Mailman 3 yet another scipy Install problem - NumPy-Discussion

10 Jun 2010

      Dear All ..
I tried to install numpy and scipy ... basicaly I want to use OMPC

I Installed SuiteSparse :
---START---
bino@bino:~/mydoc/buku/arduino/scipy/scipy-0.8.0b1$ ls -l 
/usr/local/lib/lib*a
-rw-r--r-- 1 root root   51860 2010-06-10 10:59 
/usr/local/lib/libamd.2.2.1.a
lrwxrwxrwx 1 root root      14 2010-06-10 10:59 /usr/local/lib/libamd.a 
-> libamd.2.2.1.a
-rw-r--r-- 1 root root    9466 2010-06-10 10:59 
/usr/local/lib/libbtf.1.1.1.a
lrwxrwxrwx 1 root root      14 2010-06-10 10:59 /usr/local/lib/libbtf.a 
-> libbtf.1.1.1.a
-rw-r--r-- 1 root root   53848 2010-06-10 10:59 
/usr/local/lib/libcamd.2.2.1.a
lrwxrwxrwx 1 root root      15 2010-06-10 10:59 /usr/local/lib/libcamd.a 
-> libcamd.2.2.1.a
-rw-r--r-- 1 root root   38264 2010-06-10 10:59 
/usr/local/lib/libccolamd.2.7.2.a
lrwxrwxrwx 1 root root      18 2010-06-10 10:59 
/usr/local/lib/libccolamd.a -> libccolamd.2.7.2.a
-rw-r--r-- 1 root root 1032104 2010-06-10 10:59 
/usr/local/lib/libcholmod.1.7.2.a
lrwxrwxrwx 1 root root      18 2010-06-10 10:59 
/usr/local/lib/libcholmod.a -> libcholmod.1.7.2.a
-rw-r--r-- 1 root root   26072 2010-06-10 10:59 
/usr/local/lib/libcolamd.2.7.2.a
lrwxrwxrwx 1 root root      17 2010-06-10 10:59 
/usr/local/lib/libcolamd.a -> libcolamd.2.7.2.a
-rw-r--r-- 1 root root  361906 2010-06-10 10:59 
/usr/local/lib/libcxsparse.2.2.4.a
lrwxrwxrwx 1 root root      19 2010-06-10 10:59 
/usr/local/lib/libcxsparse.a -> libcxsparse.2.2.4.a
-rw-r--r-- 1 root root  468572 2010-06-10 00:17 /usr/local/lib/libfblas.a
-rw-r--r-- 1 root root 6227200 2010-06-10 00:00 /usr/local/lib/libflapack.a
-rw-r--r-- 1 root root  475472 2010-05-20 10:16 /usr/local/lib/libgarmin.a
-rw-r--r-- 1 root root  216520 2010-06-10 10:59 
/usr/local/lib/libklu.1.1.1.a
lrwxrwxrwx 1 root root      14 2010-06-10 10:59 /usr/local/lib/libklu.a 
-> libklu.1.1.1.a
-rw-r--r-- 1 root root    5548 2010-06-10 10:59 
/usr/local/lib/libldl.2.0.2.a
lrwxrwxrwx 1 root root      14 2010-06-10 10:59 /usr/local/lib/libldl.a 
-> libldl.2.0.2.a
-rw-r--r-- 1 root root   28642 2010-06-10 10:59 
/usr/local/lib/librbio.2.0.0.a
lrwxrwxrwx 1 root root      15 2010-06-10 10:59 /usr/local/lib/librbio.a 
-> librbio.2.0.0.a
-rw-r--r-- 1 root root  255520 2010-06-10 10:59 
/usr/local/lib/libspqr.1.2.0.a
lrwxrwxrwx 1 root root      15 2010-06-10 10:59 /usr/local/lib/libspqr.a 
-> libspqr.1.2.0.a
-rw-r--r-- 1 root root    1412 2010-06-10 10:59 
/usr/local/lib/libufconfig.3.5.0.a
lrwxrwxrwx 1 root root      19 2010-06-10 10:59 
/usr/local/lib/libufconfig.a -> libufconfig.3.5.0.a
-rw-r--r-- 1 root root 1064532 2010-06-10 10:59 
/usr/local/lib/libumfpack.5.5.0.a
lrwxrwxrwx 1 root root      18 2010-06-10 10:59 
/usr/local/lib/libumfpack.a -> libumfpack.5.5.0.a
----------------
bino@bino:~/mydoc/buku/arduino/scipy/scipy-0.8.0b1$ ls -l 
/usr/local/include/
total 736
-rw-r--r-- 1 root root 17293 2010-06-10 10:59 amd.h
-rw-r--r-- 1 root root 12129 2010-06-10 10:59 btf.h
-rw-r--r-- 1 root root 16975 2010-06-10 10:59 camd.h
-rw-r--r-- 1 root root 10713 2010-06-10 10:59 ccolamd.h
-rw-r--r-- 1 root root 13990 2010-06-10 10:59 cholmod_blas.h
-rw-r--r-- 1 root root 14685 2010-06-10 10:59 cholmod_check.h
-rw-r--r-- 1 root root 20091 2010-06-10 10:59 cholmod_cholesky.h
-rw-r--r-- 1 root root  9380 2010-06-10 10:59 cholmod_complexity.h
-rw-r--r-- 1 root root  3162 2010-06-10 10:59 cholmod_config.h
-rw-r--r-- 1 root root 96574 2010-06-10 10:59 cholmod_core.h
-rw-r--r-- 1 root root  3858 2010-06-10 10:59 cholmod.h
-rw-r--r-- 1 root root  1710 2010-06-10 10:59 cholmod_io64.h
-rw-r--r-- 1 root root  8606 2010-06-10 10:59 cholmod_matrixops.h
-rw-r--r-- 1 root root 12969 2010-06-10 10:59 cholmod_modify.h
-rw-r--r-- 1 root root  8850 2010-06-10 10:59 cholmod_partition.h
-rw-r--r-- 1 root root  6435 2010-06-10 10:59 cholmod_supernodal.h
-rw-r--r-- 1 root root  9217 2010-06-10 10:59 cholmod_template.h
-rw-r--r-- 1 root root  8666 2010-06-10 10:59 colamd.h
-rw-r--r-- 1 root root 30977 2010-06-10 10:59 cs.h
-rw-r--r-- 1 root root 29336 2010-06-10 10:59 klu.h
-rw-r--r-- 1 root root  3934 2010-06-10 10:59 ldl.h
-rw-r--r-- 1 root root  6150 2010-05-20 10:16 libgarmin.h
-rw-r--r-- 1 root root 11648 2010-06-10 10:59 RBio.h
-rw-r--r-- 1 root root 34283 2010-06-10 10:59 spqr.hpp
-rw-r--r-- 1 root root  9652 2010-06-10 10:59 SuiteSparseQR_C.h
-rw-r--r-- 1 root root  2906 2010-06-10 10:59 SuiteSparseQR_definitions.h
-rw-r--r-- 1 root root 24518 2010-06-10 10:59 SuiteSparseQR.hpp
-rw-r--r-- 1 root root  5467 2010-06-10 10:59 UFconfig.h
-rw-r--r-- 1 root root  3712 2010-06-10 10:59 umfpack_col_to_triplet.h
-rw-r--r-- 1 root root  1892 2010-06-10 10:59 umfpack_defaults.h
-rw-r--r-- 1 root root  1690 2010-06-10 10:59 umfpack_free_numeric.h
-rw-r--r-- 1 root root  1708 2010-06-10 10:59 umfpack_free_symbolic.h
-rw-r--r-- 1 root root  6270 2010-06-10 10:59 umfpack_get_determinant.h
-rw-r--r-- 1 root root  3989 2010-06-10 10:59 umfpack_get_lunz.h
-rw-r--r-- 1 root root  9019 2010-06-10 10:59 umfpack_get_numeric.h
-rw-r--r-- 1 root root 13040 2010-06-10 10:59 umfpack_get_symbolic.h
-rw-r--r-- 1 root root  1029 2010-06-10 10:59 umfpack_global.h
-rw-r--r-- 1 root root 19268 2010-06-10 10:59 umfpack.h
-rw-r--r-- 1 root root  2585 2010-06-10 10:59 umfpack_load_numeric.h
-rw-r--r-- 1 root root  2612 2010-06-10 10:59 umfpack_load_symbolic.h
-rw-r--r-- 1 root root 23181 2010-06-10 10:59 umfpack_numeric.h
-rw-r--r-- 1 root root  7500 2010-06-10 10:59 umfpack_qsymbolic.h
-rw-r--r-- 1 root root  2197 2010-06-10 10:59 umfpack_report_control.h
-rw-r--r-- 1 root root  2639 2010-06-10 10:59 umfpack_report_info.h
-rw-r--r-- 1 root root  6997 2010-06-10 10:59 umfpack_report_matrix.h
-rw-r--r-- 1 root root  3612 2010-06-10 10:59 umfpack_report_numeric.h
-rw-r--r-- 1 root root  3520 2010-06-10 10:59 umfpack_report_perm.h
-rw-r--r-- 1 root root  2563 2010-06-10 10:59 umfpack_report_status.h
-rw-r--r-- 1 root root  3551 2010-06-10 10:59 umfpack_report_symbolic.h
-rw-r--r-- 1 root root  4893 2010-06-10 10:59 umfpack_report_triplet.h
-rw-r--r-- 1 root root  4507 2010-06-10 10:59 umfpack_report_vector.h
-rw-r--r-- 1 root root  2243 2010-06-10 10:59 umfpack_save_numeric.h
-rw-r--r-- 1 root root  2274 2010-06-10 10:59 umfpack_save_symbolic.h
-rw-r--r-- 1 root root  3161 2010-06-10 10:59 umfpack_scale.h
-rw-r--r-- 1 root root 10693 2010-06-10 10:59 umfpack_solve.h
-rw-r--r-- 1 root root 21739 2010-06-10 10:59 umfpack_symbolic.h
-rw-r--r-- 1 root root  2225 2010-06-10 10:59 umfpack_tictoc.h
-rw-r--r-- 1 root root  1719 2010-06-10 10:59 umfpack_timer.h
-rw-r--r-- 1 root root  7938 2010-06-10 10:59 umfpack_transpose.h
-rw-r--r-- 1 root root 10442 2010-06-10 10:59 umfpack_triplet_to_col.h
-rw-r--r-- 1 root root  5542 2010-06-10 10:59 umfpack_wsolve.h
---STOP---

Environtment :
LAPACK_SRC=/home/bino/mydoc/buku/arduino/scipy/lapack/lapack-3.2.1/SRC/
bino@bino:~/mydoc/buku/arduino/scipy/scipy-0.8.0b1$ env |grep BLAS
BLAS_SRC=/home/bino/mydoc/buku/arduino/scipy/blas/BLAS/

But I still got no success installing scipy

Here is the error msg :

----START----
bino@bino:~/mydoc/buku/arduino/scipy/scipy-0.8.0b1$ ./setup.py build
Warning: No configuration returned, assuming unavailable.
blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  NOT AVAILABLE

/usr/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1340: 
UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
blas_info:
  libraries blas not found in /usr/local/lib
  NOT AVAILABLE

/usr/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1349: 
UserWarning:
    Blas (http://www.netlib.org/blas/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [blas]) or by setting
    the BLAS environment variable.
  warnings.warn(BlasNotFoundError.__doc__)
blas_src_info:
  FOUND:
    sources = ['/home/bino/mydoc/buku/arduino/scipy/blas/BLAS/caxpy.f', 
'/home/bino/mydoc/buku/arduino/scipy/blas/BLAS/csscal.f', '/ho...
...
...mm.f', '/home/bino/mydoc/buku/arduino/scipy/blas/BLAS/zsymm.f', 
'/home/bino/mydoc/buku/arduino/scipy/blas/BLAS/ztrsm.f']
    language = f77

  FOUND:
    libraries = [('fblas_src', {'sources': 
['/home/bino/mydoc/buku/arduino/scipy/blas/BLAS/caxpy.f', 
'/home/bino/mydoc/buku/arduino/scip...
...
...oc/buku/arduino/scipy/blas/BLAS/zsymm.f', 
'/home/bino/mydoc/buku/arduino/scipy/blas/BLAS/ztrsm.f'], 'language': 
'f77'})]
    define_macros = [('NO_ATLAS_INFO', 1)]

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  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
  NOT AVAILABLE

atlas_info:
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
numpy.distutils.system_info.atlas_info
  NOT AVAILABLE

/usr/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1247: 
UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
  libraries lapack not found in /usr/local/lib
  NOT AVAILABLE

/usr/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1258: 
UserWarning:
    Lapack (http://www.netlib.org/lapack/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [lapack]) or by setting
    the LAPACK environment variable.
  warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
  FOUND:
    sources = 
['/home/bino/mydoc/buku/arduino/scipy/lapack/lapack-3.2.1/SRC/sbdsdc.f', 
'/home/bino/mydoc/buku/arduino/scipy/lapack/lap...
...
...apack-3.2.1/SRC/../INSTALL/slamch.f', 
'/home/bino/mydoc/buku/arduino/scipy/lapack/lapack-3.2.1/SRC/../INSTALL/dlamch.f']
    language = f77

/usr/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1271: 
UserWarning:
    Blas (http://www.netlib.org/blas/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [blas]) or by setting
    the BLAS environment variable.
  warnings.warn(BlasNotFoundError.__doc__)
  FOUND:
    libraries = [('flapack_src', {'sources': 
['/home/bino/mydoc/buku/arduino/scipy/lapack/lapack-3.2.1/SRC/sbdsdc.f', 
'/home/bino/mydoc/...
...
...oc/buku/arduino/scipy/blas/BLAS/zsymm.f', 
'/home/bino/mydoc/buku/arduino/scipy/blas/BLAS/ztrsm.f'], 'language': 
'f77'})]
    define_macros = [('NO_ATLAS_INFO', 1)]

umfpack_info:
amd_info:
  FOUND:
    libraries = ['amd']
    library_dirs = ['/usr/local/lib']
    swig_opts = ['-I/usr/local/include']
    define_macros = [('SCIPY_AMD_H', None)]
    include_dirs = ['/usr/local/include']

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

Traceback (most recent call last):
  File "./setup.py", line 160, in <module>
    setup_package()
  File "./setup.py", line 152, in setup_package
    configuration=configuration )
  File "/usr/lib/python2.6/dist-packages/numpy/distutils/core.py", line 
150, in setup
    config = configuration()
  File "./setup.py", line 118, in configuration
    config.add_subpackage('scipy')
  File "/usr/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", 
line 851, in add_subpackage
    caller_level = 2)
  File "/usr/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", 
line 834, in get_subpackage
    caller_level = caller_level + 1)
  File "/usr/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", 
line 781, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "scipy/setup.py", line 20, in configuration
    config.add_subpackage('special')
  File "/usr/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", 
line 851, in add_subpackage
    caller_level = 2)
  File "/usr/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", 
line 834, in get_subpackage
    caller_level = caller_level + 1)
  File "/usr/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", 
line 766, in _get_configuration_from_setup_py
    ('.py', 'U', 1))
  File "scipy/special/setup.py", line 7, in <module>
    from numpy.distutils.misc_util import get_numpy_include_dirs, get_info
ImportError: cannot import name get_info

----STOP------

Kindly please tell me how to fix it.
My system is based on ubuntu jaunty

Sincerely
-bino-

yet another scipy Install problem

Bino Oetomo

David Cournapeau

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