Several pybind errors trying to install scipy from source on Linux Mint 19.3
JustinS6626 opened this issue · 1 comments
I am working with the latest version of scipy on Linux Mint, and I am trying to install from source because I want to contribute to the scipy project, as I feel that there is an improvement that I can make to the zvode integrator class. However, when I attempt to install from source, I get the following error:
sudo python3.7 setup.py install
Note: if you need reliable uninstall behavior, then install
with pip instead of using setup.py install:
pip install .(from a git repo or downloaded source
release)pip install scipy(last SciPy release on PyPI)
Cythonizing sources
Running scipy/special/_generate_pyx.py
Running scipy/linalg/_generate_pyx.py
scipy/linalg/_generate_pyx.py: all files up-to-date
scipy/special/_generate_pyx.py: all files up-to-date
scipy/spatial/ckdtree.pyx has not changed
scipy/fftpack/convolve.pyx has not changed
scipy/stats/_stats.pyx has not changed
scipy/special/cython_special.pyx has not changed
scipy/special/_ufuncs.pyx has not changed
scipy/spatial/_hausdorff.pyx has not changed
scipy/special/_comb.pyx has not changed
scipy/special/_test_round.pyx has not changed
scipy/special/_ellip_harm_2.pyx has not changed
scipy/io/matlab/mio5_utils.pyx has not changed
scipy/io/matlab/streams.pyx has not changed
scipy/io/matlab/mio_utils.pyx has not changed
scipy/interpolate/_bspl.pyx has not changed
scipy/interpolate/_ppoly.pyx has not changed
scipy/special/_ufuncs_cxx.pyx has not changed
scipy/sparse/_csparsetools.pyx.in has not changed
scipy/spatial/_voronoi.pyx has not changed
scipy/sparse/csgraph/_min_spanning_tree.pyx has not changed
scipy/spatial/qhull.pyx has not changed
scipy/sparse/csgraph/_matching.pyx has not changed
scipy/interpolate/interpnd.pyx has not changed
scipy/sparse/csgraph/_reordering.pyx has not changed
scipy/sparse/csgraph/_flow.pyx has not changed
scipy/signal/_max_len_seq_inner.pyx has not changed
scipy/signal/_sosfilt.pyx has not changed
scipy/signal/_spectral.pyx has not changed
scipy/signal/_upfirdn_apply.pyx has not changed
scipy/signal/_peak_finding_utils.pyx has not changed
scipy/optimize/_group_columns.pyx has not changed
scipy/optimize/_bglu_dense.pyx has not changed
scipy/optimize/cython_optimize/_zeros.pyx.in has not changed
scipy/optimize/_trlib/_trlib.pyx has not changed
scipy/sparse/csgraph/_traversal.pyx has not changed
scipy/sparse/csgraph/_tools.pyx has not changed
scipy/sparse/csgraph/_shortest_path.pyx has not changed
scipy/cluster/_vq.pyx has not changed
scipy/linalg/_solve_toeplitz.pyx has not changed
scipy/cluster/_hierarchy.pyx has not changed
scipy/linalg/_decomp_update.pyx.in has not changed
scipy/linalg/cython_lapack.pyx has not changed
scipy/linalg/cython_blas.pyx has not changed
scipy/ndimage/src/_cytest.pyx has not changed
scipy/_lib/_ccallback_c.pyx has not changed
scipy/_lib/messagestream.pyx has not changed
scipy/optimize/_lsq/givens_elimination.pyx has not changed
scipy/cluster/_optimal_leaf_ordering.pyx has not changed
scipy/ndimage/src/_ni_label.pyx has not changed
Running from SciPy source directory.
lapack_opt_info:
lapack_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_lapack_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_clapack_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
flame_info:
customize UnixCCompiler
libraries flame not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries satlas,satlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
accelerate_info:
NOT AVAILABLE
lapack_info:
customize UnixCCompiler
customize UnixCCompiler
FOUND:
libraries = ['lapack', 'lapack']
library_dirs = ['/usr/lib/x86_64-linux-gnu']
language = f77
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
blis_info:
customize UnixCCompiler
libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries tatlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_blas_info:
customize UnixCCompiler
libraries satlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_blas_info:
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/usr/local/lib/python3.7/dist-packages/numpy/distutils/system_info.py:690: UserWarning:
Optimized (vendor) Blas libraries are not found.
Falls back to netlib Blas library which has worse performance.
A better performance should be easily gained by switching
Blas library.
self.calc_info()
blas_info:
customize UnixCCompiler
customize UnixCCompiler
C compiler: x86_64-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 /tmp/tmpzx8uau81/tmp
creating /tmp/tmpzx8uau81/tmp/tmpzx8uau81
compile options: '-I/usr/local/include -I/usr/include -c'
x86_64-linux-gnu-gcc: /tmp/tmpzx8uau81/source.c
x86_64-linux-gnu-gcc -pthread /tmp/tmpzx8uau81/tmp/tmpzx8uau81/source.o -lblas -o /tmp/tmpzx8uau81/a.out
customize UnixCCompiler
FOUND:
libraries = ['blas', 'blas']
library_dirs = ['/usr/lib/x86_64-linux-gnu']
include_dirs = ['/usr/local/include', '/usr/include']
language = c
define_macros = [('HAVE_CBLAS', None)]
FOUND:
define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
libraries = ['blas', 'blas']
library_dirs = ['/usr/lib/x86_64-linux-gnu']
include_dirs = ['/usr/local/include', '/usr/include']
language = c
FOUND:
libraries = ['lapack', 'lapack', 'blas', 'blas']
library_dirs = ['/usr/lib/x86_64-linux-gnu']
language = c
define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
include_dirs = ['/usr/local/include', '/usr/include']
non-existing path in 'scipy/fft/_pocketfft': '/home/justin/.local/include/python3.7m'
non-existing path in 'scipy/fft/_pocketfft': '/usr/local/include/python3.7'
non-existing path in 'scipy/interpolate': 'src/multipack.h'
/usr/local/lib/python3.7/dist-packages/numpy/distutils/system_info.py:782: UserWarning: Specified path /usr/local/include/python3.7m is invalid.
return self.get_paths(self.section, key)
non-existing path in 'scipy/signal/windows': 'tests'
[makenpz] scipy/special/tests/data/boost.npz is already up to date
[makenpz] scipy/special/tests/data/gsl.npz is already up to date
[makenpz] scipy/special/tests/data/local.npz is already up to date
running install
running bdist_egg
running egg_info
running build_src
build_src
building py_modules sources
building library "mach" sources
building library "quadpack" sources
building library "lsoda" sources
building library "vode" sources
building library "dop" sources
building library "fitpack" sources
building library "fwrappers" sources
building library "odrpack" sources
building library "minpack" sources
building library "rectangular_lsap" sources
building library "rootfind" sources
building library "superlu_src" sources
building library "arpack_scipy" sources
building library "sc_cephes" sources
building library "sc_mach" sources
building library "sc_amos" sources
building library "sc_cdf" sources
building library "sc_specfun" sources
building library "statlib" sources
building extension "scipy.cluster._vq" sources
building extension "scipy.cluster._hierarchy" sources
building extension "scipy.cluster._optimal_leaf_ordering" sources
building extension "scipy.fft._pocketfft.pypocketfft" sources
building extension "scipy.fftpack.convolve" sources
building extension "scipy.integrate._quadpack" sources
building extension "scipy.integrate._odepack" sources
building extension "scipy.integrate.vode" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/integrate/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/integrate' to include_dirs.
building extension "scipy.integrate.lsoda" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/integrate/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/integrate' to include_dirs.
building extension "scipy.integrate._dop" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/integrate/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/integrate' to include_dirs.
building extension "scipy.integrate._test_multivariate" sources
building extension "scipy.integrate._test_odeint_banded" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/integrate/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/integrate' to include_dirs.
adding 'build/src.linux-x86_64-3.7/scipy/integrate/_test_odeint_banded-f2pywrappers.f' to sources.
building extension "scipy.interpolate.interpnd" sources
building extension "scipy.interpolate._ppoly" sources
building extension "scipy.interpolate._bspl" sources
building extension "scipy.interpolate._fitpack" sources
building extension "scipy.interpolate.dfitpack" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/interpolate/src/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/interpolate/src' to include_dirs.
adding 'build/src.linux-x86_64-3.7/scipy/interpolate/src/dfitpack-f2pywrappers.f' to sources.
building extension "scipy.io._test_fortran" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/io/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/io' to include_dirs.
building extension "scipy.io.matlab.streams" sources
building extension "scipy.io.matlab.mio_utils" sources
building extension "scipy.io.matlab.mio5_utils" sources
building extension "scipy.linalg._fblas" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg' to include_dirs.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg/_fblas-f2pywrappers.f' to sources.
building extension "scipy.linalg._flapack" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg' to include_dirs.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg/_flapack-f2pywrappers.f' to sources.
building extension "scipy.linalg._flinalg" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg' to include_dirs.
building extension "scipy.linalg._interpolative" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg' to include_dirs.
building extension "scipy.linalg._solve_toeplitz" sources
building extension "scipy.linalg.cython_blas" sources
building extension "scipy.linalg.cython_lapack" sources
building extension "scipy.linalg._decomp_update" sources
building extension "scipy.odr.__odrpack" sources
building extension "scipy.optimize._minpack" sources
building extension "scipy.optimize._lsap_module" sources
building extension "scipy.optimize._zeros" sources
building extension "scipy.optimize._lbfgsb" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/optimize/lbfgsb_src/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/optimize/lbfgsb_src' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/optimize/cobyla/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/optimize/cobyla' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/optimize/minpack2/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/optimize/minpack2' to include_dirs.
building extension "scipy.optimize._slsqp" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/optimize/slsqp/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/optimize/slsqp' to include_dirs.
building extension "scipy.optimize._nnls" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/optimize/nnls/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/optimize/nnls' to include_dirs.
building extension "scipy.optimize._group_columns" sources
building extension "scipy.optimize._bglu_dense" sources
building extension "scipy.optimize._lsq.givens_elimination" sources
building extension "scipy.optimize._trlib._trlib" sources
building extension "scipy.optimize.cython_optimize._zeros" sources
building extension "scipy.signal.sigtools" sources
building extension "scipy.signal._spectral" sources
building extension "scipy.signal._max_len_seq_inner" sources
building extension "scipy.signal._peak_finding_utils" sources
building extension "scipy.signal._sosfilt" sources
building extension "scipy.signal._upfirdn_apply" sources
building extension "scipy.signal.spline" sources
building extension "scipy.sparse.linalg.isolve._iterative" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/sparse/linalg/isolve/iterative/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/sparse/linalg/isolve/iterative' to include_dirs.
building extension "scipy.sparse.linalg.dsolve._superlu" sources
building extension "scipy.sparse.linalg.eigen.arpack._arpack" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/sparse/linalg/eigen/arpack/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/sparse/linalg/eigen/arpack' to include_dirs.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/sparse/linalg/eigen/arpack/_arpack-f2pywrappers.f' to sources.
building extension "scipy.sparse.csgraph._shortest_path" sources
building extension "scipy.sparse.csgraph._traversal" sources
building extension "scipy.sparse.csgraph._min_spanning_tree" sources
building extension "scipy.sparse.csgraph._matching" sources
building extension "scipy.sparse.csgraph._flow" sources
building extension "scipy.sparse.csgraph._reordering" sources
building extension "scipy.sparse.csgraph._tools" sources
building extension "scipy.sparse._csparsetools" sources
building extension "scipy.sparse._sparsetools" sources
[generate_sparsetools] 'scipy/sparse/sparsetools/bsr_impl.h' already up-to-date
[generate_sparsetools] 'scipy/sparse/sparsetools/csr_impl.h' already up-to-date
[generate_sparsetools] 'scipy/sparse/sparsetools/csc_impl.h' already up-to-date
[generate_sparsetools] 'scipy/sparse/sparsetools/other_impl.h' already up-to-date
[generate_sparsetools] 'scipy/sparse/sparsetools/sparsetools_impl.h' already up-to-date
building extension "scipy.spatial.qhull" sources
building extension "scipy.spatial.ckdtree" sources
building extension "scipy.spatial._distance_wrap" sources
building extension "scipy.spatial._voronoi" sources
building extension "scipy.spatial._hausdorff" sources
building extension "scipy.special.specfun" sources
f2py options: ['--no-wrap-functions']
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/special/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/special' to include_dirs.
building extension "scipy.special._ufuncs" sources
building extension "scipy.special._ufuncs_cxx" sources
building extension "scipy.special._ellip_harm_2" sources
building extension "scipy.special.cython_special" sources
building extension "scipy.special._comb" sources
building extension "scipy.special._test_round" sources
building extension "scipy.stats.statlib" sources
f2py options: ['--no-wrap-functions']
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/stats/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/stats' to include_dirs.
building extension "scipy.stats._stats" sources
building extension "scipy.stats.mvn" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/stats/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/stats' to include_dirs.
adding 'build/src.linux-x86_64-3.7/scipy/stats/mvn-f2pywrappers.f' to sources.
building extension "scipy.ndimage._nd_image" sources
building extension "scipy.ndimage._ni_label" sources
building extension "scipy.ndimage._ctest" sources
building extension "scipy.ndimage._ctest_oldapi" sources
building extension "scipy.ndimage._cytest" sources
building extension "scipy._lib._ccallback_c" sources
building extension "scipy._lib._test_ccallback" sources
building extension "scipy._lib._fpumode" sources
building extension "scipy._lib.messagestream" sources
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using config
C compiler: x86_64-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/include/python3.7m -c'
x86_64-linux-gnu-gcc: _configtest.c
x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest.o.d _configtest
building extension "scipy._lib._uarray._uarray" sources
building data_files sources
build_src: building npy-pkg config files
writing scipy.egg-info/PKG-INFO
writing dependency_links to scipy.egg-info/dependency_links.txt
writing top-level names to scipy.egg-info/top_level.txt
reading manifest file 'scipy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching 'subr.f' found under directory 'scipy/linalg/src/id_dist/src'
no previously-included directories found matching 'benchmarks/env'
no previously-included directories found matching 'benchmarks/results'
no previously-included directories found matching 'benchmarks/html'
no previously-included directories found matching 'benchmarks/scipy'
no previously-included directories found matching 'doc/build'
no previously-included directories found matching 'doc/source/generated'
warning: no previously-included files matching '~' found anywhere in distribution
warning: no previously-included files matching '.bak' found anywhere in distribution
warning: no previously-included files matching '.swp' found anywhere in distribution
warning: no previously-included files matching '.pyo' found anywhere in distribution
writing manifest file 'scipy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using build_clib
building 'sc_cephes' library
compiling C sources
C compiler: x86_64-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/home/justin/scipy/scipy/special -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -Iscipy/_lib -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c'
running install_lib
running build_py
copying scipy/version.py -> build/lib.linux-x86_64-3.7/scipy
copying build/src.linux-x86_64-3.7/scipy/config.py -> build/lib.linux-x86_64-3.7/scipy
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
resetting extension 'scipy.integrate._quadpack' language from 'c' to 'f77'.
resetting extension 'scipy.integrate._odepack' language from 'c' to 'f77'.
resetting extension 'scipy.integrate.vode' language from 'c' to 'f77'.
resetting extension 'scipy.integrate.lsoda' language from 'c' to 'f77'.
resetting extension 'scipy.integrate._test_odeint_banded' language from 'c' to 'f77'.
resetting extension 'scipy.linalg._fblas' language from 'c' to 'f77'.
resetting extension 'scipy.linalg._flapack' language from 'c' to 'f77'.
resetting extension 'scipy.linalg._flinalg' language from 'c' to 'f77'.
resetting extension 'scipy.linalg._interpolative' language from 'c' to 'f77'.
resetting extension 'scipy.linalg.cython_blas' language from 'c' to 'f77'.
resetting extension 'scipy.linalg.cython_lapack' language from 'c' to 'f77'.
resetting extension 'scipy.odr.__odrpack' language from 'c' to 'f77'.
resetting extension 'scipy.optimize._lbfgsb' language from 'c' to 'f77'.
resetting extension 'scipy.sparse.linalg.isolve._iterative' language from 'c' to 'f77'.
extending extension 'scipy.sparse.linalg.dsolve._superlu' defined_macros with [('USE_VENDOR_BLAS', 1)]
resetting extension 'scipy.sparse.linalg.eigen.arpack._arpack' language from 'c' to 'f77'.
resetting extension 'scipy.special._ufuncs' language from 'c' to 'f77'.
resetting extension 'scipy.special.cython_special' language from 'c' to 'f77'.
customize UnixCCompiler
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
C compiler: x86_64-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 /tmp/tmp0jf12nzs/tmp
creating /tmp/tmp0jf12nzs/tmp/tmp0jf12nzs
compile options: '-I/usr/include/python3.7m -c'
extra options: '-std=c++14'
x86_64-linux-gnu-g++: /tmp/tmp0jf12nzs/main.c
C compiler: x86_64-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 /tmp/tmpzk513g1j/tmp
creating /tmp/tmpzk513g1j/tmp/tmpzk513g1j
compile options: '-I/usr/include/python3.7m -c'
extra options: '-std=c++14 -fvisibility=hidden'
x86_64-linux-gnu-g++: /tmp/tmpzk513g1j/main.c
C compiler: x86_64-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 /tmp/tmp_f0bta4x/tmp
creating /tmp/tmp_f0bta4x/tmp/tmp_f0bta4x
compile options: '-I/usr/include/python3.7m -c'
x86_64-linux-gnu-g++: /tmp/tmp_f0bta4x/main.c
building 'scipy.fft._pocketfft.pypocketfft' extension
compiling C++ sources
C compiler: x86_64-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: '-DPOCKETFFT_PTHREADS -I/home/justin/.local/include/python3.7m -I/usr/local/include/python3.7 -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c'
extra options: '-std=c++14 -fvisibility=hidden'
x86_64-linux-gnu-g++: scipy/fft/_pocketfft/pypocketfft.cxx
scipy/fft/_pocketfft/pypocketfft.cxx: In function ‘pocketfft::detail::shape_t {anonymous}::makeaxes(const pybind11::array&, const pybind11::object&)’:
scipy/fft/_pocketfft/pypocketfft.cxx:74:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ((sz>=ndim) || (sz<0))
~~^~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx: At global scope:
scipy/fft/_pocketfft/pypocketfft.cxx:707:16: error: expected constructor, destructor, or type conversion before ‘(’ token
PYBIND11_MODULE(pypocketfft, m)
^
scipy/fft/_pocketfft/pypocketfft.cxx: In instantiation of ‘pybind11::array_t {anonymous}::prepare_output(pybind11::object&, pocketfft::detail::shape_t&) [with T = std::complex; pocketfft::detail::shape_t = std::vector]’:
scipy/fft/_pocketfft/pypocketfft.cxx:122:40: required from ‘pybind11::array {anonymous}::c2c_internal(const pybind11::array&, const pybind11::object&, bool, int, pybind11::object&, size_t) [with T = double; size_t = long unsigned int]’
scipy/fft/_pocketfft/pypocketfft.cxx:168:5: required from here
scipy/fft/pocketfft/pypocketfft.cxx:111:12: error: ‘class pybind11::array_t<std::complex >’ has no member named ‘is’
if (!tmp.is(out)) // a new object was created during casting
~~~~^~
scipy/fft/_pocketfft/pypocketfft.cxx: In instantiation of ‘pybind11::array_t {anonymous}::prepare_output(pybind11::object&, pocketfft::detail::shape_t&) [with T = std::complex; pocketfft::detail::shape_t = std::vector]’:
scipy/fft/_pocketfft/pypocketfft.cxx:122:40: required from ‘pybind11::array {anonymous}::c2c_internal(const pybind11::array&, const pybind11::object&, bool, int, pybind11::object&, size_t) [with T = float; size_t = long unsigned int]’
scipy/fft/_pocketfft/pypocketfft.cxx:168:5: required from here
scipy/fft/_pocketfft/pypocketfft.cxx:111:12: error: ‘class pybind11::array_t<std::complex >’ has no member named ‘is’
scipy/fft/_pocketfft/pypocketfft.cxx: In instantiation of ‘pybind11::array_t {anonymous}::prepare_output(pybind11::object&, pocketfft::detail::shape_t&) [with T = std::complex; pocketfft::detail::shape_t = std::vector]’:
scipy/fft/_pocketfft/pypocketfft.cxx:122:40: required from ‘pybind11::array {anonymous}::c2c_internal(const pybind11::array&, const pybind11::object&, bool, int, pybind11::object&, size_t) [with T = long double; size_t = long unsigned int]’
scipy/fft/_pocketfft/pypocketfft.cxx:168:5: required from here
scipy/fft/_pocketfft/pypocketfft.cxx:111:12: error: ‘class pybind11::array_t<std::complex >’ has no member named ‘is’
scipy/fft/_pocketfft/pypocketfft.cxx: In instantiation of ‘pybind11::array_t {anonymous}::prepare_output(pybind11::object&, pocketfft::detail::shape_t&) [with T = double; pocketfft::detail::shape_t = std::vector]’:
scipy/fft/_pocketfft/pypocketfft.cxx:209:36: required from ‘pybind11::array {anonymous}::r2r_fftpack_internal(const pybind11::array&, const pybind11::object&, bool, bool, int, pybind11::object&, size_t) [with T = double; size_t = long unsigned int]’
scipy/fft/_pocketfft/pypocketfft.cxx:227:3: required from here
scipy/fft/_pocketfft/pypocketfft.cxx:111:12: error: ‘class pybind11::array_t’ has no member named ‘is’
scipy/fft/_pocketfft/pypocketfft.cxx: In instantiation of ‘pybind11::array_t {anonymous}::prepare_output(pybind11::object&, pocketfft::detail::shape_t&) [with T = float; pocketfft::detail::shape_t = std::vector]’:
scipy/fft/_pocketfft/pypocketfft.cxx:209:36: required from ‘pybind11::array {anonymous}::r2r_fftpack_internal(const pybind11::array&, const pybind11::object&, bool, bool, int, pybind11::object&, size_t) [with T = float; size_t = long unsigned int]’
scipy/fft/_pocketfft/pypocketfft.cxx:227:3: required from here
scipy/fft/_pocketfft/pypocketfft.cxx:111:12: error: ‘class pybind11::array_t’ has no member named ‘is’
scipy/fft/_pocketfft/pypocketfft.cxx: In instantiation of ‘pybind11::array_t {anonymous}::prepare_output(pybind11::object&, pocketfft::detail::shape_t&) [with T = long double; pocketfft::detail::shape_t = std::vector]’:
scipy/fft/_pocketfft/pypocketfft.cxx:209:36: required from ‘pybind11::array {anonymous}::r2r_fftpack_internal(const pybind11::array&, const pybind11::object&, bool, bool, int, pybind11::object&, size_t) [with T = long double; size_t = long unsigned int]’
scipy/fft/_pocketfft/pypocketfft.cxx:227:3: required from here
scipy/fft/_pocketfft/pypocketfft.cxx:111:12: error: ‘class pybind11::array_t’ has no member named ‘is’
In file included from scipy/fft/_pocketfft/pypocketfft.cxx:16:0:
/usr/include/pybind11/numpy.h: In instantiation of ‘static pybind11::dtype pybind11::dtype::of() [with T = std::complex]’:
/usr/include/pybind11/numpy.h:636:92: required from ‘static bool pybind11::array_t<T, ExtraFlags>::_check(pybind11::handle) [with T = std::complex; int ExtraFlags = 16]’
/usr/include/pybind11/pytypes.h:160:47: required from ‘bool pybind11::isinstance(pybind11::handle) [with T = pybind11::array_t<std::complex >; typename std::enable_if<std::is_base_of<pybind11::object, T>::value, int>::type = 0]’
scipy/fft/_pocketfft/pypocketfft.cxx:168:5: required from here
/usr/include/pybind11/numpy.h:260:86: error: ‘dtype’ is not a member of ‘pybind11::detail::npy_format_descriptor<std::complex, void>’
eturn detail::npy_format_descriptor<typename std::remove_cv::type>::dtype();
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
scipy/fft/_pocketfft/pypocketfft.cxx:689:14: warning: ‘{anonymous}::good_size_DS’ defined but not used [-Wunused-variable]
const char * good_size_DS = R"""(Returns a good length to pad an FFT to.
^~~~~~~~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx:651:13: warning: ‘{anonymous}::dst_DS’ defined but not used [-Wunused-variable]
const char *dst_DS = R"""(Performs a discrete sine transform.
^~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx:612:13: warning: ‘{anonymous}::dct_DS’ defined but not used [-Wunused-variable]
const char *dct_DS = R"""(Performs a discrete cosine transform.
^~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx:580:13: warning: ‘{anonymous}::genuine_hartley_DS’ defined but not used [-Wunused-variable]
const char *genuine_hartley_DS = R"""(Performs a full Hartley transform.
^~~~~~~~~~~~~~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx:549:13: warning: ‘{anonymous}::separable_hartley_DS’ defined but not used [-Wunused-variable]
const char *separable_hartley_DS = R"""(Performs a separable Hartley transform.
^~~~~~~~~~~~~~~~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx:515:13: warning: ‘{anonymous}::r2r_fftpack_DS’ defined but not used [-Wunused-variable]
const char *r2r_fftpack_DS = R"""(Performs a real-valued FFT using the FFTPACK storage scheme.
^~~~~~~~~~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx:480:13: warning: ‘{anonymous}::c2r_DS’ defined but not used [-Wunused-variable]
const char *c2r_DS = R"""(Performs an FFT whose output is strictly real.
^~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx:447:13: warning: ‘{anonymous}::r2c_DS’ defined but not used [-Wunused-variable]
const char r2c_DS = R"""(Performs an FFT whose input is strictly real.
^~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx:416:13: warning: ‘{anonymous}::c2c_DS’ defined but not used [-Wunused-variable]
const char c2c_DS = R"""(Performs a complex FFT.
^~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx:404:13: warning: ‘{anonymous}::pypocketfft_DS’ defined but not used [-Wunused-variable]
const char pypocketfft_DS = R"""(Fast Fourier and Hartley transforms.
^~~~~~~~~~~~~~
scipy/fft/_pocketfft/pypocketfft.cxx:380:13: warning: ‘PyObject {anonymous}::good_size(PyObject, PyObject)’ defined but not used [-Wunused-function]
PyObject * good_size(PyObject * self, PyObject * args)
^~~~~~~~~
scipy/fft/pocketfft/pypocketfft.cxx:373:11: warning: ‘pybind11::array {anonymous}::genuine_hartley(const pybind11::array&, const pybind11::object&, int, pybind11::object&, size_t)’ defined but not used [-Wunused-function]
py::array genuine_hartley(const py::array &in, const py::object &axes,
^~~~~~~~~~~~~~~
scipy/fft/pocketfft/pypocketfft.cxx:342:11: warning: ‘pybind11::array {anonymous}::separable_hartley(const pybind11::array&, const pybind11::object&, int, pybind11::object&, size_t)’ defined but not used [-Wunused-function]
py::array separable_hartley(const py::array &in, const py::object &axes,
^~~~~~~~~~~~~~~~~
scipy/fft/pocketfft/pypocketfft.cxx:316:11: warning: ‘pybind11::array {anonymous}::c2r(const pybind11::array&, const pybind11::object&, size_t, bool, int, pybind11::object&, size_t)’ defined but not used [-Wunused-function]
py::array c2r(const py::array &in, const py::object &axes, size_t lastsize,
^~~
scipy/fft/pocketfft/pypocketfft.cxx:283:11: warning: ‘pybind11::array {anonymous}::dst(const pybind11::array&, int, const pybind11::object&, int, pybind11::object&, size_t)’ defined but not used [-Wunused-function]
py::array dst(const py::array &in, int type, const py::object &axes,
^~~
scipy/fft/pocketfft/pypocketfft.cxx:253:11: warning: ‘pybind11::array {anonymous}::dct(const pybind11::array&, int, const pybind11::object&, int, pybind11::object&, size_t)’ defined but not used [-Wunused-function]
py::array dct(const py::array &in, int type, const py::object &axes,
^~~
scipy/fft/pocketfft/pypocketfft.cxx:223:11: warning: ‘pybind11::array {anonymous}::r2r_fftpack(const pybind11::array&, const pybind11::object&, bool, bool, int, pybind11::object&, size_t)’ defined but not used [-Wunused-function]
py::array r2r_fftpack(const py::array &in, const py::object &axes,
^~~~~~~~~~~
scipy/fft/pocketfft/pypocketfft.cxx:164:11: warning: ‘pybind11::array {anonymous}::c2c(const pybind11::array&, const pybind11::object&, bool, int, pybind11::object&, size_t)’ defined but not used [-Wunused-function]
py::array c2c(const py::array &a, const py::object &axes, bool forward,
^~~
error: Command "x86_64-linux-gnu-g++ -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPOCKETFFT_PTHREADS -I/home/justin/.local/include/python3.7m -I/usr/local/include/python3.7 -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c scipy/fft/_pocketfft/pypocketfft.cxx -o build/temp.linux-x86_64-3.7/scipy/fft/_pocketfft/pypocketfft.o -MMD -MF build/temp.linux-x86_64-3.7/scipy/fft/_pocketfft/pypocketfft.o.d -std=c++14 -fvisibility=hidden" failed with exit status 1
justin@justin-System-Product-Name:~/scipy$
Is this simply a function of having the wrong version of pybind, or is this an error in the most recent development release of the source code?
This should be fine, reopen (probably in the main repo) if not!