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

[L.C. Karssen]

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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L.C. Karssen
Utrecht
The Netherlands

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