[SciPy-dev] Building on Woody(Debian): good news, bad news.

[Prabhu Ramachandran]

hi,

First, the good news.  A while back I reported a bug with severe bug
with Python + f2py under Debian Linux that Pearu Peterson
investigated.  He filed a bug with the Python folks and found that the
bug was in the Debian packages.  He then filed a bug with the Debian
developers.  I just noticed yesterday that Woody has updated python
packages that fix this problem.  Here is the report.

    http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=135461

The f2py tests and some of my modules all work for me (they used to
segfault).

I am having some difficulties with the new build process.  I'm using
the atlas libs from Debian GNU/Linux (woody).  When I try to do a 

python setup.py build

I get an error saying atlas libs cant be found.  They are very much
installed.  I looked at the code and it seems that the code looks for
liblapack, libf77blas, libcblas, libatlas all in either /usr/lib/atlas
or /usr/local/lib/atlas (or a user specified directory).  Under debian
these libraries all exist but are not in /usr/lib/atlas.  The cblas,
f77blas and atlas libs are in /usr/lib the others in /usr/lib/atlas.
This fools the system_info.py script into thinking that there aren't
any useful atlas libs and hence the build does not proceed.  I worked
around the problem by creating links to these libraries in
/usr/lib/atlas.

After I built scipy the tests seem to run but I get the following
error:

In [1]: import scipy
/usr/local/lib/python2.1/site-packages/scipy/integrate/vode.so: undefined symbol: f2py_report_on_exit

I dont know why this happens.  When I run the tests I get 4 failures.
But it does run and does not segfault anymore. :)

In [2]: scipy.test()
[snip]
======================================================================
FAIL: check_default_cols (test_misc.test_mean)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.1/site-packages/scipy/tests/test_misc.py", line 53, in check_default_cols
    assert_array_equal(val,desired)
  File "/usr/local/lib/python2.1/site-packages/scipy_test/scipy_test.py", line 301, in assert_array_equal
    assert alltrue(ravel(reduced)),\
AssertionError: 
Arrays are not equal:
        
======================================================================
FAIL: check_qnan (test_misc.test_isnan)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.1/site-packages/scipy/tests/test_misc.py", line 112, in check_qnan
    assert(isnan(log(-1.)) == 1)
AssertionError
======================================================================

======================================================================
FAIL: check_qnan (test_misc.test_isfinite)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.1/site-packages/scipy/tests/test_misc.py", line 132, in check_qnan
    assert(isfinite(log(-1.)) == 0)
AssertionError
======================================================================
FAIL: check_qnan (test_misc.test_isinf)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.1/site-packages/scipy/tests/test_misc.py", line 157, in check_qnan
    assert(isnan(log(-1.)) == 1)
AssertionError
----------------------------------------------------------------------
Ran 262 tests in 3.281s

FAILED (failures=4)


Thanks,
prabhu