sci-biology/plink: Version BUmp, #510716

Package-Manager: portage-2.2.10/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 84 insertions, 41 deletions

diff --git a/sci-biology/plink/ChangeLog b/sci-biology/plink/ChangeLog
index e30718097355..0b36a02ac637 100644
--- a/sci-biology/plink/ChangeLog
+++ b/sci-biology/plink/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/plink
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.14 2013/03/11 16:47:09 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.15 2014/05/19 14:13:36 jlec Exp $
+
+*plink-1.90_pre140514 (19 May 2014)
+
+  19 May 2014; Justin Lecher <jlec@gentoo.org> -plink-1.07.ebuild,
+  +plink-1.90_pre140514.ebuild:
+  Version BUmp, #510716
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest
index 98e88f433bc3..610d9c15a6d3 100644
--- a/sci-biology/plink/Manifest
+++ b/sci-biology/plink/Manifest
@@ -1,17 +1,30 @@
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-Hash: SHA256
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 DIST plink-1.07-src.zip 2257297 SHA256 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b SHA512 493f9f32ecd9eb20c5d11dc8ac98c47a9e695059cec3d1ad6f17465b71609577032368c0fee0d3d564e9451c3c07761e444717bec0f4628caefc587fceb1f6c3 WHIRLPOOL 01e69f605e1b52c6087dd75b506a7705d3bdb8e7dfdd0158e125f4fc4d962fad70c4ec430a139029b3b4ae91b822eb10123fab062c6552b946ec96ca7caf37da
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-EBUILD plink-1.07.ebuild 940 SHA256 5f25e15a86ff772662d909160fe626389685705a1568cdb70a14e00e49659ee5 SHA512 5c8f4fbd9234c67acbcb2cb8b23cf3a523f2a018caf244a1dab0ce89c08f17206a8cd602b58f298641e3506e1e4a096267f64fde9de059b3ad40731835d01d39 WHIRLPOOL 6c0ec262c9d7cf611f9621422bf4c13caa02cdaba4cff765d5b67d64ede11e94ffdfe72649054eddfd1087a94251a950f4d3e7a7af5d306667c5ac20c975dd6e
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+EBUILD plink-1.90_pre140514.ebuild 1342 SHA256 5aac661c4b7034b541731b2958c93afc2ea970931acd083fc042289589722354 SHA512 69464371a612ff7824b8c3570e5be2ba0bb9b64457a9cb44cbe54789f685afbc03f95b988cc8859e86ae744e70edff5088ecbb2dbcbe12421be7a168b3381e69 WHIRLPOOL 9d63607ac612553f420ab0bad714a1960429592d70a45fe3b0061a1552aa9203c1aaf474c3745524e4b6dfd25353d2d9b262e5ad4acf121e232b74fc1f13f12e
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diff --git a/sci-biology/plink/plink-1.07.ebuild b/sci-biology/plink/plink-1.07.ebuild
deleted file mode 100644
index 30fe6ae83437..000000000000
--- a/sci-biology/plink/plink-1.07.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/plink-1.07.ebuild,v 1.3 2010/04/05 12:13:23 phajdan.jr Exp $
-
-EAPI="2"
-
-DESCRIPTION="Whole genome association analysis toolset"
-HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
-SRC_URI="http://pngu.mgh.harvard.edu/~purcell/plink/dist/${P}-src.zip"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="-webcheck"
-KEYWORDS="amd64 x86"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-S="${WORKDIR}/${P}-src"
-
-# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
-# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
-
-src_prepare() {
-	sed -i -e '/CXXFLAGS =/ s/^/#/' -e 's/-static//' "${S}/Makefile" || die
-	use webcheck || sed -i '/WITH_WEBCHECK =/ s/^/#/' "${S}/Makefile" || die
-}
-
-src_install() {
-	newbin plink p-link || die
-	dodoc README.txt
-}
diff --git a/sci-biology/plink/plink-1.90_pre140514.ebuild b/sci-biology/plink/plink-1.90_pre140514.ebuild
new file mode 100644
index 000000000000..8c959627996c
--- /dev/null
+++ b/sci-biology/plink/plink-1.90_pre140514.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/plink-1.90_pre140514.ebuild,v 1.1 2014/05/19 14:13:36 jlec Exp $
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Whole genome association analysis toolset"
+HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
+SRC_URI="http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> ${P}.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="lapack"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	app-arch/unzip
+	virtual/pkgconfig"
+RDEPEND="
+	sys-libs/zlib
+	lapack? ( virtual/lapack )"
+
+S="${WORKDIR}/"
+
+# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
+# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
+
+src_prepare() {
+	use lapack || sed -i '/NO_LAPACK =/s/$/1/' "${S}/Makefile" || die
+
+	sed \
+		-e 's:zlib-1.2.8/zlib.h:zlib.h:g' \
+		-i *.{c,h} || die
+
+	sed \
+		-e 's:g++:$(CXX):g' \
+		-e 's:gcc:$(CC):g' \
+		-e 's:gfortran:$(FC):g' \
+		-i Makefile || die
+	tc-export PKG_CONFIG
+}
+
+src_compile() {
+	local blas
+	emake \
+		CXX=$(tc-getCXX) \
+		CFLAGS="${CFLAGS}" \
+		ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \
+		BLASFLAGS="$(usex lapack "" "$($(tc-getPKG_CONFIG) --libs lapack)")"
+}
+
+src_install() {
+	newbin plink p-link
+}