec 10, 2018

Pretty sure the tarball fixes it. Which means we have to release 0.20.2.

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@adrinjalali adrinjalali commented Dec 20, 2018

I suppose 0.20.2 release has fixed this. Please comment/reopen if the issue persists.

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