fonnesbeck
6/5/2016 - 8:11 PM
scipybuild.txt
fonnescj on Marichal.local in ~
$ pip install -U git+https://github.com/numpy/numpy.git
Collecting git+https://github.com/numpy/numpy.git
Cloning https://github.com/numpy/numpy.git to /var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-ko75h2ub-build
Installing collected packages: numpy
Found existing installation: numpy 1.12.0.dev0+cc51ba8
Uninstalling numpy-1.12.0.dev0+cc51ba8:
Successfully uninstalled numpy-1.12.0.dev0+cc51ba8
Running setup.py install for numpy ... done
Successfully installed numpy-1.12.0.dev0+f65b233
fonnescj on Marichal.local in ~
$ pip install -U git+https://github.com/scipy/scipy.git
Collecting git+https://github.com/scipy/scipy.git
Cloning https://github.com/scipy/scipy.git to /var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build
Installing collected packages: scipy
Found existing installation: scipy 0.17.0
Uninstalling scipy-0.17.0:
Successfully uninstalled scipy-0.17.0
Running setup.py install for scipy ... error
Complete output from command /Users/fonnescj/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-x0vdohp2-record/install-record.txt --single-version-externally-managed --compile:
Cythonizing sources
Processing scipy/cluster/_hierarchy.pyx
Processing scipy/cluster/_vq.pyx
Processing scipy/interpolate/_ppoly.pyx
Processing scipy/interpolate/interpnd.pyx
Processing scipy/io/matlab/mio5_utils.pyx
Processing scipy/io/matlab/mio_utils.pyx
Processing scipy/io/matlab/streams.pyx
Processing scipy/linalg/_decomp_update.pyx.in
Processing scipy/linalg/_solve_toeplitz.pyx
Processing scipy/linalg/cython_blas.pyx
Processing scipy/linalg/cython_lapack.pyx
Processing scipy/ndimage/src/_ni_label.pyx
Processing scipy/optimize/_group_columns.pyx
Processing scipy/optimize/_lsq/givens_elimination.pyx
Processing scipy/signal/_max_len_seq_inner.pyx
Processing scipy/signal/_spectral.pyx
Processing scipy/signal/_upfirdn_apply.pyx
Processing scipy/sparse/_csparsetools.pyx.in
Processing scipy/sparse/csgraph/_min_spanning_tree.pyx
Processing scipy/sparse/csgraph/_reordering.pyx
Processing scipy/sparse/csgraph/_shortest_path.pyx
Processing scipy/sparse/csgraph/_tools.pyx
Processing scipy/sparse/csgraph/_traversal.pyx
Processing scipy/spatial/ckdtree.pyx
Processing scipy/spatial/qhull.pyx
Processing scipy/special/_comb.pyx
Processing scipy/special/_ellip_harm_2.pyx
Processing scipy/special/_ufuncs.pyx
Processing scipy/special/_ufuncs_cxx.pyx
Processing scipy/stats/_stats.pyx
lapack_opt_info:
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in ['/Users/fonnescj/anaconda3/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
NOT AVAILABLE
openblas_lapack_info:
libraries openblas not found in ['/Users/fonnescj/anaconda3/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas,tatlas not found in /Users/fonnescj/anaconda3/lib
libraries lapack_atlas not found in /Users/fonnescj/anaconda3/lib
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
libraries satlas,satlas not found in /Users/fonnescj/anaconda3/lib
libraries lapack_atlas not found in /Users/fonnescj/anaconda3/lib
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in /Users/fonnescj/anaconda3/lib
libraries lapack_atlas not found in /Users/fonnescj/anaconda3/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
libraries f77blas,cblas,atlas not found in /Users/fonnescj/anaconda3/lib
libraries lapack_atlas not found in /Users/fonnescj/anaconda3/lib
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries f77blas,cblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
FOUND:
extra_compile_args = ['-msse3']
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
Running from scipy source directory.
Splitting linalg.interpolative Fortran source files
/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/system_info.py:645: UserWarning: Specified path /usr/local/include/python3.5m is invalid.
warnings.warn('Specified path %s is invalid.' % d)
/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/system_info.py:645: UserWarning: Specified path /usr/include/python3.5m is invalid.
warnings.warn('Specified path %s is invalid.' % d)
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in ['/Users/fonnescj/anaconda3/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
blis_info:
libraries blis not found in ['/Users/fonnescj/anaconda3/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
openblas_info:
libraries openblas not found in ['/Users/fonnescj/anaconda3/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas not found in ['/Users/fonnescj/anaconda3/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_3_10_blas_info:
libraries satlas not found in ['/Users/fonnescj/anaconda3/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in ['/Users/fonnescj/anaconda3/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in ['/Users/fonnescj/anaconda3/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
FOUND:
extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
non-existing path in '/private/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/scipy/sparse': 'sparsetools/sparsetools_impl.h'
non-existing path in '/private/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/scipy/sparse': 'sparsetools/bsr_impl.h'
non-existing path in '/private/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/scipy/sparse': 'sparsetools/csc_impl.h'
non-existing path in '/private/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/scipy/sparse': 'sparsetools/csr_impl.h'
non-existing path in '/private/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/scipy/sparse': 'sparsetools/other_impl.h'
Traceback (most recent call last):
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/npy_pkg_config.py", line 373, in read_config
return _CACHE[pkgname]
KeyError: 'npymath'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/setup.py", line 265, in <module>
setup_package()
File "/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/setup.py", line 262, in setup_package
setup(**metadata)
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/core.py", line 135, in setup
config = configuration()
File "/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/setup.py", line 182, in configuration
config.add_subpackage('scipy')
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
caller_level = 2)
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
caller_level = caller_level + 1)
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/setup.py", line 22, in configuration
config.add_subpackage('spatial')
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
caller_level = 2)
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
caller_level = caller_level + 1)
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "/private/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/scipy/spatial/setup.py", line 80, in configuration
extra_info=get_misc_info("npymath"))
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 2171, in get_info
pkg_info = get_pkg_info(pkgname, dirs)
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 2123, in get_pkg_info
return read_config(pkgname, dirs)
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/npy_pkg_config.py", line 375, in read_config
v = _read_config_imp(pkg_to_filename(pkgname), dirs)
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/npy_pkg_config.py", line 311, in _read_config_imp
meta, vars, sections, reqs = _read_config(filenames)
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/npy_pkg_config.py", line 294, in _read_config
meta, vars, sections, reqs = parse_config(f, dirs)
File "/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/distutils/npy_pkg_config.py", line 266, in parse_config
raise PkgNotFound("Could not find file(s) %s" % str(filenames))
numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/Users/fonnescj/anaconda3/lib/python3.5/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini']
----------------------------------------
Rolling back uninstall of scipy
Command "/Users/fonnescj/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-x0vdohp2-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/pip-yb2g0d12-build/