From lennart at karssen.org Sun May 1 17:11:47 2016 From: lennart at karssen.org (L.C. Karssen) Date: Sun, 1 May 2016 17:11:47 +0200 Subject: [GenABEL-dev] Upcoming ProbABEL release and Eigen lib inclusion In-Reply-To: <5724B7D6.1040804@karssen.org> References: <5724B7D6.1040804@karssen.org> Message-ID: <57261CB3.2070108@karssen.org> 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" > > > > _______________________________________________ > genabel-devel mailing list > genabel-devel at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel > -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen Utrecht The Netherlands lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: