[Numpy-discussion] Help - numpy / scipy binary compatibility

[Ralf Gommers]

On Mon, Aug 11, 2014 at 8:39 AM, Ralf Gommers <ralf.gommers at gmail.com>
wrote:

>
>
>
> On Sat, Aug 9, 2014 at 5:04 AM, David Cournapeau <cournape at gmail.com>
> wrote:
>
>>
>>
>>
>> On Sat, Aug 9, 2014 at 10:41 AM, Matthew Brett <matthew.brett at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I would be very happy of some help trying to work out a numpy package
>>> binary incompatibility.
>>>
>>> I'm trying to work out what's happening for this ticket:
>>>
>>> https://github.com/scipy/scipy/issues/3863
>>>
>>> which I summarized at the end:
>>>
>>> https://github.com/scipy/scipy/issues/3863#issuecomment-51669861
>>>
>>> but basically, we're getting these errors:
>>>
>>> RuntimeWarning: numpy.dtype size changed, may indicate binary
>>> incompatibility
>>>
>>> I now realize I am lost in the world of numpy / scipy etc binary
>>> compatibility, I'd really like some advice.    In this case
>>>
>>> numpy == 1.8.1
>>> scipy == 0.14.0 - compiled against numpy 1.5.1
>>> scikit-learn == 0.15.1 compiled against numpy 1.6.0
>>>
>>> Can y'all see any potential problem with those dependencies in binary
>>> builds?
>>>
>>> The relevant scipy Cython c files seem to guard against raising this
>>> error by doing not-strict checks of the e.g. numpy dtype, so I am
>>> confused how these errors come about.  Can anyone give any pointers?
>>>
>>
>> Assuming the message is not bogus, I would try import von_mises with a
>> venv containing numpy 1.5.1, then 1.6.0, etc... to detect when the change
>> happened.
>>
>
> That should be a recent change in 1.8.1, either because the dtype size did
> actually change or because the silencing of this message in NoseTester
> (numpy.testing) is not effective anymore.
>
> Note that the warning is too agressive, because it triggers both on ABI
> breaks and on backwards-compatible extensions to dtype. That's why it's
> filtered in numpy.testing. This was reported to Cython a while ago, not
> sure they've fixed the issue in the meantime or not.
>

Never mind, saw that you already figured out that it's due to scikit-learn:
https://github.com/scipy/scipy/issues/3863

Ralf
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