>>> ====================================================================== >>> ERROR: test_multiarray.TestNewBufferProtocol.test_relaxed_strides >>> ---------------------------------------------------------------------- >>> Traceback (most recent call last): >>> File >>> "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/nose/case.py", >>> line 197, in runTest >>> self.test(*self.arg) >>> File >>> "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/core/tests/test_multiarray.py", >>> line 5366, in test_relaxed_strides >>> fd.write(c.data) >>> TypeError: 'buffer' does not have the buffer interface >>> >>> ---------------------------------------------------------------------- >>> >>> >>> * Scipy tests pass with one error in TestNanFuncs, but the interpreter >>> crashes immediately afterwards. >>> >>> >>> Same machine, python 3.5: both numpy and scipy tests pass. >> >> Ouch - great that you found these, I'll take a look, > > I think these are problems with numpy and Python 2.7.3 - because I got > the same "TypeError: 'buffer' does not have the buffer interface" on > numpy with OS X with Python.org python 2.7.3, installing from a wheel, > or installing from source.
Indeed --- updated to python 2.7.11 (Thanks Felix Krull!) and the failure is gone, `numpy.test()` passes. However: >>> numpy.test("full") Running unit tests for numpy NumPy version 1.10.4 NumPy relaxed strides checking option: False NumPy is installed in /home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy Python version 2.7.11 (default, Dec 14 2015, 22:56:59) [GCC 4.6.3] nose version 1.3.7 <snip> ====================================================================== ERROR: test_kind.TestKind.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/nose/util.py", line 471, in try_run return func() File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 367, in setUp module_name=self.module_name) File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 79, in wrapper memo[key] = func(*a, **kw) File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 150, in build_module __import__(module_name) ImportError: /home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/core/../.libs/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /tmp/tmpPVjYDE/_test_ext_module_5405.so) ====================================================================== ERROR: test_mixed.TestMixed.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/nose/util.py", line 471, in try_run return func() File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 367, in setUp module_name=self.module_name) File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 79, in wrapper memo[key] = func(*a, **kw) File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 150, in build_module __import__(module_name) ImportError: /home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/core/../.libs/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /tmp/tmpPVjYDE/_test_ext_module_5405.so) ====================================================================== ERROR: test_mixed.TestMixed.test_docstring ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/nose/util.py", line 471, in try_run return func() File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 367, in setUp module_name=self.module_name) File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 85, in wrapper raise ret ImportError: /home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/core/../.libs/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /tmp/tmpPVjYDE/_test_ext_module_5405.so) ====================================================================== ERROR: test_basic (test_function_base.TestMedian) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/lib/tests/test_function_base.py", line 2361, in test_basic assert_(w[0].category is RuntimeWarning) IndexError: list index out of range ====================================================================== ERROR: test_nan_behavior (test_function_base.TestMedian) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/lib/tests/test_function_base.py", line 2464, in test_nan_behavior assert_(w[0].category is RuntimeWarning) IndexError: list index out of range ====================================================================== FAIL: test_default (test_numeric.TestSeterr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/core/tests/test_numeric.py", line 281, in test_default under='ignore', AssertionError: {'over': 'raise', 'divide': 'warn', 'invalid': 'warn', 'under': 'ignore'} != {'over': 'warn', 'divide': 'warn', 'invalid': 'warn', 'under': 'ignore'} - {'divide': 'warn', 'invalid': 'warn', 'over': 'raise', 'under': 'ignore'} ? ^^^^ + {'divide': 'warn', 'invalid': 'warn', 'over': 'warn', 'under': 'ignore'} ? ++ ^ ====================================================================== FAIL: test_allnans (test_nanfunctions.TestNanFunctions_Median) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/lib/tests/test_nanfunctions.py", line 544, in test_allnans assert_(len(w) == 1) File "/home/br/virtualenvs/manylinux/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 53, in assert_ raise AssertionError(smsg) AssertionError ---------------------------------------------------------------------- Ran 6148 tests in 77.301s FAILED (KNOWNFAIL=3, SKIP=6, errors=5, failures=2) <nose.result.TextTestResult run=6148 errors=5 failures=2> Not sure if any of these are present for python 2.7.3 and can no longer easily test. `scipy.test("full")` almost passes, there's a bunch of warnings-related noise and https://github.com/scipy/scipy/issues/5823 Nothing too bad on that machine, it seems :-). > I also get a scipy segfault with scipy 0.17.0 installed from an OSX > wheel, with output ending: > > test_check_finite (test_basic.TestLstsq) ... > /Users/mb312/.virtualenvs/test/lib/python2.7/site-packages/scipy/linalg/basic.py:884: > RuntimeWarning: internal gelsd driver lwork query error, required > iwork dimension not returned. This is likely the result of LAPACK bug > 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to > 'gelss' driver. > warnings.warn(mesg, RuntimeWarning) > ok > test_random_complex_exact (test_basic.TestLstsq) ... FAIL > test_random_complex_overdet (test_basic.TestLstsq) ... Bus error Oh, that one again... > This is so whether scipy is running on top of source- or wheel-built > numpy, and for a scipy built from source. > > Same numpy error installing on a bare Ubuntu 12.04, either installing > from a wheel built on 12.04 on travis: > > pip install -f http://travis-wheels.scikit-image.org --trusted-host > travis-wheels.scikit-image.org --no-index numpy > > or from numpy built from source. > > I can't replicate the segfault with manylinux wheels and scipy. On > the other hand, I get a new test error for numpy from manylinux, scipy > from manylinux, like this: > > $ python -c 'import scipy.linalg; scipy.linalg.test()' > > ====================================================================== > FAIL: test_decomp.test_eigh('general ', 6, 'F', True, False, False, (2, 4)) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line > 197, in runTest > self.test(*self.arg) > File > "/usr/local/lib/python2.7/dist-packages/scipy/linalg/tests/test_decomp.py", > line 658, in eigenhproblem_general > assert_array_almost_equal(diag2_, ones(diag2_.shape[0]), DIGITS[dtype]) > File "/usr/local/lib/python2.7/dist-packages/numpy/testing/utils.py", > line 892, in assert_array_almost_equal > precision=decimal) > File "/usr/local/lib/python2.7/dist-packages/numpy/testing/utils.py", > line 713, in assert_array_compare > raise AssertionError(msg) > AssertionError: > Arrays are not almost equal to 4 decimals > > (mismatch 100.0%) > x: array([ 0., 0., 0.], dtype=float32) > y: array([ 1., 1., 1.]) > > ---------------------------------------------------------------------- > Ran 1507 tests in 14.928s > > FAILED (KNOWNFAIL=4, SKIP=1, failures=1) > > This is a very odd error, which we don't get when running over a numpy > installed from source, linked to ATLAS, and doesn't happen when > running the tests via: > > nosetests /usr/local/lib/python2.7/dist-packages/scipy/linalg > > So, something about the copy of numpy (linked to openblas) is > affecting the results of scipy (also linked to openblas), and only > with a particular environment / test order. > > If you'd like to try and see whether y'all can do a better job of > debugging than me: > > # Run this script inside a docker container started with this incantation: > # docker run -ti --rm ubuntu:12.04 /bin/bash > apt-get update > apt-get install -y python curl > apt-get install libpython2.7 # this won't be necessary with next > iteration of manylinux wheel builds > curl -LO https://bootstrap.pypa.io/get-pip.py > python get-pip.py > pip install -f https://nipy.bic.berkeley.edu/manylinux numpy scipy nose > python -c 'import scipy.linalg; scipy.linalg.test()' > > Cheers, > > Matthew > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion@scipy.org > https://mail.scipy.org/mailman/listinfo/numpy-discussion _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org https://mail.scipy.org/mailman/listinfo/numpy-discussion