[SciPy-user] Installing scipy-5.2 on fedora 64 bit: cannot import

Niels L Ellegaard niels.ellegaard at gmail.com
Wed Dec 20 09:07:15 CST 2006


Niels L Ellegaard <niels.ellegaard <at> gmail.com> writes:
> I am trying to install scipy 5.2 on a fedora 64 bit machine with 
> numpy 1.0.1. When I try to run scipy.test() i get the following 
> error
>
>    from scipy.linalg import flapack
>ImportError: cannot import name flapack

I did a little more testing. Apparently the problem is clapack.so (See below) 
I hope somebody can give me a hint. Otherwise i will have to install Ubuntu.

                                  Niels

Some more info:

$ python -c 'import os,sys;print os.name,sys.platform'
posix linux2

$ python -c 'import sys;print sys.version'
2.4.3 (#1, Jun 13 2006, 11:46:22)
[GCC 4.1.1 20060525 (Red Hat 4.1.1-1)]

$ python -c 'import Numeric;print Numeric.__version__'
23.7

$ f2py -v
2_3396

$ uname -a
Linux xx.ac.in 2.6.17-1.2139_FC5 #1 SMP Fri Jun 23 12:40:11 EDT 
2006 x86_64
x86_64 x86_64 GNU/Linux


$ python /usr/lib64/python2.4/site-packages/scipy/linalg/lapack.py
.......
 File "/usr/lib64/python2.4/site-packages/scipy/linalg/lapack.py", 
line 18, in ?
    from scipy.linalg import clapack
ImportError: /usr/lib64/python2.4/site-packages/scipy/linalg/
clapack.so:
undefined symbol: clapack_sgesv

$ldd /usr/lib64/python2.4/site-packages/scipy/linalg/clapack.so
shell-init: error retrieving current directory: getcwd: cannot 
access parent
directories: No such file or directory
        liblapack.so.3 => /usr/lib64/atlas/liblapack.so.3 
(0x00002aaaaabdc000)
        libblas.so.3 => /usr/lib64/atlas/libblas.so.3 
(0x00002aaaab1ef000)
        libg2c.so.0 => /usr/lib64/libg2c.so.0 
(0x00002aaaaba81000)
        libm.so.6 => /lib64/libm.so.6 (0x00002aaaabba4000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002aaaabd26000)
        libc.so.6 => /lib64/libc.so.6 (0x00002aaaabe34000)
        libgfortran.so.1 => /usr/lib64/libgfortran.so.1 
(0x00002aaaac07e000)
        /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)

$ python setup_atlas_version.py
/usr/lib64/python2.4/site-packages/numpy/distutils/
misc_util.py:1391:
UserWarning: Use Configuration('linalg','',top_path=None) instead
 of deprecated
default_config_dict('linalg','',None)
  warnings.warn('Use Configuration(%r,%r,top_path=%r) instead of '\
Traceback (most recent call last):
  File "setup_atlas_version.py", line 29, in ?
    setup(**configuration())
  File "setup_atlas_version.py", line 13, in configuration
    del config['fortran_libraries']
KeyError: 'fortran_libraries'

$ gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-libgcj-multifile
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada 
--enable-java-awt=gtk
--disable-dssi --with-java-home=/usr/lib/jvm/
java-1.4.2-gcj-1.4.2.0/jre
--with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.1 20060525 (Red Hat 4.1.1-1)

$ g77 --version
GNU Fortran (GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-55.fc5)) 
3.2.3 
20030502 (Red Hat Linux 3.2.3-13)
Copyright (C) 2002 Free Software Foundation, Inc.

$ python /usr/lib64/python2.4/test/test_distutils.py
test_home_installation_scheme (distutils.tests.test_install.
InstallTestCase)
 ... FAIL
test_package_data (distutils.tests.test_build_py.BuildPyTestCase) 
... ok
test_build (distutils.tests.test_build_scripts.BuildScriptsTestCase) 
... ok
test_default_settings (distutils.tests.test_build_scripts.
BuildScriptsTestCase)
... ok
test_command_packages_cmdline (distutils.tests.test_dist.
DistributionTestCase)
... ok
test_command_packages_configfile
(distutils.tests.test_dist.DistributionTestCase) ... ok
test_command_packages_unspecified
(distutils.tests.test_dist.DistributionTestCase) ... ok
test_default_settings
(distutils.tests.test_install_scripts.InstallScriptsTestCase) 
... ok
test_installation (distutils.tests.test_install_scripts.
InstallScriptsTestCase)
... ok

=================================================================
FAIL: test_home_installation_scheme (distutils.tests.test_install.
InstallTestCase)
-----------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python2.4/distutils/tests/test_install.py", 
line 43, in test_home_installation_scheme
    check_path(cmd.install_platlib, libdir)
  File "/usr/lib64/python2.4/distutils/tests/test_install.py", 
ine 39, in check_path
    self.assertEqual(got, expected)
AssertionError: '/tmp/tmpddXPuo/installation/lib64/python' !=
'/tmp/tmpddXPuo/installation/lib/python'

----------------------------------------------------------------
Ran 9 tests in 0.075s

FAILED (failures=1)
Traceback (most recent call last):
  File "/usr/lib64/python2.4/test/test_distutils.py", line 17,
 in ?
    test_main()
  File "/usr/lib64/python2.4/test/test_distutils.py", line 13,
 in 
test_main
    test.test_support.run_unittest(distutils.tests.
test_suite())
  File "/usr/lib64/python2.4/test/test_support.py", line 290, 
in run_unittest
    run_suite(suite, testclass)
  File "/usr/lib64/python2.4/test/test_support.py", line 275, 
in run_suite
    raise TestFailed(err)
test.test_support.TestFailed: Traceback (most recent call last):
  File "/usr/lib64/python2.4/distutils/tests/test_install.py",
 line 43, in test_home_installation_scheme
    check_path(cmd.install_platlib, libdir)
  File "/usr/lib64/python2.4/distutils/tests/test_install.py", 
line 39, in check_path
    self.assertEqual(got, expected)
AssertionError: '/tmp/tmpddXPuo/installation/lib64/python' !=
'/tmp/tmpddXPuo/installation/lib/python'




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