ubuntu@ip-10-174-23-251:~/bioinfo/scipy-0.12.0$ sudo python setup.py install
Running from scipy source directory.
blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
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 -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/usr/lib/atlas-base -lptf77blas -lptcblas -latlas -o _configtest
ATLAS version 3.8.4 built by buildd on Sat Sep 10 23:12:12 UTC 2011:
   UNAME    : Linux crested 2.6.24-29-server #1 SMP Wed Aug 10 15:58:57 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_HAMMER -DATL_CPUMHZ=1993 -DATL_USE64BITS -DATL_GAS_x8664
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 393216
   F77      : gfortran, version GNU Fortran (Ubuntu/Linaro 4.6.1-9ubuntu2) 4.6.1
   F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -Wa,--noexecstack -fPIC -m64
   SMC      : gcc, version gcc (Ubuntu/Linaro 4.6.1-9ubuntu2) 4.6.1
   SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -Wa,--noexecstack -fPIC -m64
   SKC      : gcc, version gcc (Ubuntu/Linaro 4.6.1-9ubuntu2) 4.6.1
   SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -Wa,--noexecstack -fPIC -m64
success!
removing: _configtest.c _configtest.o _configtest
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/lib/atlas-base']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
    include_dirs = ['/usr/include/atlas']

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

ATLAS version: 3.8.4
lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/lib/atlas-base/atlas', '/usr/lib/atlas-base']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
    include_dirs = ['/usr/include/atlas']

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

ATLAS version: 3.8.4
ATLAS version: 3.8.4
non-existing path in 'scipy/linalg': 'cblas.pyf.src'
non-existing path in 'scipy/linalg': 'cblas.pyf.src'
non-existing path in 'scipy/linalg': 'cblas_l1.pyf.src'
non-existing path in 'scipy/linalg': 'clapack.pyf.src'
non-existing path in 'scipy/linalg': 'clapack.pyf.src'
umfpack_info:
amd_info:
  FOUND:
    libraries = ['amd']
    library_dirs = ['/usr/lib']
    swig_opts = ['-I/usr/include/suitesparse']
    define_macros = [('SCIPY_AMD_H', None)]
    include_dirs = ['/usr/include/suitesparse']

  FOUND:
    libraries = ['umfpack', 'amd']
    library_dirs = ['/usr/lib']
    swig_opts = ['-I/usr/include/suitesparse', '-I/usr/include/suitesparse']
    define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]
    include_dirs = ['/usr/include/suitesparse']

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 "linpack_lite" sources
building library "mach" sources
building library "quadpack" sources
building library "odepack" sources
building library "dop" sources
building library "fitpack" 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_wrap" 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.interpolate.interpnd" 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.lib.blas.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/lib/blas/fblas-f2pywrappers.f' to sources.
building extension "scipy.lib.blas.cblas" sources
  adding 'scipy/lib/blas/cblas.pyf.src' to 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.lib.lapack.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.
building extension "scipy.lib.lapack.clapack" sources
  adding 'scipy/lib/lapack/clapack.pyf.src' to 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.lib.lapack.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._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
from_template:> build/src.linux-x86_64-2.7/cblas.pyf
error: cblas.pyf.src: No such file or directory