[pymvpa] error py26-pywavelets installation on snow leopard Mac
James Kyle
krunk7+pymvpa at gmail.com
Sat Jan 29 21:49:12 UTC 2011
> make unittest-nonlabile
Alright, that greatly the failed tests to just these two (besides a lot of warnings similar to the original log):
> .....
> ======================================================================
> ERROR: testDetrend (mvpa.tests.test_datasetfx_sp.MiscDatasetFxSpTests)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/tests/test_datasetfx_sp.py", line 71, in testDetrend
> detrend(ds, perchunk=False, model='regress', polyord=1)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/datasets/miscfx_sp.py", line 85, in detrend
> polyord=polyord, opt_reg=opt_reg)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/datasets/miscfx_sp.py", line 179, in __detrend_regress
> res = lstsq(regs, dataset.samples)
> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/linalg/basic.py", line 352, in lstsq
> a1, b1 = map(asarray_chkfinite, (a, b))
> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/lib/function_base.py", line 547, in asarray_chkfinite
> "array must not contain infs or NaNs")
> ValueError: array must not contain infs or NaNs
>
> ======================================================================
> ERROR: testSplitFeaturewiseDatasetMeasure (mvpa.tests.test_datameasure.SensitivityAnalysersTests)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/tests/test_datameasure.py", line 290, in testSplitFeaturewiseDatasetMeasure
> error = ce(ds)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/measures/base.py", line 105, in __call__
> result = self._call(dataset)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/algorithms/cvtranserror.py", line 190, in _call
> result = transerror(split[1], split[0])
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/clfs/transerror.py", line 1309, in __call__
> self._precall(testdataset, trainingdataset)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/clfs/transerror.py", line 1265, in _precall
> self.__clf.train(trainingdataset)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/clfs/base.py", line 394, in train
> result = self._train(dataset)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/clfs/meta.py", line 1297, in _train
> self.__testdataset)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/featsel/base.py", line 116, in __call__
> sensitivity = self.__sensitivity_analyzer(dataset)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/measures/base.py", line 105, in __call__
> result = self._call(dataset)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/measures/base.py", line 620, in _call
> sensitivity = analyzer(ds)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/measures/base.py", line 450, in __call__
> return FeaturewiseDatasetMeasure.__call__(self, dataset)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/measures/base.py", line 106, in __call__
> result = self._postcall(dataset, result)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/measures/base.py", line 336, in _postcall
> result = DatasetMeasure._postcall(self, dataset, result)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/measures/base.py", line 128, in _postcall
> result = self.__transformer(result)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/misc/transformers.py", line 291, in __call__
> **hist_kwargs)
> TypeError: histogram() got an unexpected keyword argument 'new'
>
> ======================================================================
> ERROR: Basic testing of DistPValue
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/tests/test_transformers.py", line 120, in testDistPValue
> result = distPValue(x)
> File "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.4/mvpa/misc/transformers.py", line 291, in __call__
> **hist_kwargs)
> TypeError: histogram() got an unexpected keyword argument 'new'
>
> ----------------------------------------------------------------------
> Ran 238 tests in 82.195s
>
> FAILED (errors=3)
> MVPA_SEED=1703053983
> make: *** [unittest-nonlabile] Error 1
On Jan 29, 2011, at 11:42 AM, Yaroslav Halchenko wrote:
> hm... I guess I would need to have a look at it -- there was a reason for using
> old interface on how we treated returned bins... THANKS! -- we haven't got to
> the 1.5.1 (although it is available... should upgrade ;))
>
> as for running unittests -- if only "do not fail for sure" ones to be
> ran, do
>
> make unittest-nonlabile
>
> because otherwise some tests are "ok" to fail from time to time to
> effects of random data, e.g. like this one
>
> Traceback (most recent call last):
> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/tests/test_datameasure.py", line 112, in testAnalyzerWithSplitClassifier
> len(self.dataset.uniquelabels)))
> AssertionError:
> Single scenario lead to failures of unittest testAnalyzerWithSplitClassifier:
> on
> clf=FeatureSelectionClassifier(clf=SVM(kernel_type='linear', svm_impl='C_SVC', probability=1), enable_states=['training_confusion'], descr='LinSVM on 5%(ANOVA)') :
> We must have trained on each one more or less correctly. Got 66.666667% correct on 2 labels
> clf=FeatureSelectionClassifier(clf=SVM(kernel_type='linear', svm_impl='C_SVC', probability=1), enable_states=['training_confusion'], descr='LinSVM on 5%(SVM)') :
> We must have trained on each one more or less correctly. Got 66.666667% correct on 2 labels
>
>
> On Sat, 29 Jan 2011, James Kyle wrote:
>
>> Ok, here's a patch that fixes the first failed test aside from the lxml dep missing.
>
>> On line #253 of mvpa/misc/transformers.py there's a version test for numpy that evaluates to True and creates a **kwargs hash of {'new': False} for N.histogram(). The 'new' kwarg is no longer supported as of Numpy version >= 1.4. I modified the test to provide a **kwarg of {} for all versions < 1.4 resolving the test error.
>
>
>
>
>
>> -james
>
>> On Jan 29, 2011, at 11:00 AM, James Kyle wrote:
>
>>> Ok, I rolled back to the 0.4 HEAD (maint/0.4).
>
>>> This compiles without error, but running the unittests produces some errors. The output of the log was quite large (2.5M) so rather than attaching I uploaded it to our server.
>
>>> The full log can be found here:
>
>>> http://www.kspacemri.com/data/tests.log
>
>
>>> -james
>>> On Jan 28, 2011, at 5:43 PM, Yaroslav Halchenko wrote:
>
>
>>>> On Fri, 28 Jan 2011, James Kyle wrote:
>>>>>> ah... I guess it is time to release 0.4.6 of pymvpa -- we have that
>>>>>> libsvm3.0 compatibility fix past 0.4.5 release:
>
>>>>> I've actually been toying with the 0.6.0.dev branch, is that not ready for the masses yet?
>>>> well... it has been used by users and we hope to release it soon (
>>>> probably as soon as our extensive testing battery shows no bad symptomps ;-) )
>
>>>> the problem is that it is not compatible, so it might come as a surprise
>>>> to macport users... for Debian users we ship python-mvpa-snapshot which
>>>> provides 0.6.x functionality before we release it
>
>>>> so altogether it would be better to stick with 0.4.x series until 0.6.0
>>>> gets released
>
>>>>>> or could macports simply build off a specific git branch? (i.e. maint/0.4)
>>>>> I can setup the macports build script for whichever branch is preferred/recommended.
>
>>>> So you would not need to tune it up later on, probably let it stay as
>>>> is -- HEAD of that repository corresponds to debian releases... I
>>>> progressed it forward (merged maint/0.4)...
>
>>>> is port taking a HEAD or releases (tags), as given by
>>>> livecheck.regex {upstream\/([0-9.]+)}
>>>> (and that is how it assigns the version according to (...) above)?
>
>>>> --
>>>> =------------------------------------------------------------------=
>>>> Keep in touch www.onerussian.com
>>>> Yaroslav Halchenko www.ohloh.net/accounts/yarikoptic
>
>>>> _______________________________________________
>>>> Pkg-ExpPsy-PyMVPA mailing list
>>>> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
>>>> http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
>
>
>
>> _______________________________________________
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>
>
> --
> =------------------------------------------------------------------=
> Keep in touch www.onerussian.com
> Yaroslav Halchenko www.ohloh.net/accounts/yarikoptic
>
> _______________________________________________
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