Dear Sona, I guess with this: 'spyder-3.3.2-foss-2019b-3.6.6' you mean 'Spyder-3.3.2-foss-2018b-Python-3.6.6.eb'? The error: 'g++: internal compiler error: Killed (program cc1plus)' often occurs when the build runs out of memory, did you check that?
Kind regards, Sam On Sat, Apr 27, 2019 at 6:47 AM Ms. Sona CP <[email protected]> wrote: > Hi, > I am facing following error while installing spyder-3.3.2-foss-2019b-3.6.6 > ^~~~~~~~~ > scipy/sparse/csgraph/_shortest_path.c:2519:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_shortest_path.c:2532:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_5 = __Pyx_PyBool_FromLong((!__pyx_t_4)); if > (unlikely(!__pyx_t_5)) __PYX_ERR(0, 133, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_shortest_path.c:2532:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_shortest_path.c: In function > '__pyx_pf_5scipy_6sparse_7csgraph_14_shortest_path_2floyd_warshall': > scipy/sparse/csgraph/_shortest_path.c:3563:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_5 = __Pyx_PyBool_FromLong((!__pyx_t_4)); if > (unlikely(!__pyx_t_5)) __PYX_ERR(0, 237, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_shortest_path.c:3563:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > gcc -shared > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/bzip2/1.0.6-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/zlib/1.2.11-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libreadline/7.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ncurses/6.1-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/SQLite/3.24.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GMP/6.1.2-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib > -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > build/temp.linux-x86_64-2.7/scipy/sparse/csgraph/_shortest_path.o > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib > -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o > build/lib.linux-x86_64-2.7/scipy/sparse/csgraph/_shortest_path.so > -Wl,--version-script=build/temp.linux-x86_64-2.7/link-version-scipy.sparse.csgraph._shortest_path.map > building 'scipy.sparse.csgraph._traversal' extension > compiling C sources > C compiler: gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O2 > -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > -fPIC > > compile options: > '-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/include/python2.7 > -c' > gcc: scipy/sparse/csgraph/_traversal.c > In file included from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1816:0, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4, > from scipy/sparse/csgraph/_traversal.c:566: > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/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 " \ > ^~~~~~~ > scipy/sparse/csgraph/_traversal.c: In function > '__pyx_pf_5scipy_6sparse_7csgraph_10_traversal_connected_components': > scipy/sparse/csgraph/_traversal.c:2099:5: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __Pyx_INCREF(Py_False); > ^~~~~~~~~~~~ > gcc -shared > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/bzip2/1.0.6-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/zlib/1.2.11-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libreadline/7.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ncurses/6.1-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/SQLite/3.24.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GMP/6.1.2-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib > -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > build/temp.linux-x86_64-2.7/scipy/sparse/csgraph/_traversal.o > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib > -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o > build/lib.linux-x86_64-2.7/scipy/sparse/csgraph/_traversal.so > -Wl,--version-script=build/temp.linux-x86_64-2.7/link-version-scipy.sparse.csgraph._traversal.map > building 'scipy.sparse.csgraph._min_spanning_tree' extension > compiling C sources > C compiler: gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O2 > -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > -fPIC > > compile options: > '-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/include/python2.7 > -c' > gcc: scipy/sparse/csgraph/_min_spanning_tree.c > In file included from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1816:0, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4, > from scipy/sparse/csgraph/_min_spanning_tree.c:566: > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/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 " \ > ^~~~~~~ > scipy/sparse/csgraph/_min_spanning_tree.c: In function > '__pyx_pf_5scipy_6sparse_7csgraph_18_min_spanning_tree_minimum_spanning_tree': > scipy/sparse/csgraph/_min_spanning_tree.c:2583:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __Pyx_INCREF(Py_True); > ^~~~~~~~~~~~ > scipy/sparse/csgraph/_min_spanning_tree.c:2601:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_5 = __Pyx_PyBool_FromLong((!__pyx_t_4)); if > (unlikely(!__pyx_t_5)) __PYX_ERR(0, 86, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_min_spanning_tree.c:2601:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_min_spanning_tree.c: In function > '__pyx_array_get_memview': > scipy/sparse/csgraph/_min_spanning_tree.c:7301:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if > (unlikely(!__pyx_t_2)) __PYX_ERR(2, 227, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_min_spanning_tree.c:7301:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_min_spanning_tree.c: In function > '__pyx_memoryview_is_slice': > scipy/sparse/csgraph/_min_spanning_tree.c:9551:9: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); > if (unlikely(!__pyx_t_7)) __PYX_ERR(2, 430, __pyx_L4_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_min_spanning_tree.c:9551:9: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_min_spanning_tree.c: In function > '__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig': > scipy/sparse/csgraph/_min_spanning_tree.c:12037:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_1 = > __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig((__pyx_v_mslice[0]), > 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 618, > __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_min_spanning_tree.c:12037:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_min_spanning_tree.c: In function > '__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig': > scipy/sparse/csgraph/_min_spanning_tree.c:12108:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_1 = > __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig((__pyx_v_mslice[0]), > 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 624, > __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_min_spanning_tree.c:12108:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_min_spanning_tree.c: In function > '__pyx_memoryview_new': > scipy/sparse/csgraph/_min_spanning_tree.c:12449:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if > (unlikely(!__pyx_t_2)) __PYX_ERR(2, 653, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_min_spanning_tree.c:12449:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_min_spanning_tree.c: In function '_unellipsify': > scipy/sparse/csgraph/_min_spanning_tree.c:12953:5: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if > (unlikely(!__pyx_t_4)) __PYX_ERR(2, 693, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_min_spanning_tree.c:12953:5: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_min_spanning_tree.c: In function > '__pyx_memoryview_fromslice': > scipy/sparse/csgraph/_min_spanning_tree.c:15353:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if > (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1008, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_min_spanning_tree.c:15353:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > gcc -shared > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/bzip2/1.0.6-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/zlib/1.2.11-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libreadline/7.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ncurses/6.1-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/SQLite/3.24.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GMP/6.1.2-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib > -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > build/temp.linux-x86_64-2.7/scipy/sparse/csgraph/_min_spanning_tree.o > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib > -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o > build/lib.linux-x86_64-2.7/scipy/sparse/csgraph/_min_spanning_tree.so > -Wl,--version-script=build/temp.linux-x86_64-2.7/link-version-scipy.sparse.csgraph._min_spanning_tree.map > building 'scipy.sparse.csgraph._reordering' extension > compiling C sources > C compiler: gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O2 > -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > -fPIC > > compile options: > '-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/include/python2.7 > -c' > gcc: scipy/sparse/csgraph/_reordering.c > In file included from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1816:0, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4, > from scipy/sparse/csgraph/_reordering.c:566: > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/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 " \ > ^~~~~~~ > scipy/sparse/csgraph/_reordering.c: In function '__pyx_array_get_memview': > scipy/sparse/csgraph/_reordering.c:14462:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if > (unlikely(!__pyx_t_2)) __PYX_ERR(2, 227, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:14462:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_reordering.c: In function > '__pyx_memoryview_is_slice': > scipy/sparse/csgraph/_reordering.c:16712:9: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); > if (unlikely(!__pyx_t_7)) __PYX_ERR(2, 430, __pyx_L4_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:16712:9: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_reordering.c: In function > '__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig': > scipy/sparse/csgraph/_reordering.c:19198:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_1 = > __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig((__pyx_v_mslice[0]), > 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 618, > __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:19198:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_reordering.c: In function > '__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig': > scipy/sparse/csgraph/_reordering.c:19269:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_1 = > __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig((__pyx_v_mslice[0]), > 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 624, > __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:19269:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_reordering.c: In function '__pyx_memoryview_new': > scipy/sparse/csgraph/_reordering.c:19610:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if > (unlikely(!__pyx_t_2)) __PYX_ERR(2, 653, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:19610:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_reordering.c: In function '_unellipsify': > scipy/sparse/csgraph/_reordering.c:20114:5: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if > (unlikely(!__pyx_t_4)) __PYX_ERR(2, 693, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:20114:5: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_reordering.c: In function > '__pyx_memoryview_fromslice': > scipy/sparse/csgraph/_reordering.c:22514:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if > (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1008, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:22514:3: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_reordering.c: In function '__Pyx_PyInt_EqObjC': > scipy/sparse/csgraph/_reordering.c:29199:9: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:29206:13: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:29208:13: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_FALSE; > ^~~~~~~~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:29262:17: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > default: Py_RETURN_FALSE; > ^~~~~~~ > scipy/sparse/csgraph/_reordering.c:29267:17: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:29269:17: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_FALSE; > ^~~~~~~~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:29277:17: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/csgraph/_reordering.c:29279:17: warning: dereferencing > type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_FALSE; > ^~~~~~~~~~~~~~~ > gcc -shared > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/bzip2/1.0.6-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/zlib/1.2.11-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libreadline/7.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ncurses/6.1-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/SQLite/3.24.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GMP/6.1.2-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib > -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > build/temp.linux-x86_64-2.7/scipy/sparse/csgraph/_reordering.o > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib > -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o > build/lib.linux-x86_64-2.7/scipy/sparse/csgraph/_reordering.so > -Wl,--version-script=build/temp.linux-x86_64-2.7/link-version-scipy.sparse.csgraph._reordering.map > building 'scipy.sparse.csgraph._tools' extension > compiling C sources > C compiler: gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O2 > -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > -fPIC > > compile options: > '-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/include/python2.7 > -c' > gcc: scipy/sparse/csgraph/_tools.c > In file included from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1816:0, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4, > from scipy/sparse/csgraph/_tools.c:566: > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/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 " \ > ^~~~~~~ > scipy/sparse/csgraph/_tools.c: In function > '__pyx_pf_5scipy_6sparse_7csgraph_6_tools_2csgraph_masked_from_dense': > scipy/sparse/csgraph/_tools.c:2899:7: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > __Pyx_INCREF(Py_True); > ^~~~~~~~~~~~ > scipy/sparse/csgraph/_tools.c:2988:7: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > __Pyx_INCREF(Py_True); > ^~~~~~~~~~~~ > scipy/sparse/csgraph/_tools.c: In function > '__pyx_pf_5scipy_6sparse_7csgraph_6_tools_12construct_dist_matrix': > scipy/sparse/csgraph/_tools.c:5944:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_3 = __Pyx_PyBool_FromLong((!__pyx_t_4)); if > (unlikely(!__pyx_t_3)) __PYX_ERR(0, 405, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/csgraph/_tools.c:5944:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/csgraph/_tools.c: In function '__Pyx_PyInt_EqObjC': > scipy/sparse/csgraph/_tools.c:11883:9: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/csgraph/_tools.c:11890:13: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/csgraph/_tools.c:11892:13: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_FALSE; > ^~~~~~~~~~~~~~~ > scipy/sparse/csgraph/_tools.c:11946:17: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > default: Py_RETURN_FALSE; > ^~~~~~~ > scipy/sparse/csgraph/_tools.c:11951:17: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/csgraph/_tools.c:11953:17: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_FALSE; > ^~~~~~~~~~~~~~~ > scipy/sparse/csgraph/_tools.c:11961:17: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/csgraph/_tools.c:11963:17: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_FALSE; > ^~~~~~~~~~~~~~~ > gcc -shared > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/bzip2/1.0.6-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/zlib/1.2.11-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libreadline/7.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ncurses/6.1-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/SQLite/3.24.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GMP/6.1.2-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib > -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > build/temp.linux-x86_64-2.7/scipy/sparse/csgraph/_tools.o > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib > -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o > build/lib.linux-x86_64-2.7/scipy/sparse/csgraph/_tools.so > -Wl,--version-script=build/temp.linux-x86_64-2.7/link-version-scipy.sparse.csgraph._tools.map > building 'scipy.sparse._csparsetools' extension > compiling C sources > C compiler: gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O2 > -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > -fPIC > > compile options: > '-I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/include/python2.7 > -c' > gcc: scipy/sparse/_csparsetools.c > In file included from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1816:0, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4, > from scipy/sparse/_csparsetools.c:566: > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/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 " \ > ^~~~~~~ > scipy/sparse/_csparsetools.c: In function '__pyx_array_get_memview': > scipy/sparse/_csparsetools.c:18564:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if > (unlikely(!__pyx_t_2)) __PYX_ERR(2, 227, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/_csparsetools.c:18564:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/_csparsetools.c: In function '__pyx_memoryview_is_slice': > scipy/sparse/_csparsetools.c:20814:9: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); > if (unlikely(!__pyx_t_7)) __PYX_ERR(2, 430, __pyx_L4_error) > ^~~~~~~~~ > scipy/sparse/_csparsetools.c:20814:9: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/_csparsetools.c: In function > '__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig': > scipy/sparse/_csparsetools.c:23300:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_1 = > __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig((__pyx_v_mslice[0]), > 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 618, > __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/_csparsetools.c:23300:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/_csparsetools.c: In function > '__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig': > scipy/sparse/_csparsetools.c:23371:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_1 = > __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig((__pyx_v_mslice[0]), > 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 624, > __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/_csparsetools.c:23371:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/_csparsetools.c: In function '__pyx_memoryview_new': > scipy/sparse/_csparsetools.c:23712:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if > (unlikely(!__pyx_t_2)) __PYX_ERR(2, 653, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/_csparsetools.c:23712:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/_csparsetools.c: In function '_unellipsify': > scipy/sparse/_csparsetools.c:24216:5: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if > (unlikely(!__pyx_t_4)) __PYX_ERR(2, 693, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/_csparsetools.c:24216:5: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/_csparsetools.c: In function '__pyx_memoryview_fromslice': > scipy/sparse/_csparsetools.c:26616:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if > (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1008, __pyx_L1_error) > ^~~~~~~~~ > scipy/sparse/_csparsetools.c:26616:3: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > scipy/sparse/_csparsetools.c: In function '__Pyx_PyInt_EqObjC': > scipy/sparse/_csparsetools.c:35323:9: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/_csparsetools.c:35330:13: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/_csparsetools.c:35332:13: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_FALSE; > ^~~~~~~~~~~~~~~ > scipy/sparse/_csparsetools.c:35386:17: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > default: Py_RETURN_FALSE; > ^~~~~~~ > scipy/sparse/_csparsetools.c:35391:17: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/_csparsetools.c:35393:17: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_FALSE; > ^~~~~~~~~~~~~~~ > scipy/sparse/_csparsetools.c:35401:17: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_TRUE; > ^~~~~~~~~~~~~~ > scipy/sparse/_csparsetools.c:35403:17: warning: dereferencing type-punned > pointer will break strict-aliasing rules [-Wstrict-aliasing] > Py_RETURN_FALSE; > ^~~~~~~~~~~~~~~ > gcc -shared > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GCCcore/7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/bzip2/1.0.6-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/zlib/1.2.11-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libreadline/7.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/ncurses/6.1-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/SQLite/3.24.0-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/GMP/6.1.2-GCCcore-7.3.0/lib > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib64 > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/libffi/3.2.1-GCCcore-7.3.0/lib > -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > build/temp.linux-x86_64-2.7/scipy/sparse/_csparsetools.o > -L/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib > -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o > build/lib.linux-x86_64-2.7/scipy/sparse/_csparsetools.so > -Wl,--version-script=build/temp.linux-x86_64-2.7/link-version-scipy.sparse._csparsetools.map > building 'scipy.sparse._sparsetools' extension > compiling C++ sources > C compiler: g++ -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize > -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > -fPIC > > creating build/temp.linux-x86_64-2.7/scipy/sparse/sparsetools > compile options: '-D__STDC_FORMAT_MACROS=1 -Iscipy/sparse/sparsetools > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/include/python2.7 > -c' > g++: scipy/sparse/sparsetools/sparsetools.cxx > In file included from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1816:0, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18, > from scipy/sparse/sparsetools/sparsetools.cxx:34: > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/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 " \ > ^~~~~~~ > g++: scipy/sparse/sparsetools/csr.cxx > In file included from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1816:0, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18, > from scipy/sparse/sparsetools/sparsetools.h:5, > from scipy/sparse/sparsetools/csr.cxx:4: > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/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 " \ > ^~~~~~~ > g++: scipy/sparse/sparsetools/bsr.cxx > In file included from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1816:0, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18, > from scipy/sparse/sparsetools/sparsetools.h:5, > from scipy/sparse/sparsetools/bsr.cxx:4: > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/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 " \ > ^~~~~~~ > g++: internal compiler error: Killed (program cc1plus) > Please submit a full bug report, > with preprocessed source if appropriate. > See <https://gcc.gnu.org/bugs/> for instructions. > In file included from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1816:0, > from > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18, > from scipy/sparse/sparsetools/sparsetools.h:5, > from scipy/sparse/sparsetools/bsr.cxx:4: > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/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 " \ > ^~~~~~~ > g++: internal compiler error: Killed (program cc1plus) > Please submit a full bug report, > with preprocessed source if appropriate. > See <https://gcc.gnu.org/bugs/> for instructions. > error: Command "g++ -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize > -march=native -fno-math-errno -fPIC > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/FFTW/3.3.8-gompi-2018b/include > -fPIC -D__STDC_FORMAT_MACROS=1 -Iscipy/sparse/sparsetools > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/numpy-1.14.5-py2.7-linux-x86_64.egg/numpy/core/include > -I/sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/include/python2.7 > -c scipy/sparse/sparsetools/bsr.cxx -o > build/temp.linux-x86_64-2.7/scipy/sparse/sparsetools/bsr.o -MMD -MF > build/temp.linux-x86_64-2.7/scipy/sparse/sparsetools/bsr.o.d" failed with > exit status 4 > (at > easybuild/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_framework-3.9.0-py2.7.egg/easybuild/tools/run.py:501 > in parse_cmd_output) > == 2019-04-26 23:58:44,463 easyblock.py:3010 WARNING build failed (first > 300 chars): cmd " unset LDFLAGS && > /sNow/easybuild/centos/7.3.1611/Broadwell/software/Python/2.7.15-foss-2018b/bin/python > setup.py build --fcompiler=gnu95 " exited with exit code 1 and output: > lapack_opt_info: > lapack_mkl_info: > customize UnixCCompiler > libraries mkl_rt not found in ['/sNow/easybuild/centos/7 > Can anyone please help me with error. > > With Regards > Sona >
