numpy build/installation problems ?
I wanted to finally upgrade my numpy, so I can build scipy trunk again, but I get test failures with numpy. And running the tests of the previously compiled version of scipy crashes in signaltools. Is this a problem with my build (the usual official MingW on WindowsXP), or are there still ABI problems in numpy trunk? I did the build twice with (I think) clean directories and get the same result. Thanks, Josef Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information.
import numpy numpy.__file__ 'C:\\Josef\\_progs\\Subversion\\numpy-trunk\\dist\\numpy-1.4.0.dev7539.win32\\Pr ograms\\Python25\\Lib\\site-packages\\numpy\\__init__.py' numpy.test() Running unit tests for numpy NumPy version 1.4.0.dev7539 NumPy is installed in C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.de v7539.win32\Programs\Python25\Lib\site-packages\numpy Python version 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Int el)] nose version 0.11.1 ................................. \u03a3 .[[' abc' ''] ['12345' 'MixedCase'] ['123 345' 'UPPER']] ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ............................K................................................... ..FF.......................FFFF................................................. ................................................................................ ................................................................................ ................................................................................ ................................................................................ ............................................................................C:\J osef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Programs\Pytho n25\Lib\site-packages\numpy\lib\io.py:1332: ConversionWarning: Some errors were detected ! Line #2 (got 4 columns instead of 5) Line #12 (got 4 columns instead of 5) Line #22 (got 4 columns instead of 5) Line #32 (got 4 columns instead of 5) Line #42 (got 4 columns instead of 5) warnings.warn(errmsg, ConversionWarning) .C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Programs\ Python25\Lib\site-packages\numpy\lib\io.py:1332: ConversionWarning: Some errors were detected ! Line #2 (got 4 columns instead of 2) Line #12 (got 4 columns instead of 2) Line #22 (got 4 columns instead of 2) Line #32 (got 4 columns instead of 2) Line #42 (got 4 columns instead of 2) warnings.warn(errmsg, ConversionWarning) ................E.E.EE....................K........K............F............... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ..S............................................................................. ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ............................. ====================================================================== ERROR: Test giving usecols with a comma-separated string
Traceback (most recent call last):
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\lib\tests\test_io.py", line 747, in test
_usecols_as_css
names="a, b, c", usecols="a, c")
File "\Programs\Python25\Lib\site-packages\numpy\lib\io.py", line 1099, in gen
fromtxt
the docstring of the `genfromtxt` function.
AttributeError: 'tuple' object has no attribute 'index'
======================================================================
ERROR: Test usecols with named columns
----------------------------------------------------------------------
Traceback (most recent call last):
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\lib\tests\test_io.py", line 773, in test
_usecols_with_named_columns
usecols=('a', 'c'), **kwargs)
File "\Programs\Python25\Lib\site-packages\numpy\lib\io.py", line 1099, in gen
fromtxt
the docstring of the `genfromtxt` function.
AttributeError: 'tuple' object has no attribute 'index'
======================================================================
ERROR: Test with missing and filling values
----------------------------------------------------------------------
Traceback (most recent call last):
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\lib\tests\test_io.py", line 861, in test
_user_filling_values
test = np.genfromtxt(StringIO.StringIO(data), **kwargs)
File "\Programs\Python25\Lib\site-packages\numpy\lib\io.py", line 1127, in gen
fromtxt
See Also
AttributeError: 'tuple' object has no attribute 'index'
======================================================================
ERROR: test_user_missing_values (test_io.TestFromTxt)
----------------------------------------------------------------------
Traceback (most recent call last):
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\lib\tests\test_io.py", line 845, in test
_user_missing_values
**basekwargs)
File "\Programs\Python25\Lib\site-packages\numpy\lib\io.py", line 1481, in maf
romtxt
File "\Programs\Python25\Lib\site-packages\numpy\lib\io.py", line 1127, in gen
fromtxt
See Also
AttributeError: 'tuple' object has no attribute 'index'
======================================================================
FAIL: test_umath.test_hypot_special_values(1.#QNAN, 1.#INF)
----------------------------------------------------------------------
Traceback (most recent call last):
File "c:\programs\python25\lib\site-packages\nose-0.11.1-py2.5.egg\nose\case.p
y", line 183, in runTest
self.test(*self.arg)
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\core\tests\test_umath.py", line 211, in
assert_hypot_isinf
assert np.isinf(ncu.hypot(x, y))
AssertionError
======================================================================
FAIL: test_umath.test_hypot_special_values(1.#INF, 1.#QNAN)
----------------------------------------------------------------------
Traceback (most recent call last):
File "c:\programs\python25\lib\site-packages\nose-0.11.1-py2.5.egg\nose\case.p
y", line 183, in runTest
self.test(*self.arg)
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\core\tests\test_umath.py", line 211, in
assert_hypot_isinf
assert np.isinf(ncu.hypot(x, y))
AssertionError
======================================================================
FAIL: test_umath.test_arctan2_special_values(nan, 2.3561944901923448)
----------------------------------------------------------------------
Traceback (most recent call last):
File "c:\programs\python25\lib\site-packages\nose-0.11.1-py2.5.egg\nose\case.p
y", line 183, in runTest
self.test(*self.arg)
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\testing\utils.py", line 449, in assert_a
lmost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal
ACTUAL: nan
DESIRED: 2.3561944901923448
======================================================================
FAIL: test_umath.test_arctan2_special_values(nan, -2.3561944901923448)
----------------------------------------------------------------------
Traceback (most recent call last):
File "c:\programs\python25\lib\site-packages\nose-0.11.1-py2.5.egg\nose\case.p
y", line 183, in runTest
self.test(*self.arg)
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\testing\utils.py", line 449, in assert_a
lmost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal
ACTUAL: nan
DESIRED: -2.3561944901923448
======================================================================
FAIL: test_umath.test_arctan2_special_values(nan, 0.78539816339744828)
----------------------------------------------------------------------
Traceback (most recent call last):
File "c:\programs\python25\lib\site-packages\nose-0.11.1-py2.5.egg\nose\case.p
y", line 183, in runTest
self.test(*self.arg)
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\testing\utils.py", line 449, in assert_a
lmost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal
ACTUAL: nan
DESIRED: 0.78539816339744828
======================================================================
FAIL: test_umath.test_arctan2_special_values(nan, -0.78539816339744828)
----------------------------------------------------------------------
Traceback (most recent call last):
File "c:\programs\python25\lib\site-packages\nose-0.11.1-py2.5.egg\nose\case.p
y", line 183, in runTest
self.test(*self.arg)
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\testing\utils.py", line 449, in assert_a
lmost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal
ACTUAL: nan
DESIRED: -0.78539816339744828
======================================================================
FAIL: test_doctests (test_polynomial.TestDocs)
----------------------------------------------------------------------
Traceback (most recent call last):
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\lib\tests\test_polynomial.py", line 90,
in test_doctests
return rundocs()
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Pr
ograms\Python25\Lib\site-packages\numpy\testing\utils.py", line 951, in rundocs
raise AssertionError("Some doctests failed:\n%s" % "\n".join(msg))
AssertionError: Some doctests failed:
**********************************************************************
File "C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.dev7539.win32\Prog
rams\Python25\Lib\site-packages\numpy\lib\tests\test_polynomial.py", line 20, in
test_polynomial
Failed example:
print poly1d([100e-90, 1.234567e-9j+3, -1234.999e8])
Expected:
2
1e-88 x + (3 + 1.235e-09j) x - 1.235e+11
Got:
2
1e-088 x + (3 + 1.235e-009j) x - 1.235e+011
----------------------------------------------------------------------
Ran 2140 tests in 13.281s
FAILED (KNOWNFAIL=3, SKIP=1, errors=4, failures=7)
import scipy scipy.__file__ 'c:\\josef\\eclipsegworkspace\\scipy-trunk-work\\scipytrunkcopy\\scipy\\__init__ .pyc' scipy.test() Running unit tests for scipy NumPy version 1.4.0.dev7539 NumPy is installed in C:\Josef\_progs\Subversion\numpy-trunk\dist\numpy-1.4.0.de v7539.win32\Programs\Python25\Lib\site-packages\numpy SciPy version 0.8.0.dev SciPy is installed in c:\josef\eclipsegworkspace\scipy-trunk-work\scipytrunkcopy \scipy Python version 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Int el)] nose version 0.11.1 E..... ...
crash with verbose the last tests are test_rank1 (test_signaltools.TestCorrelateComplexSingle) ... ok test_rank3 (test_signaltools.TestCorrelateComplexSingle) ... ok test_rank1 (test_signaltools.TestCorrelateDouble) ... ok test_rank3 (test_signaltools.TestCorrelateDouble) ... ok test_rank1 (test_signaltools.TestCorrelateExtended) ... ok test_rank3 (test_signaltools.TestCorrelateExtended) ... ok test_rank1 (test_signaltools.TestCorrelateObject) ... ok test_rank3 (test_signaltools.TestCorrelateObject) ... ok test_rank1 (test_signaltools.TestCorrelateSingle) ... ok test_rank3 (test_signaltools.TestCorrelateSingle) ... ok test_signaltools.TestDecimate.test_basic ... crash
On Mon, Oct 19, 2009 at 10:40 AM,
I wanted to finally upgrade my numpy, so I can build scipy trunk again, but I get test failures with numpy. And running the tests of the previously compiled version of scipy crashes in signaltools.
Is this a problem with my build (the usual official MingW on WindowsXP), or are there still ABI problems in numpy trunk? I did the build twice with (I think) clean directories and get the same result.
Thanks,
Josef
Forgot to mention my previous version of scipy was build against numpy release 1.3.0 I recompiled scipy, and have no problems building and running scipy trunk against numpy trunk. One problem I had, was that during the build of scipy, gcc failed with unknown npymath. I had to copy the file libnpymath.a to my Python libs directory, then the build finished without problems. Josef
On Oct 19, 2009, at 10:40 AM, josef.pktd@gmail.com wrote:
I wanted to finally upgrade my numpy, so I can build scipy trunk again, but I get test failures with numpy. And running the tests of the previously compiled version of scipy crashes in signaltools.
The ConversionWarnings are expected. I'm probably to be blamed for the AttributeErrors (I'm testing on 2.6 where tuples do have an index Attribute), I gonna check that.
I had the same 4 errors in genfromtext yesterday when I upgraded numpy r 7539.
mac os x python 2.5.2.
--George.
2009/10/19 Pierre GM
On Oct 19, 2009, at 10:40 AM, josef.pktd@gmail.com wrote:
I wanted to finally upgrade my numpy, so I can build scipy trunk again, but I get test failures with numpy. And running the tests of the previously compiled version of scipy crashes in signaltools.
The ConversionWarnings are expected. I'm probably to be blamed for the AttributeErrors (I'm testing on 2.6 where tuples do have an index Attribute), I gonna check that. _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
On Oct 19, 2009, at 12:01 PM, George Nurser wrote:
I had the same 4 errors in genfromtext yesterday when I upgraded numpy r 7539. mac os x python 2.5.2.
I'm on it, should be fixed in a few hours. Please, don't hesitate to open a ticket next time (so that I remember to test on 2.5 as well...). Thx
participants (3)
-
George Nurser -
josef.pktd＠gmail.com -
Pierre GM