scipy 0.16.0 failure log

scipy installation failure

/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
  warnings.warn(msg)
/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'setup_requires'
  warnings.warn(msg)
/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
lapack_opt_info:
openblas_lapack_info:
  libraries openblas not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64
  libraries lapack_atlas not found in /usr/local/lib64
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/lib64/atlas
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}

C compiler: gcc -pthread -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -I/usr/local/include -I/sw/include -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/usr/lib64/atlas -lptf77blas -lptcblas -latlas -o _configtest
ATLAS version 3.8.4 built by mockbuild on Fri Sep  2 01:16:43 UTC 2011:
   UNAME    : Linux x86-04.phx2.fedoraproject.org 2.6.32-131.2.1.el6.x86_64 #1 SMP Wed May 18 07:07:37 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_Core2 -DATL_CPUMHZ=2333 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 98304
   F77      : gfortran, version GNU Fortran (GCC) 4.6.1 20110804 (Red Hat 4.6.1-7)
   F77FLAGS : -O -g -Wa,--noexecstack -fPIC -m64
   SMC      : gcc, version gcc (GCC) 4.6.1 20110804 (Red Hat 4.6.1-7)
   SMCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse2 -O2 -g -Wa,--noexecstack -fPIC -m64
   SKC      : gcc, version gcc (GCC) 4.6.1 20110804 (Red Hat 4.6.1-7)
   SKCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse2 -O2 -g -Wa,--noexecstack -fPIC -m64
success!
removing: _configtest.c _configtest.o _configtest
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/lib64/atlas']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
    include_dirs = ['/usr/include']

  FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/lib64/atlas']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
    include_dirs = ['/usr/include']

Running from scipy source directory.
/usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:581: UserWarning: Specified path /usr/lib64/python2.7/site-packages/numpy/__init__.pyc/include/python2.7 is invalid.
  warnings.warn('Specified path %s is invalid.' % d)
/usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:581: UserWarning: Specified path /usr/local/include/python2.7 is invalid.
  warnings.warn('Specified path %s is invalid.' % d)
ATLAS version: 3.8.4
Splitting linalg.interpolative Fortran source files
blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

openblas_info:
  libraries openblas not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/lib64/atlas']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
    include_dirs = ['/usr/include']

  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/lib64/atlas']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
    include_dirs = ['/usr/include']

non-existing path in 'scipy/spatial': 'ckdtree.cxx'
non-existing path in 'scipy/spatial': 'ckdtree/src/ckdtree_decl.h'
non-existing path in 'scipy/spatial': 'ckdtree/src/ckdtree_exc.h'
non-existing path in 'scipy/spatial': 'ckdtree/src/ckdtree_methods.h'
non-existing path in 'scipy/spatial': 'ckdtree/src/ckdtree_utils.h'
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
building library "dfftpack" sources
building library "fftpack" sources
building library "mach" sources
building library "quadpack" sources
building library "odepack" sources
building library "dop" sources
building library "fitpack" sources
building library "fwrappers" sources
building library "odrpack" sources
building library "minpack" sources
building library "rootfind" sources
building library "superlu_src" sources
building library "arpack_scipy" sources
building library "sc_c_misc" 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.fftpack._fftpack" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
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_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.integrate.lsoda" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.integrate._dop" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' 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_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/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._fitpack" sources
building extension "scipy.interpolate.dfitpack" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/scipy/interpolate/src/dfitpack-f2pywrappers.f' to sources.
building extension "scipy.interpolate._interpolate" sources
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_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/linalg/_fblas-f2pywrappers.f' to sources.
building extension "scipy.linalg._flapack" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/linalg/_flapack-f2pywrappers.f' to sources.
building extension "scipy.linalg._cblas" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.linalg._clapack" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.linalg._flinalg" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.linalg._interpolative" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.linalg._calc_lwork" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' 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._zeros" sources
building extension "scipy.optimize._lbfgsb" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.optimize._slsqp" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.optimize._nnls" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.signal.sigtools" sources
building extension "scipy.signal._spectral" sources
building extension "scipy.signal._max_len_seq" sources
building extension "scipy.signal.spline" sources
building extension "scipy.sparse.linalg.isolve._iterative" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' 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_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/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._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.special.specfun" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' 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.stats.statlib" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.stats.vonmises_cython" sources
building extension "scipy.stats._rank" sources
building extension "scipy.stats.futil" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.stats.mvn" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/scipy/stats/mvn-f2pywrappers.f' to sources.
building extension "scipy.ndimage._nd_image" sources
building extension "scipy.ndimage._ni_label" sources
building data_files sources
build_src: building npy-pkg config files
running build_py
copying scipy/version.py -> build/lib.linux-x86_64-2.7/scipy
copying build/src.linux-x86_64-2.7/scipy/__config__.py -> build/lib.linux-x86_64-2.7/scipy
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using build_clib
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
resetting extension 'scipy.odr.__odrpack' language from 'c' to 'f77'.
extending extension 'scipy.sparse.linalg.dsolve._superlu' defined_macros with [('USE_VENDOR_BLAS', 1)]
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'scipy.cluster._vq' extension
compiling C sources
C compiler: gcc -pthread -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -I/usr/local/include -I/sw/include -fPIC

compile options: '-DATLAS_INFO="\"3.8.4\"" -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c'
gcc: scipy/cluster/_vq.c
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from scipy/cluster/_vq.c:257:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/cluster/_vq.c: In function ‘__pyx_fuse_0__pyx_f_5scipy_7cluster_3_vq_cal_M’:
scipy/cluster/_vq.c:1533:3: warning: implicit declaration of function ‘sgemm_’ [-Wimplicit-function-declaration]
scipy/cluster/_vq.c: In function ‘__pyx_fuse_1__pyx_f_5scipy_7cluster_3_vq_cal_M’:
scipy/cluster/_vq.c:1570:3: warning: implicit declaration of function ‘dgemm_’ [-Wimplicit-function-declaration]
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from scipy/cluster/_vq.c:258:
scipy/cluster/_vq.c: At top level:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
/usr/bin/gfortran -Wall -g -L/usr/local/lib -L/sw/lib build/temp.linux-x86_64-2.7/scipy/cluster/_vq.o -L/usr/lib64/atlas -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/scipy/cluster/_vq.so
/usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: error: ld returned 1 exit status
/usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: error: ld returned 1 exit status
error: Command "/usr/bin/gfortran -Wall -g -L/usr/local/lib -L/sw/lib build/temp.linux-x86_64-2.7/scipy/cluster/_vq.o -L/usr/lib64/atlas -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/scipy/cluster/_vq.so" failed with exit status 1