[SciPy-User] Building Scipy for Mac OS X 10.6

Scott Stephens stephens.js@gmail....
Mon Jun 7 22:22:29 CDT 2010


On Mon, Jun 7, 2010 at 1:23 AM, David <david@silveregg.co.jp> wrote:
> On 06/07/2010 12:42 PM, Scott Stephens wrote:
>> On Sat, Jun 5, 2010 at 10:49 PM, Ralf Gommers
>> <ralf.gommers@googlemail.com>  wrote:
>>> Could you try the 0.8.0 beta (http://sourceforge.net/projects/scipy/files/)?
>>> Some of this may be fixed, and you also get another 18 months worth or so of
>>> new features and bug fixes.
>>
>> 0.8.0b1 doesn't build for me using numscons.  Build log is attached.
>> I'm using numpy 1.4.1 built from source (and tested, no errors or
>> unknown failures) and numscons freshly checked out from the git
>> repository (at least numscons-0.11 is required to build scipy-0.8.0b1,
>> and only numscons-0.10 is available via easy_install; couldn't find
>> source for numscons-0.11).
>
> Could you see whether r6487 fixes it for you ?
>

Checked out and built the trunk (r6490).  r6487 fixed the build
problem, and some of the test failures I was getting in 0.7.1, but not
all.  The errors and failures I get now are:

ERROR: test_decomp.test_lapack_misaligned(<function solve at
0x103da4f50>, (array([[  1.734e-255,   8.189e-217,   4.025e-178,
1.903e-139,   9.344e-101,
ERROR: test_complex_nonsymmetric_modes
(test_arpack.TestEigenComplexNonSymmetric)
ERROR: test_nonsymmetric_modes (test_arpack.TestEigenNonSymmetric)
ERROR: test_starting_vector (test_arpack.TestEigenNonSymmetric)
ERROR: test_continuous_basic.test_cont_basic(<scipy.stats.distributions.wald_gen
object at 0x104608e50>, (), 'wald')
ERROR: test_continuous_basic.test_cont_basic(<scipy.stats.distributions.wald_gen
object at 0x104608e50>, (), 'wald')
ERROR: test_continuous_basic.test_cont_basic(<scipy.stats.distributions.wald_gen
object at 0x104608e50>, (), 'wald')
FAIL: test_complex_symmetric_modes (test_arpack.TestEigenComplexSymmetric)

Full text of the test run is attached.

-- Scott
-------------- next part --------------
>>> import scipy
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.4.1
NumPy is installed in /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy
SciPy version 0.9.0.dev6493
SciPy is installed in /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy
Python version 2.6.4 (r264:75706, Mar 27 2010, 11:45:57) [GCC 4.2.1 (Apple Inc. build 5646) (dot 1)]
nose version 0.11.3
............................................................................................................................................................................................................................................................................../Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:639: UserWarning: 
The coefficients of the spline returned have been computed as the
minimal norm least-squares solution of a (numerically) rank deficient
system (deficiency=7). If deficiency is large, the results may be
inaccurate. Deficiency may strongly depend on the value of eps.
  warnings.warn(message)
...../Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:580: UserWarning: 
The required storage space exceeds the available storage space: nxest
or nyest too small, or s too small.
The weighted least-squares spline corresponds to the current set of
knots.
  warnings.warn(message)
...........................................K..K.........................................................................................................................................................................................................................................................................................................................Warning: 1000000 bytes requested, 20 bytes read.
./Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/lib/utils.py:140: DeprecationWarning: `write_array` is deprecated!

This function is replaced by numpy.savetxt which allows the same functionality
through a different syntax.

  warnings.warn(depdoc, DeprecationWarning)
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/lib/utils.py:140: DeprecationWarning: `read_array` is deprecated!

The functionality of read_array is in numpy.loadtxt which allows the same
functionality using different syntax.

  warnings.warn(depdoc, DeprecationWarning)
...........................................Exception AttributeError: "'netcdf_file' object has no attribute 'mode'" in <bound method netcdf_file.close of <scipy.io.netcdf.netcdf_file object at 0x104bbe650>> ignored
............/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/lib/utils.py:140: DeprecationWarning: `npfile` is deprecated!

You can achieve the same effect as using npfile using numpy.save and
numpy.load.

You can use memory-mapped arrays and data-types to map out a
file format for direct manipulation in NumPy.

  warnings.warn(depdoc, DeprecationWarning)
........./Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/io/wavfile.py:30: WavFileWarning: Unfamiliar format bytes
  warnings.warn("Unfamiliar format bytes", WavFileWarning)
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/io/wavfile.py:120: WavFileWarning: chunk not understood
  warnings.warn("chunk not understood", WavFileWarning)
...............................................................................................................................................................................................................................SSSSSS......SSSSSS......SSSS...............................................................S...................................................................................................................................................................................................................E.....................................................................................................................................................................................................SSS.........S........................................................................................................................................................................................................................................................................................................................................................................................................................................................** On entry to DGEEV , parameter number  5 had an illegal value
** On entry to DGEEV , parameter number  5 had an illegal value
............/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/filter_design.py:247: BadCoefficients: Badly conditioned filter coefficients (numerator): the results may be meaningless
  "results may be meaningless", BadCoefficients)
..................................................................................................................................................................................................................................................................................SSSSSSSSSSS.........EFEE..K.......................................................................................................................................K...............................................................K.........................................................................................................................................................KK.......................................................................................................................................................................................................................................................................................................................................................................................................K.K...................................................................................................................................................................................................................................................................................................................................................................................K........K.........SSSSS.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................EEE.........................................................................................................................................................S......................................................................................................................................................................................./Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/morestats.py:736: UserWarning: Ties preclude use of exact statistic.
  warnings.warn("Ties preclude use of exact statistic.")
......................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
ERROR: test_decomp.test_lapack_misaligned(<function solve at 0x103da4f50>, (array([[  1.734e-255,   8.189e-217,   4.025e-178,   1.903e-139,   9.344e-101,
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/nose-0.11.3-py2.6.egg/nose/case.py", line 186, in runTest
    self.test(*self.arg)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/linalg/tests/test_decomp.py", line 1074, in check_lapack_misaligned
    func(*a,**kwargs)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/linalg/basic.py", line 49, in solve
    a1, b1 = map(asarray_chkfinite,(a,b))
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/lib/function_base.py", line 586, in asarray_chkfinite
    raise ValueError, "array must not contain infs or NaNs"
ValueError: array must not contain infs or NaNs

======================================================================
ERROR: test_complex_nonsymmetric_modes (test_arpack.TestEigenComplexNonSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 267, in test_complex_nonsymmetric_modes
    self.eval_evec(m,typ,k,which)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 248, in eval_evec
    eval,evec=eigen(a,k,which=which)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 397, in eigen
    params.iterate()
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 222, in iterate
    raise RuntimeError("Error info=%d in arpack" % self.info)
RuntimeError: Error info=-8 in arpack

======================================================================
ERROR: test_nonsymmetric_modes (test_arpack.TestEigenNonSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 204, in test_nonsymmetric_modes
    self.eval_evec(m,typ,k,which)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 186, in eval_evec
    eval,evec=eigen(a,k,which=which,**kwds)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 397, in eigen
    params.iterate()
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 222, in iterate
    raise RuntimeError("Error info=%d in arpack" % self.info)
RuntimeError: Error info=-8 in arpack

======================================================================
ERROR: test_starting_vector (test_arpack.TestEigenNonSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 214, in test_starting_vector
    self.eval_evec(self.symmetric[0],typ,k,which='LM',v0=v0)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 186, in eval_evec
    eval,evec=eigen(a,k,which=which,**kwds)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 397, in eigen
    params.iterate()
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 222, in iterate
    raise RuntimeError("Error info=%d in arpack" % self.info)
RuntimeError: Error info=-8 in arpack

======================================================================
ERROR: test_continuous_basic.test_cont_basic(<scipy.stats.distributions.wald_gen object at 0x104608e50>, (), 'wald')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/nose-0.11.3-py2.6.egg/nose/case.py", line 186, in runTest
    self.test(*self.arg)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/tests/test_continuous_basic.py", line 291, in check_cdf_ppf
    npt.assert_almost_equal(distfn.cdf(distfn.ppf([0.001,0.5,0.999], *arg), *arg),
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py", line 1324, in ppf
    place(output,cond,self._ppf(*goodargs)*scale + loc)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py", line 1028, in _ppf
    return self.vecfunc(q,*args)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/lib/function_base.py", line 1804, in __call__
    theout = self.thefunc(*newargs)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py", line 974, in _ppf_single_call
    return optimize.brentq(self._ppf_to_solve, self.xa, self.xb, args=(q,)+args, xtol=self.xtol)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/optimize/zeros.py", line 262, in brentq
    r = _zeros._brentq(f,a,b,xtol,maxiter,args,full_output,disp)
ValueError: f(a) and f(b) must have different signs

======================================================================
ERROR: test_continuous_basic.test_cont_basic(<scipy.stats.distributions.wald_gen object at 0x104608e50>, (), 'wald')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/nose-0.11.3-py2.6.egg/nose/case.py", line 186, in runTest
    self.test(*self.arg)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/tests/test_continuous_basic.py", line 296, in check_sf_isf
    npt.assert_almost_equal(distfn.sf(distfn.isf([0.1,0.5,0.9], *arg), *arg),
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py", line 1366, in isf
    place(output,cond,self._isf(*goodargs)*scale + loc) #PB use _isf instead of _ppf
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py", line 1031, in _isf
    return self._ppf(1.0-q,*args) #use correct _ppf for subclasses
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py", line 1028, in _ppf
    return self.vecfunc(q,*args)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/lib/function_base.py", line 1804, in __call__
    theout = self.thefunc(*newargs)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py", line 974, in _ppf_single_call
    return optimize.brentq(self._ppf_to_solve, self.xa, self.xb, args=(q,)+args, xtol=self.xtol)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/optimize/zeros.py", line 262, in brentq
    r = _zeros._brentq(f,a,b,xtol,maxiter,args,full_output,disp)
ValueError: f(a) and f(b) must have different signs

======================================================================
ERROR: test_continuous_basic.test_cont_basic(<scipy.stats.distributions.wald_gen object at 0x104608e50>, (), 'wald')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/nose-0.11.3-py2.6.egg/nose/case.py", line 186, in runTest
    self.test(*self.arg)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/tests/test_continuous_basic.py", line 306, in check_pdf
    median = distfn.ppf(0.5, *arg)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py", line 1324, in ppf
    place(output,cond,self._ppf(*goodargs)*scale + loc)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py", line 1028, in _ppf
    return self.vecfunc(q,*args)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/lib/function_base.py", line 1804, in __call__
    theout = self.thefunc(*newargs)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py", line 974, in _ppf_single_call
    return optimize.brentq(self._ppf_to_solve, self.xa, self.xb, args=(q,)+args, xtol=self.xtol)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/optimize/zeros.py", line 262, in brentq
    r = _zeros._brentq(f,a,b,xtol,maxiter,args,full_output,disp)
ValueError: f(a) and f(b) must have different signs

======================================================================
FAIL: test_complex_symmetric_modes (test_arpack.TestEigenComplexSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 156, in test_complex_symmetric_modes
    self.eval_evec(self.symmetric[0],typ,k,which)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 145, in eval_evec
    assert_array_almost_equal(eval,exact_eval,decimal=_ndigits[typ])
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 765, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 609, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal

(mismatch 100.0%)
 x: array([ 1.07188725 +6.23436023e-08j,  4.91291142 -3.25412906e-08j], dtype=complex64)
 y: array([ 5.+0.j,  6.+0.j], dtype=complex64)

----------------------------------------------------------------------
Ran 4613 tests in 89.389s

FAILED (KNOWNFAIL=11, SKIP=38, errors=7, failures=1)
<nose.result.TextTestResult run=4613 errors=7 failures=1>


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