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

Ralf Gommers ralf.gommers at gmail.com
Mon Aug 11 02:39:12 EDT 2014


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.

Ralf
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