[GenABEL-dev] Upcoming ProbABEL release and Eigen lib inclusion

[L.C. Karssen]

Dear list,

Thanks Yurii and Diego for your replies. Glad to get some feedback on
this. Inclusion of Eigen 3.2.1 it will be!

Looking forward to the release in a few days.

Lennart.


On 30-04-16 15:49, L.C. Karssen wrote:
> cDear list,
> 
> I'm preparing a new release of ProbABEL (probably v0.5.0), with a bunch
> of bug fixes (see the Changelog [1]). One of the major changes is that
> ProbABEL now fully depends on the Eigen library for matrix manipulation.
> 
> Currently, only one thing stands in the way of finalising the release:
> Issue #11 [2]. Due to a change in the Eigen library starting from
> version 3.2.2, some of the ProbABEL checks where we compare R output
> with ProbABEL output fail. Luckily these failures are only in those
> checks that test corner cases (e.g. our test SNP 6, where only 1 out of
> 182 samples has a different genotype).
> What I observe is that with Eigen v3.2.1 the output of ProbABEL is equal
> to that produced by R. With newer Eigen versions, there are differences
> (although in the end, the result is still that there is no association,
> e.g. small betas and huge standard errors).
> 
> In my opinion the proper solution of issue #11 would be to write proper
> checks for these corner case (like singular matrices) and output
> warnings if they occur. However, that would delay the release of
> ProbABEL too much.
> 
> So my suggestion is to include Eigen v3.2.1 with ProbABEL v0.5.0. This
> way we will be certain that ProbABEL and R give the same output, and,
> addtionally, having Eigen included in the ProbABEL tar.gz will make life
> easier for a (novice) user installing ProbABEL from source. Meanwhile
> this will buy us time to fix issue #11.
> 
> Regarding licences, I don't see a problem. Eigen is licensed under the
> Mozilla Public Licence (MPL) [3, 4], which allows distribution of
> (unmodified code) in GPL software [5].
> 
> I would like to hear your opinions on distribution Eigen with ProbABEL.
> Is there anything I overlooked?
> 
> 
> Best regards,
> 
> Lennart.
> 
> 
> [1] https://github.com/GenABEL-Project/ProbABEL/blob/master/doc/ChangeLog
> [2] https://github.com/GenABEL-Project/ProbABEL/issues/11
> [3] http://eigen.tuxfamily.org/index.php?title=Main_Page#License
> [4] https://www.mozilla.org/en-US/MPL/2.0/
> [5] https://www.mozilla.org/en-US/MPL/2.0/combining-mpl-and-gpl/,
> especially section "Unmodified MPL-licensed Files - MPL-only"
> 
> 
> 
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-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
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