[SciPy-User] 1.8.0rc1

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[SciPy-User] 1.8.0rc1

Charles R Harris
Hi All,

NumPy 1.8.0rc1 is up now on sourceforge .The binary builds are included except for Python 3.3 on windows, which will arrive later. Many thanks to Ralf for the binaries, and to those who found and fixed the bugs in the last beta. Any remaining bugs are all my fault ;) I hope this will be the last release before final, so please test it thoroughly.

Chuck

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Re: [SciPy-Dev] 1.8.0rc1

Nathaniel Smith
Everyone please do actually test this! It is really in your best
interest, and I think people don't always realize this.

Here's how it works:
- If you test it *now*, and it breaks your code that worked with 1.7,
and you *tell* us this now, then it's *our* problem and we hold up the
release to fix the bug.
- If you test it *after* we release, and it breaks your code, then we
are sad but you have to work around it (because we can't magically
make that release not have happened, your users will be using it
anyway), and we put it on the stack with all the other bugs. All of
which we care about but it's a large enough stack that it's not going
to get any special priority, because, see above about how at this
point you'll have had to work around it anyway.

-n

On Mon, Sep 30, 2013 at 4:17 PM, Charles R Harris
<[hidden email]> wrote:

> Hi All,
>
> NumPy 1.8.0rc1 is up now on sourceforge .The binary builds are included
> except for Python 3.3 on windows, which will arrive later. Many thanks to
> Ralf for the binaries, and to those who found and fixed the bugs in the last
> beta. Any remaining bugs are all my fault ;) I hope this will be the last
> release before final, so please test it thoroughly.
>
> Chuck
>
> _______________________________________________
> SciPy-Dev mailing list
> [hidden email]
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
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Re: [Numpy-discussion] 1.8.0rc1

Daπid
In reply to this post by Charles R Harris

On 30 September 2013 17:17, Charles R Harris <[hidden email]> wrote:
NumPy 1.8.0rc1 is up now on sourceforge .The binary builds are included except for Python 3.3 on windows, which will arrive later. Many thanks to Ralf for the binaries, and to those who found and fixed the bugs in the last beta. Any remaining bugs are all my fault ;) I hope this will be the last release before final, so please test it thoroughly.

I installed it with

# python setup.py install

But something is wrong there:

>>> import numpy as np
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib64/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
  File "/usr/lib64/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib64/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
  File "/usr/lib64/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
  File "/usr/lib64/python2.7/site-packages/numpy/core/__init__.py", line 45, in <module>
    from numpy.testing import Tester
  File "/usr/lib64/python2.7/site-packages/numpy/testing/__init__.py", line 10, in <module>
    import decorators as dec
  File "/usr/lib64/python2.7/site-packages/numpy/testing/decorators.py", line 19, in <module>
    from numpy.testing.utils import \
  File "/usr/lib64/python2.7/site-packages/numpy/testing/utils.py", line 12, in <module>
    from .nosetester import import_nose
  File "/usr/lib64/python2.7/site-packages/numpy/testing/nosetester.py", line 12, in <module>
    from numpy.compat import basestring
ImportError: cannot import name basestring


I am using Python27 on Fedora 19.

$ gcc --version
gcc (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1)

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Re: [Numpy-discussion] 1.8.0rc1

Daπid
Disregard that, I had not cleaned the previous installation properly.

Sorry for the noise.


On 1 October 2013 12:11, Daπid <[hidden email]> wrote:

On 30 September 2013 17:17, Charles R Harris <[hidden email]> wrote:
NumPy 1.8.0rc1 is up now on sourceforge .The binary builds are included except for Python 3.3 on windows, which will arrive later. Many thanks to Ralf for the binaries, and to those who found and fixed the bugs in the last beta. Any remaining bugs are all my fault ;) I hope this will be the last release before final, so please test it thoroughly.

I installed it with

# python setup.py install

But something is wrong there:

>>> import numpy as np

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib64/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
  File "/usr/lib64/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib64/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
  File "/usr/lib64/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
  File "/usr/lib64/python2.7/site-packages/numpy/core/__init__.py", line 45, in <module>
    from numpy.testing import Tester
  File "/usr/lib64/python2.7/site-packages/numpy/testing/__init__.py", line 10, in <module>
    import decorators as dec
  File "/usr/lib64/python2.7/site-packages/numpy/testing/decorators.py", line 19, in <module>
    from numpy.testing.utils import \
  File "/usr/lib64/python2.7/site-packages/numpy/testing/utils.py", line 12, in <module>
    from .nosetester import import_nose
  File "/usr/lib64/python2.7/site-packages/numpy/testing/nosetester.py", line 12, in <module>
    from numpy.compat import basestring
ImportError: cannot import name basestring


I am using Python27 on Fedora 19.

$ gcc --version
gcc (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1)


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Re: [SciPy-Dev] 1.8.0rc1

Jack Howarth
In reply to this post by Charles R Harris
On Mon, Sep 30, 2013 at 09:17:14AM -0600, Charles R Harris wrote:

> Hi All,
>
> NumPy 1.8.0rc1 is up now on
> sourceforge<http://sourceforge.net/projects/numpy/files/NumPy/1.8.0rc1/>.The
> binary builds are included except for Python 3.3 on windows, which
> will arrive later. Many thanks to Ralf for the binaries, and to those who
> found and fixed the bugs in the last beta. Any remaining bugs are all my
> fault ;) I hope this will be the last release before final, so please test
> it thoroughly.
>
> Chuck
Chuck,
   The NumPy 1.8.0rc1 release fails to build on Mac OS X 10.6.8 under fink using the
build command...

/sw/bin/python2.7 setup.py build

which fails at...

/sw/bin/gfortran -Wall -L/sw/lib build/temp.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_lite/python_xerbla.o -L/sw/lib -L/sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin10.8.0/4.8.1 -Lbuild/temp.macosx-10.6-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lgfortran -o build/lib.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_lite.so
Undefined symbols for architecture x86_64:
  "_main", referenced from:
      start in crt1.10.6.o
  "_PyOS_snprintf", referenced from:
      _xerbla_ in python_xerbla.o
  "_PyGILState_Ensure", referenced from:
      _xerbla_ in python_xerbla.o
  "_PyExc_ValueError", referenced from:
      _xerbla_ in python_xerbla.o
etc

The full build log is attached.
        Jack
ps The same build approach works fine for the current numpy 1.7.1 release.

> _______________________________________________
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> http://mail.scipy.org/mailman/listinfo/scipy-dev


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Re: [SciPy-Dev] 1.8.0rc1

Robert Kern-2
In reply to this post by Charles R Harris
On Tue, Oct 1, 2013 at 4:41 PM, Pauli Virtanen <[hidden email]> wrote:
>
> Hi,
>
> 01.10.2013 16:28, Jack Howarth kirjoitti:
> [clip]
> > /sw/bin/python2.7 setup.py build
> >
> > which fails at...
> >
> > /sw/bin/gfortran -Wall -L/sw/lib build/temp.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_lite/python_xerbla.o -L/sw/lib -L/sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin10.8.0/4.8.1 -Lbuild/temp.macosx-10.6-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lgfortran -o build/lib.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_lite.so
> > Undefined symbols for architecture x86_64:
> >   "_main", referenced from:
> >       start in crt1.10.6.o
> [clip]
>
> Something is screwed up in your build environment: the `-shared` flag is
> missing from the link command.
>
> Perhaps you have set one of the the environment variables FFLAGS,
> CFLAGS, LDFLAGS?

Also the `-undefined dynamic_lookup` flag.

--
Robert Kern

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Re: [SciPy-Dev] 1.8.0rc1

Jack Howarth
On Tue, Oct 01, 2013 at 04:52:06PM +0100, Robert Kern wrote:

> On Tue, Oct 1, 2013 at 4:41 PM, Pauli Virtanen <[hidden email]> wrote:
> >
> > Hi,
> >
> > 01.10.2013 16:28, Jack Howarth kirjoitti:
> > [clip]
> > > /sw/bin/python2.7 setup.py build
> > >
> > > which fails at...
> > >
> > > /sw/bin/gfortran -Wall -L/sw/lib
> build/temp.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_litemodule.o
> build/temp.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_lite/python_xerbla.o
> -L/sw/lib -L/sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin10.8.0/4.8.1
> -Lbuild/temp.macosx-10.6-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas
> -lgfortran -o build/lib.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_lite.so
> > > Undefined symbols for architecture x86_64:
> > >   "_main", referenced from:
> > >       start in crt1.10.6.o
> > [clip]
> >
> > Something is screwed up in your build environment: the `-shared` flag is
> > missing from the link command.
> >
> > Perhaps you have set one of the the environment variables FFLAGS,
> > CFLAGS, LDFLAGS?
>
> Also the `-undefined dynamic_lookup` flag.

The consensus of the fink developers is that you are introducing a bug in both
scipy and numpy. The build should be able to pass additional flags on these
variables and the scipy/numpy build should be able to append any additional
flags required. In particular, both MacPorts and fink will want to be able to
pass -L/opt/local/lib or -L/sw/lib via LDFLAGS. The changes added to scipy and
numpy have broken this and now require that these additional flags be manually
patched into the Makefiles of numpy and scipy rather than just passing them
on LDFLAGS as has always worked in the past.
         Jack

>
> --
> Robert Kern

> _______________________________________________
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Re: [SciPy-Dev] 1.8.0rc1

Robert Kern-2
On Tue, Oct 1, 2013 at 5:02 PM, Jack Howarth <[hidden email]> wrote:
>
> On Tue, Oct 01, 2013 at 04:52:06PM +0100, Robert Kern wrote:
> > On Tue, Oct 1, 2013 at 4:41 PM, Pauli Virtanen <[hidden email]> wrote:
> > >
> > > Hi,
> > >
> > > 01.10.2013 16:28, Jack Howarth kirjoitti:
> > > [clip]
> > > > /sw/bin/python2.7 setup.py build
> > > >
> > > > which fails at...
> > > >
> > > > /sw/bin/gfortran -Wall -L/sw/lib
> > build/temp.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_litemodule.o
> > build/temp.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_lite/python_xerbla.o
> > -L/sw/lib -L/sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin10.8.0/4.8.1
> > -Lbuild/temp.macosx-10.6-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas
> > -lgfortran -o build/lib.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_lite.so
> > > > Undefined symbols for architecture x86_64:
> > > >   "_main", referenced from:
> > > >       start in crt1.10.6.o
> > > [clip]
> > >
> > > Something is screwed up in your build environment: the `-shared` flag is
> > > missing from the link command.
> > >
> > > Perhaps you have set one of the the environment variables FFLAGS,
> > > CFLAGS, LDFLAGS?
> >
> > Also the `-undefined dynamic_lookup` flag.
>
> The consensus of the fink developers is that you are introducing a bug in both
> scipy and numpy. The build should be able to pass additional flags on these
> variables and the scipy/numpy build should be able to append any additional
> flags required. In particular, both MacPorts and fink will want to be able to
> pass -L/opt/local/lib or -L/sw/lib via LDFLAGS. The changes added to scipy and
> numpy have broken this and now require that these additional flags be manually
> patched into the Makefiles of numpy and scipy rather than just passing them
> on LDFLAGS as has always worked in the past.

Oh no it hasn't. It has been a consistent thorn in our side for a very long time. In the case of Fortran modules built by numpy.distutils, $LDFLAGS has replaced rather than appended flags since time immemorial. It is a compromise solution to work around the fact that the wide variety of Fortran compilers are very finicky about their flags, and distutils is not very accommodating about letting users change the flags to suit their local environments. If you think you have a better solution to this problem that does not degrade the existing flexibility, your PR will be cheerfully accepted. No one thinks this is desirable behavior, but it is most certainly not *new* behavior.

--
Robert Kern

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Re: [SciPy-Dev] 1.8.0rc1

Jack Howarth
On Tue, Oct 01, 2013 at 05:10:39PM +0100, Robert Kern wrote:

> On Tue, Oct 1, 2013 at 5:02 PM, Jack Howarth <[hidden email]>
> wrote:
> >
> > On Tue, Oct 01, 2013 at 04:52:06PM +0100, Robert Kern wrote:
> > > On Tue, Oct 1, 2013 at 4:41 PM, Pauli Virtanen <[hidden email]> wrote:
> > > >
> > > > Hi,
> > > >
> > > > 01.10.2013 16:28, Jack Howarth kirjoitti:
> > > > [clip]
> > > > > /sw/bin/python2.7 setup.py build
> > > > >
> > > > > which fails at...
> > > > >
> > > > > /sw/bin/gfortran -Wall -L/sw/lib
> > > build/temp.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_litemodule.o
> > >
> build/temp.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_lite/python_xerbla.o
> > > -L/sw/lib -L/sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin10.8.0/4.8.1
> > > -Lbuild/temp.macosx-10.6-x86_64-2.7 -llapack -lptf77blas -lptcblas
> -latlas
> > > -lgfortran -o
> build/lib.macosx-10.6-x86_64-2.7/numpy/linalg/lapack_lite.so
> > > > > Undefined symbols for architecture x86_64:
> > > > >   "_main", referenced from:
> > > > >       start in crt1.10.6.o
> > > > [clip]
> > > >
> > > > Something is screwed up in your build environment: the `-shared` flag
> is
> > > > missing from the link command.
> > > >
> > > > Perhaps you have set one of the the environment variables FFLAGS,
> > > > CFLAGS, LDFLAGS?
> > >
> > > Also the `-undefined dynamic_lookup` flag.
> >
> > The consensus of the fink developers is that you are introducing a bug in
> both
> > scipy and numpy. The build should be able to pass additional flags on
> these
> > variables and the scipy/numpy build should be able to append any
> additional
> > flags required. In particular, both MacPorts and fink will want to be
> able to
> > pass -L/opt/local/lib or -L/sw/lib via LDFLAGS. The changes added to
> scipy and
> > numpy have broken this and now require that these additional flags be
> manually
> > patched into the Makefiles of numpy and scipy rather than just passing
> them
> > on LDFLAGS as has always worked in the past.
>
> Oh no it hasn't. It has been a consistent thorn in our side for a very long
> time. In the case of Fortran modules built by numpy.distutils, $LDFLAGS has
> replaced rather than appended flags since time immemorial. It is a
> compromise solution to work around the fact that the wide variety of
> Fortran compilers are very finicky about their flags, and distutils is not
> very accommodating about letting users change the flags to suit their local
> environments. If you think you have a better solution to this problem that
> does not degrade the existing flexibility, your PR will be cheerfully
> accepted. No one thinks this is desirable behavior, but it is most
> certainly not *new* behavior.

Robert,
  Okay. Good news, bad news. The good news is that on fink for both darwin12 and darwin13,
using 'NoSetLDFLAGS: true' is sufficient to solve the linkage problems while retaining the
passing of -L/sw/lib for both numpy 1.8.0rc1 and current git of scipy 0.13.0. The resulting
numpy 1.8.0rc1, against python 2.7.5, on both darwin12 and darwin13 shows....

OK (KNOWNFAIL=5, SKIP=19)

The bad news is that while the scipy 0.13.0 git builds fine on darwin12 and darwin13 without
testsuite regressions against numpy 1.7.1, scipy 0.13.0 git shows failures against numpy 1.8.0rc1.
On darwin12, I get...

======================================================================
ERROR: Test that bode() finds a reasonable frequency range.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/tests/test_ltisys.py", line 473, in test_05
    w, mag, phase = bode(system, n=n)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/ltisys.py", line 1015, in bode
    w, y = freqresp(system, w=w, n=n)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/ltisys.py", line 1085, in freqresp
    w, h = freqs(sys.num.ravel(), sys.den, worN=worN)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/filter_design.py", line 142, in freqs
    w = findfreqs(b, a, N)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/filter_design.py", line 70, in findfreqs
    1.5 * ez.imag)) + 0.5)
  File "/sw/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2130, in amax
    out=out, keepdims=keepdims)
  File "/sw/lib/python2.7/site-packages/numpy/core/_methods.py", line 17, in _amax
    out=out, keepdims=keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

======================================================================
FAIL: test_cases (test_solvers.TestSolveDiscreteARE)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/linalg/tests/test_solvers.py", line 132, in test_cases
    self.check_case(case[0], case[1], case[2], case[3])
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/linalg/tests/test_solvers.py", line 128, in check_case
    a.getH()*x*a-(a.getH()*x*b)*inv(r+b.getH()*x*b)*(b.getH()*x*a)+q-x, 0.0)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

(mismatch 100.0%)
 x: matrix([[ 101.68132940 +8.47322212e-13j, -149.17526406 -1.74130113e+02j],
        [-149.17526406 +1.74130113e+02j,  517.05220513 +3.88311605e-12j]])
 y: array(0.0)

======================================================================
FAIL: Test method='gbt' with alpha=0.25 for tf and zpk cases.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/tests/test_cont2discrete.py", line 218, in test_gbt_with_sio_tf_and_zpk
    assert_allclose(dnum, c2dnum)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 1181, in assert_allclose
    verbose=verbose, header=header)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=1e-07, atol=0

(mismatch 100.0%)
 x: array([[ 0.7,  0. ]])
 y: array([[ 0. +0.00000000e+00j,  0. -2.32036388e+77j]])

======================================================================
FAIL: test_dimpulse (test_dltisys.TestDLTI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/tests/test_dltisys.py", line 172, in test_dimpulse
    assert_array_almost_equal(yout[0].flatten(), yout_tfimpulse)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

(mismatch 33.3333333333%)
 x: array([ 0.,  1.,  0.])
 y: array([ 0.,  1., -1.])

======================================================================
FAIL: test_dstep (test_dltisys.TestDLTI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/tests/test_dltisys.py", line 132, in test_dstep
    assert_array_almost_equal(yout[0].flatten(), yout_tfstep)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

(mismatch 33.3333333333%)
 x: array([ 0.,  1.,  1.])
 y: array([ 0.,  1.,  0.])

----------------------------------------------------------------------
Ran 9659 tests in 157.525s

FAILED (KNOWNFAIL=119, SKIP=444, errors=1, failures=4)

and on darwin13, I get...

======================================================================
ERROR: Test that bode() finds a reasonable frequency range.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/tests/test_ltisys.py", line 473, in test_05
    w, mag, phase = bode(system, n=n)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/ltisys.py", line 1015, in bode
    w, y = freqresp(system, w=w, n=n)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/ltisys.py", line 1085, in freqresp
    w, h = freqs(sys.num.ravel(), sys.den, worN=worN)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/filter_design.py", line 142, in freqs
    w = findfreqs(b, a, N)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/filter_design.py", line 70, in findfreqs
    1.5 * ez.imag)) + 0.5)
  File "/sw/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2130, in amax
    out=out, keepdims=keepdims)
  File "/sw/lib/python2.7/site-packages/numpy/core/_methods.py", line 17, in _amax
    out=out, keepdims=keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

======================================================================
ERROR: test_ltisys.Test_freqresp.test_freq_range
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/tests/test_ltisys.py", line 570, in test_freq_range
    w, H = freqresp(system, n=n)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/ltisys.py", line 1085, in freqresp
    w, h = freqs(sys.num.ravel(), sys.den, worN=worN)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/filter_design.py", line 142, in freqs
    w = findfreqs(b, a, N)
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/filter_design.py", line 70, in findfreqs
    1.5 * ez.imag)) + 0.5)
  File "/sw/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2130, in amax
    out=out, keepdims=keepdims)
  File "/sw/lib/python2.7/site-packages/numpy/core/_methods.py", line 17, in _amax
    out=out, keepdims=keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

======================================================================
FAIL: test_cases (test_solvers.TestSolveDiscreteARE)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/linalg/tests/test_solvers.py", line 132, in test_cases
    self.check_case(case[0], case[1], case[2], case[3])
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/linalg/tests/test_solvers.py", line 128, in check_case
    a.getH()*x*a-(a.getH()*x*b)*inv(r+b.getH()*x*b)*(b.getH()*x*a)+q-x, 0.0)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

(mismatch 100.0%)
 x: matrix([[ -2.42159197e+221 +1.62702106e+235j,
           2.78628694e+235 -2.38697996e+235j],
        [ -2.78628694e+235 -2.38697996e+235j,
          -1.06747728e+222 +8.27344440e+235j]])
 y: array(0.0)

======================================================================
FAIL: Test method='gbt' with alpha=0.25 for tf and zpk cases.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/tests/test_cont2discrete.py", line 218, in test_gbt_with_sio_tf_and_zpk
    assert_allclose(dnum, c2dnum)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 1181, in assert_allclose
    verbose=verbose, header=header)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=1e-07, atol=0

(mismatch 100.0%)
 x: array([[ 0.7,  1.4]])
 y: array([[ 0.5 +1.07561885e-232j,  1.0 -2.00390128e+000j]])

======================================================================
FAIL: test_dimpulse (test_dltisys.TestDLTI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/tests/test_dltisys.py", line 172, in test_dimpulse
    assert_array_almost_equal(yout[0].flatten(), yout_tfimpulse)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

(mismatch 33.3333333333%)
 x: array([ 0.,  1., -2.])
 y: array([ 0.,  1., -1.])

======================================================================
FAIL: test_dstep (test_dltisys.TestDLTI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/src/fink.build/root-scipy-py27-0.13.0b1-0/sw/lib/python2.7/site-packages/scipy/signal/tests/test_dltisys.py", line 132, in test_dstep
    assert_array_almost_equal(yout[0].flatten(), yout_tfstep)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

(mismatch 33.3333333333%)
 x: array([ 0.,  1., -1.])
 y: array([ 0.,  1.,  0.])

----------------------------------------------------------------------
Ran 9659 tests in 148.120s

FAILED (KNOWNFAIL=119, SKIP=444, errors=2, failures=4)

FYI.


>
> --
> Robert Kern

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Re: 1.8.0rc1

Piet van Oostrum
In reply to this post by Charles R Harris
Charles R Harris <[hidden email]> writes:

> Hi All,
>
> NumPy 1.8.0rc1 is up now on sourceforge .The binary builds are included except for Python 3.3 on
> windows, which will arrive later. Many thanks to Ralf for the binaries, and to those who found and
> fixed the bugs in the last beta. Any remaining bugs are all my fault ;) I hope this will be the
> last release before final, so please test it thoroughly.

I have installed 1.0.8rc1 on Python 3.3.2 on Mac OS X Snow Leopard (10.6.8) from the binary installer http://ufpr.dl.sourceforge.net/project/numpy/NumPy/1.8.0rc1/numpy-1.8.0rc1-py3.3-python.org-macosx10.6.dmg an the test fails with 20 errors. I have tried it also with installing from source but it also gives these erros (I haven't checked if the errors are the same bit for bit, but they were also 20). Here is the output of the test run.



--
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WWW: http://pietvanoostrum.com/
PGP key: [8DAE142BE17999C4]

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Re: 1.8.0rc1

Charles R Harris



On Wed, Oct 2, 2013 at 2:31 PM, Piet van Oostrum <[hidden email]> wrote:
Charles R Harris <[hidden email]> writes:

> Hi All,
>
> NumPy 1.8.0rc1 is up now on sourceforge .The binary builds are included except for Python 3.3 on
> windows, which will arrive later. Many thanks to Ralf for the binaries, and to those who found and
> fixed the bugs in the last beta. Any remaining bugs are all my fault ;) I hope this will be the
> last release before final, so please test it thoroughly.

I have installed 1.0.8rc1 on Python 3.3.2 on Mac OS X Snow Leopard (10.6.8) from the binary installer http://ufpr.dl.sourceforge.net/project/numpy/NumPy/1.8.0rc1/numpy-1.8.0rc1-py3.3-python.org-macosx10.6.dmg an the test fails with 20 errors. I have tried it also with installing from source but it also gives these erros (I haven't checked if the errors are the same bit for bit, but they were also 20). Here is the output of the test run.

 
I'd guess you have the wrong Fortran. IIRC, you have to get it somewhere else than from Apple. Someone else here would know.

Chuck


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Re: 1.8.0rc1

Matthew Brett
Hi,

On Wed, Oct 2, 2013 at 3:42 PM, Charles R Harris
<[hidden email]> wrote:

>
>
>
> On Wed, Oct 2, 2013 at 2:31 PM, Piet van Oostrum <[hidden email]>
> wrote:
>>
>> Charles R Harris <[hidden email]> writes:
>>
>> > Hi All,
>> >
>> > NumPy 1.8.0rc1 is up now on sourceforge .The binary builds are included
>> > except for Python 3.3 on
>> > windows, which will arrive later. Many thanks to Ralf for the binaries,
>> > and to those who found and
>> > fixed the bugs in the last beta. Any remaining bugs are all my fault ;)
>> > I hope this will be the
>> > last release before final, so please test it thoroughly.
>>
>> I have installed 1.0.8rc1 on Python 3.3.2 on Mac OS X Snow Leopard
>> (10.6.8) from the binary installer
>> http://ufpr.dl.sourceforge.net/project/numpy/NumPy/1.8.0rc1/numpy-1.8.0rc1-py3.3-python.org-macosx10.6.dmg
>> an the test fails with 20 errors. I have tried it also with installing from
>> source but it also gives these erros (I haven't checked if the errors are
>> the same bit for bit, but they were also 20). Here is the output of the test
>> run.
>>
>
> I'd guess you have the wrong Fortran. IIRC, you have to get it somewhere
> else than from Apple. Someone else here would know.

I don't think he should need Fortran installing from the binary
installer - should he?

Cheers,

Matthew
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Re: 1.8.0rc1

Charles R Harris



On Wed, Oct 2, 2013 at 4:48 PM, Matthew Brett <[hidden email]> wrote:
Hi,

On Wed, Oct 2, 2013 at 3:42 PM, Charles R Harris
<[hidden email]> wrote:
>
>
>
> On Wed, Oct 2, 2013 at 2:31 PM, Piet van Oostrum <[hidden email]>
> wrote:
>>
>> Charles R Harris <[hidden email]> writes:
>>
>> > Hi All,
>> >
>> > NumPy 1.8.0rc1 is up now on sourceforge .The binary builds are included
>> > except for Python 3.3 on
>> > windows, which will arrive later. Many thanks to Ralf for the binaries,
>> > and to those who found and
>> > fixed the bugs in the last beta. Any remaining bugs are all my fault ;)
>> > I hope this will be the
>> > last release before final, so please test it thoroughly.
>>
>> I have installed 1.0.8rc1 on Python 3.3.2 on Mac OS X Snow Leopard
>> (10.6.8) from the binary installer
>> http://ufpr.dl.sourceforge.net/project/numpy/NumPy/1.8.0rc1/numpy-1.8.0rc1-py3.3-python.org-macosx10.6.dmg
>> an the test fails with 20 errors. I have tried it also with installing from
>> source but it also gives these erros (I haven't checked if the errors are
>> the same bit for bit, but they were also 20). Here is the output of the test
>> run.
>>
>
> I'd guess you have the wrong Fortran. IIRC, you have to get it somewhere
> else than from Apple. Someone else here would know.

I don't think he should need Fortran installing from the binary
installer - should he?

Cheers,


The f2py tests use it. Apparently he has a Fortran, it is just the wrong one.

Chuck


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Re: 1.8.0rc1

Matthew Brett
On Wed, Oct 2, 2013 at 4:07 PM, Charles R Harris
<[hidden email]> wrote:

>
>
>
> On Wed, Oct 2, 2013 at 4:48 PM, Matthew Brett <[hidden email]>
> wrote:
>>
>> Hi,
>>
>> On Wed, Oct 2, 2013 at 3:42 PM, Charles R Harris
>> <[hidden email]> wrote:
>> >
>> >
>> >
>> > On Wed, Oct 2, 2013 at 2:31 PM, Piet van Oostrum <[hidden email]>
>> > wrote:
>> >>
>> >> Charles R Harris <[hidden email]> writes:
>> >>
>> >> > Hi All,
>> >> >
>> >> > NumPy 1.8.0rc1 is up now on sourceforge .The binary builds are
>> >> > included
>> >> > except for Python 3.3 on
>> >> > windows, which will arrive later. Many thanks to Ralf for the
>> >> > binaries,
>> >> > and to those who found and
>> >> > fixed the bugs in the last beta. Any remaining bugs are all my fault
>> >> > ;)
>> >> > I hope this will be the
>> >> > last release before final, so please test it thoroughly.
>> >>
>> >> I have installed 1.0.8rc1 on Python 3.3.2 on Mac OS X Snow Leopard
>> >> (10.6.8) from the binary installer
>> >>
>> >> http://ufpr.dl.sourceforge.net/project/numpy/NumPy/1.8.0rc1/numpy-1.8.0rc1-py3.3-python.org-macosx10.6.dmg
>> >> an the test fails with 20 errors. I have tried it also with installing
>> >> from
>> >> source but it also gives these erros (I haven't checked if the errors
>> >> are
>> >> the same bit for bit, but they were also 20). Here is the output of the
>> >> test
>> >> run.
>> >>
>> >
>> > I'd guess you have the wrong Fortran. IIRC, you have to get it somewhere
>> > else than from Apple. Someone else here would know.
>>
>> I don't think he should need Fortran installing from the binary
>> installer - should he?
>>
>> Cheers,
>>
>
> The f2py tests use it. Apparently he has a Fortran, it is just the wrong
> one.

Aha - yes - that makes sense,

Thanks,

Matthew
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Re: 1.8.0rc1

ralfgommers
In reply to this post by Charles R Harris



On Thu, Oct 3, 2013 at 1:07 AM, Charles R Harris <[hidden email]> wrote:



On Wed, Oct 2, 2013 at 4:48 PM, Matthew Brett <[hidden email]> wrote:
Hi,

On Wed, Oct 2, 2013 at 3:42 PM, Charles R Harris
<[hidden email]> wrote:
>
>
>
> On Wed, Oct 2, 2013 at 2:31 PM, Piet van Oostrum <[hidden email]>
> wrote:
>>
>> Charles R Harris <[hidden email]> writes:
>>
>> > Hi All,
>> >
>> > NumPy 1.8.0rc1 is up now on sourceforge .The binary builds are included
>> > except for Python 3.3 on
>> > windows, which will arrive later. Many thanks to Ralf for the binaries,
>> > and to those who found and
>> > fixed the bugs in the last beta. Any remaining bugs are all my fault ;)
>> > I hope this will be the
>> > last release before final, so please test it thoroughly.
>>
>> I have installed 1.0.8rc1 on Python 3.3.2 on Mac OS X Snow Leopard
>> (10.6.8) from the binary installer
>> http://ufpr.dl.sourceforge.net/project/numpy/NumPy/1.8.0rc1/numpy-1.8.0rc1-py3.3-python.org-macosx10.6.dmg
>> an the test fails with 20 errors. I have tried it also with installing from
>> source but it also gives these erros (I haven't checked if the errors are
>> the same bit for bit, but they were also 20). Here is the output of the test
>> run.
>>
>
> I'd guess you have the wrong Fortran. IIRC, you have to get it somewhere
> else than from Apple. Someone else here would know.

I don't think he should need Fortran installing from the binary
installer - should he?

Cheers,


The f2py tests use it. Apparently he has a Fortran, it is just the wrong one.

Piet, you should get one of the ones recommended at http://scipy.org/scipylib/building/macosx.html#fortran 

The last error, test_io.TestSavezLoad, is real though. I can reproduce it, will try to figure it out.

Ralf


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Re: 1.8.0rc1

Piet van Oostrum
Ralf Gommers <[hidden email]> writes:

> Piet, you should get one of the ones recommended at http://scipy.org/scipylib/building/macosx.html
> #fortran 
>
> The last error, test_io.TestSavezLoad, is real though. I can reproduce it, will try to figure it
> out.
>
I have installed gfortran 4.2.3, which is the one recommended for Snow leopard:

bash-3.2$ gfortran -v
Using built-in specs.
Target: i686-apple-darwin8
Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/local --mandir=/share/man --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --build=i686-apple-darwin8 --host=i686-apple-darwin8 --target=i686-apple-darwin8 --enable-languages=fortran
Thread model: posix
gcc version 4.2.3

--
Piet van Oostrum <[hidden email]>
WWW: http://pietvanoostrum.com/
PGP key: [8DAE142BE17999C4]

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Re: 1.8.0rc1

ralfgommers



On Sat, Oct 5, 2013 at 5:34 AM, Piet van Oostrum <[hidden email]> wrote:
Ralf Gommers <[hidden email]> writes:

> Piet, you should get one of the ones recommended at http://scipy.org/scipylib/building/macosx.html
> #fortran 
>
> The last error, test_io.TestSavezLoad, is real though. I can reproduce it, will try to figure it
> out.
>
I have installed gfortran 4.2.3, which is the one recommended for Snow leopard:

bash-3.2$ gfortran -v
Using built-in specs.
Target: i686-apple-darwin8
Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/local --mandir=/share/man --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --build=i686-apple-darwin8 --host=i686-apple-darwin8 --target=i686-apple-darwin8 --enable-languages=fortran
Thread model: posix
gcc version 4.2.3

I can't reproduce it with the exact same OS and Fortran compiler. Looking at the tracebacks a bit more carefully, I see that the compile fails on missing symbols from the Python C API. Did you install Python with the dmg installer from python.org? And can you give the output of "$ locate Python.h"?

Ralf

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Re: 1.8.0rc1

Piet van Oostrum
I should have added that yes, I have installed the DMG from python.org.
--
Piet van Oostrum <[hidden email]>
WWW: http://pietvanoostrum.com/
PGP key: [8DAE142BE17999C4]

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Re: 1.8.0rc1

Piet van Oostrum
In reply to this post by ralfgommers
Ralf Gommers <[hidden email]> writes:

> On Sat, Oct 5, 2013 at 5:34 AM, Piet van Oostrum <[hidden email]> wrote:
>
>     Ralf Gommers <[hidden email]> writes:
>    
>     > Piet, you should get one of the ones recommended at http://scipy.org/scipylib/building/
>     macosx.html
>     > #fortran 
>     >
>     > The last error, test_io.TestSavezLoad, is real though. I can reproduce it, will try to
>     figure it
>     > out.
>     >
>     I have installed gfortran 4.2.3, which is the one recommended for Snow leopard:
>    
>     bash-3.2$ gfortran -v
>     Using built-in specs.
>     Target: i686-apple-darwin8
>     Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/local --mandir=/share/man
>     --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --build=i686-apple-darwin8 --host=
>     i686-apple-darwin8 --target=i686-apple-darwin8 --enable-languages=fortran
>     Thread model: posix
>     gcc version 4.2.3
>
> I can't reproduce it with the exact same OS and Fortran compiler. Looking at the tracebacks a bit
> more carefully, I see that the compile fails on missing symbols from the Python C API. Did you
> install Python with the dmg installer from python.org? And can you give the output of "$ locate
> Python.h"?

It does contain (among others) /Library/Frameworks/Python.framework/Versions/3.3/include/python3.3m/Python.h (I am using Python 3.3.2)

I have some progress: I reinstalled XCode 3.2.6 after removing the old XCode. And I run the test with the default gcc, which is gcc-4.2 (=version 4.2.1).

$ gcc-4.2 -v
Using built-in specs.
Target: i686-apple-darwin10
Configured with: /var/tmp/gcc/gcc-5666.3~6/src/configure --disable-checking --enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10- --host=x86_64-apple-darwin10 --target=i686-apple-darwin10 --with-gxx-include-dir=/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Apple Inc. build 5666) (dot 3)

On my previous test I used

$ export CC=/usr/bin/gcc-4.0
$ export CXX=/usr/bin/g++-4.0

as recommended in http://scipy.org/scipylib/building/macosx.html, but maybe this recommendation is outdated as the Python is compiled with gcc version 4.2.1

Now there is only one error left:

ERROR: test_big_arrays (test_io.TestSavezLoad)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/testing/decorators.py", line 146, in skipper_func
    return f(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/lib/tests/test_io.py", line 149, in test_big_arrays
    np.savez(tmp, a=a)
  File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/lib/npyio.py", line 530, in savez
    _savez(file, args, kwds, False)
  File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/lib/npyio.py", line 589, in _savez
    format.write_array(fid, np.asanyarray(val))
  File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/lib/format.py", line 417, in write_array
    fp.write(array.tostring('C'))
OSError: [Errno 22] Invalid argument

That's the one you mentioned I think.
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WWW: http://pietvanoostrum.com/
PGP key: [8DAE142BE17999C4]

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Re: 1.8.0rc1

ralfgommers



On Mon, Oct 7, 2013 at 1:48 PM, Piet van Oostrum <[hidden email]> wrote:
Ralf Gommers <[hidden email]> writes:

> On Sat, Oct 5, 2013 at 5:34 AM, Piet van Oostrum <[hidden email]> wrote:
>
>     Ralf Gommers <[hidden email]> writes:
>
>     > Piet, you should get one of the ones recommended at http://scipy.org/scipylib/building/
>     macosx.html
>     > #fortran 
>     >
>     > The last error, test_io.TestSavezLoad, is real though. I can reproduce it, will try to
>     figure it
>     > out.
>     >
>     I have installed gfortran 4.2.3, which is the one recommended for Snow leopard:
>
>     bash-3.2$ gfortran -v
>     Using built-in specs.
>     Target: i686-apple-darwin8
>     Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/local --mandir=/share/man
>     --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --build=i686-apple-darwin8 --host=
>     i686-apple-darwin8 --target=i686-apple-darwin8 --enable-languages=fortran
>     Thread model: posix
>     gcc version 4.2.3
>
> I can't reproduce it with the exact same OS and Fortran compiler. Looking at the tracebacks a bit
> more carefully, I see that the compile fails on missing symbols from the Python C API. Did you
> install Python with the dmg installer from python.org? And can you give the output of "$ locate
> Python.h"?

It does contain (among others) /Library/Frameworks/Python.framework/Versions/3.3/include/python3.3m/Python.h (I am using Python 3.3.2)

I have some progress: I reinstalled XCode 3.2.6 after removing the old XCode. And I run the test with the default gcc, which is gcc-4.2 (=version 4.2.1).

$ gcc-4.2 -v
Using built-in specs.
Target: i686-apple-darwin10
Configured with: /var/tmp/gcc/gcc-5666.3~6/src/configure --disable-checking --enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10- --host=x86_64-apple-darwin10 --target=i686-apple-darwin10 --with-gxx-include-dir=/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Apple Inc. build 5666) (dot 3)

On my previous test I used

$ export CC=/usr/bin/gcc-4.0
$ export CXX=/usr/bin/g++-4.0

as recommended in http://scipy.org/scipylib/building/macosx.html, but maybe this recommendation is outdated as the Python is compiled with gcc version 4.2.1

Ah yes. The recommendation is still valid for Python 2.6, which was the highest Python version available at the time those instructions were written. Python 2.7 from python.org was compiled with gcc 4.2 instead of 4.0.
 

Now there is only one error left:

ERROR: test_big_arrays (test_io.TestSavezLoad)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/testing/decorators.py", line 146, in skipper_func
    return f(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/lib/tests/test_io.py", line 149, in test_big_arrays
    np.savez(tmp, a=a)
  File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/lib/npyio.py", line 530, in savez
    _savez(file, args, kwds, False)
  File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/lib/npyio.py", line 589, in _savez
    format.write_array(fid, np.asanyarray(val))
  File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/lib/format.py", line 417, in write_array
    fp.write(array.tostring('C'))
OSError: [Errno 22] Invalid argument

That's the one you mentioned I think.

Indeed. That error will be silenced in the final 1.8.0 release. You've got everything working correctly now.

Cheers,
Ralf

 
--
Piet van Oostrum <[hidden email]>
WWW: http://pietvanoostrum.com/
PGP key: [8DAE142BE17999C4]

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