Hi,
I just copied the first 4 rows of the warning, it is actually repeated many,
many times.
The change Greg suggests fixes things, thanks.
Chris
> On 19 Jan 2017, at 03:32, Greg Landrum <greg.land...@gmail.com> wrote:
>
> Peter is correct, those are just warnings. But they are irritating warnings.
> You should be able to get rid of them by changing the call to:
> fig, maxweight = SimilarityMaps.GetSimilarityMapForModel(m5,
> SimilarityMaps.GetMorganFingerprint, lambda x: getProba((x,),
> rf.predict_proba))
> This passes getProba() a tuple with the fingerprint in question.
>
> -greg
>
>
> On Thu, Jan 19, 2017 at 12:12 AM, Peter S. Shenkin <shen...@gmail.com
> <mailto:shen...@gmail.com>> wrote:
> These are not errors. They are warnings, as stated in the messages.
>
> Do you have any evidence that the procedure is not working? If not, the
> reason is unlikely to be these warnings.
>
> What the message is saying is that in a future release of sklearn
> (scikit-learn), the calling code will have to use the validation module
> differently.
>
> I don't know this part of RDKit, but the purport is presumably that whoever
> is maintaining the part of RDKit that calls the validation module (directly
> or indirectly) will have to make the change described in the warning messages
> before RDKit starts using version 0.19 of sklearn. A quick google search
> indicates that version 0.19 hasn't been released yet, so the current calling
> protocol should work for now. But we have been forewarned....
>
> -P.
>
> On Wed, Jan 18, 2017 at 2:26 PM, Chris Swain <sw...@mac.com
> <mailto:sw...@mac.com>> wrote:
> Hi,
>
> I’ve been trying a few o the examples in
> http://www.rdkit.org/docs/Cookbook.html
> <http://www.rdkit.org/docs/Cookbook.html>
>
> and I’d like to use the Similarity Maps as shown below
>
> from rdkit.Chem.Draw import SimilarityMaps
>
> # helper function
> def getProba(fp, predictionFunction):
> return predictionFunction(fp)[0][1]
>
> m5 = Chem.MolFromSmiles('c1ccccc1O')
> fig, maxweight = SimilarityMaps.GetSimilarityMapForModel(m5,
> SimilarityMaps.GetMorganFingerprint, lambda x: getProba(x, rf.predict_proba))
> But I get this error.
>
> /usr/local/lib/python2.7/site-packages/sklearn/utils/validation.py:395:
> DeprecationWarning: Passing 1d arrays as data is deprecated in 0.17 and will
> raise ValueError in 0.19. Reshape your data either using X.reshape(-1, 1) if
> your data has a single feature or X.reshape(1, -1) if it contains a single
> sample.
> DeprecationWarning)
> /usr/local/lib/python2.7/site-packages/sklearn/utils/validation.py:395:
> DeprecationWarning: Passing 1d arrays as data is deprecated in 0.17 and will
> raise ValueError in 0.19. Reshape your data either using X.reshape(-1, 1) if
> your data has a single feature or X.reshape(1, -1) if it contains a single
> sample.
> DeprecationWarning)
> /usr/local/lib/python2.7/site-packages/sklearn/utils/validation.py:395:
> DeprecationWarning: Passing 1d arrays as data is deprecated in 0.17 and will
> raise ValueError in 0.19. Reshape your data either using X.reshape(-1, 1) if
> your data has a single feature or X.reshape(1, -1) if it contains a single
> sample.
> DeprecationWarning)
> /usr/local/lib/python2.7/site-packages/sklearn/utils/validation.py:395:
> DeprecationWarning: Passing 1d arrays as data is deprecated in 0.17 and will
> raise ValueError in 0.19. Reshape your data either using X.reshape(-1, 1) if
> your data has a single feature or X.reshape(1, -1) if it contains a single
> sample.
> DeprecationWarning)
>
> Cheers,
>
> Chris
>
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