Bump EAPI

Package-Manager: portage-2.2.17/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 74 insertions, 15 deletions

diff --git a/sci-biology/paml/ChangeLog b/sci-biology/paml/ChangeLog
index 2d77e45920b4..9fb8082bd9c5 100644
--- a/sci-biology/paml/ChangeLog
+++ b/sci-biology/paml/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/paml
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/ChangeLog,v 1.15 2010/09/12 17:19:45 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/ChangeLog,v 1.16 2015/03/03 15:26:16 jlec Exp $
+
+*paml-4.4c-r1 (03 Mar 2015)
+
+  03 Mar 2015; Justin Lecher <jlec@gentoo.org> +paml-4.4c-r1.ebuild,
+  metadata.xml:
+  Bump EAPI
 
   12 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> -paml-4.3a.ebuild,
   -paml-4.3b.ebuild:
@@ -69,4 +75,3 @@
   21 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; +metadata.xml,
   +paml-3.15.ebuild:
   New package: Phylogenetic Analysis by Maximum Likelihood.
-
diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
index 1c065cd72f5f..23e1d3432d6e 100644
--- a/sci-biology/paml/Manifest
+++ b/sci-biology/paml/Manifest
@@ -1,16 +1,27 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
-DIST paml4.4c.tar.gz 2891715 RMD160 9a9307b1d32d60ac2b02d76c62d522e49ef50da2 SHA1 4e9cfa207fa08e4eb39efa99091b22bb46c22563 SHA256 08aad25b6b06a359d4f2f12a60ea601c95694864d5f29f7028f67b80890974d6
-EBUILD paml-4.4c.ebuild 1209 RMD160 e6d5e5531287647cbac89f5c4578c5523abe4563 SHA1 833b902f4342f2499d9f0074d26374a70bf76dee SHA256 558abe2195e74b8759b55a46c87e2381fa052956b75fb286925b5fc45516e1be
-MISC ChangeLog 2124 RMD160 a8d5aff7d25f8babdd9e11dd32f36da731fb0e2a SHA1 72a9fee2b75c86b270e9417911805fca67ea767a SHA256 037df509a4b45f1d45bbf907dd07edf5321c9b2cb6da96d66fa91e5560aac0f7
-MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
+DIST paml4.4c.tar.gz 2891715 SHA256 08aad25b6b06a359d4f2f12a60ea601c95694864d5f29f7028f67b80890974d6 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a WHIRLPOOL 44ae42dd6088039be1041cdce70ce9ee907b8f85d4e25f9d556df4738ea3ea91f700f96f627f20a13d226038132fd23aecbc5b452bfb6716b9499c8d2be491e4
+EBUILD paml-4.4c-r1.ebuild 1072 SHA256 ac32f96ce8442f53bda109afeb01807552b8b1ef5549031b8a1496104e6ee57f SHA512 c93f49ac3c499ad4197ba8bcb1b0af3f819e1daf260e59fe8467e02fc12c722d4ef7fedd4a83b2c38430e5f9da5a77b1fe1281f4636af274fab0b1471bfb5fc1 WHIRLPOOL f7e0a04ad080cf8068d40b112f35620d642970c090784f819d6b76b57e3d62b9c758c374dac211bce530ec03a77ebcdd1be0253522461b40b883a29b1ead9a08
+EBUILD paml-4.4c.ebuild 1209 SHA256 558abe2195e74b8759b55a46c87e2381fa052956b75fb286925b5fc45516e1be SHA512 2163475154045d40417fe66af89a5be253beeea514ae4fd4a619dcd9cfb09c78d24a4f7c4652b7235d340731b1b8877a2a2a2a46c1210196dd8da15005abd2ba WHIRLPOOL 100802ed26aea0ef176ee4ea7557330e86ca3e62dd579741ef13ed045a479ddcb67bc1cd9521e15be8c4991d3488758338f00f8631039b65c9a66463f9c6992b
+MISC ChangeLog 2244 SHA256 d3fdde62dd7906ca74a46f9ef1931f27c2f31f2517dbb64e28ce36fd8f50e8cd SHA512 248eab8e448310832d5dd533dc473523b265081693deff864680d4dbc02a5e48a07c9cf48db413112aa99b3e4d480f296290fe9412208fbc6daf0fe23e8ee600 WHIRLPOOL acb9524aad47608dca2049e2363967e080d8ce2e94a49302728e62527b044a005e6d23d7b70492f6add875cac8f28af3877d5f876282f50c7c2f8133e2159fc7
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
+Version: GnuPG v2.0
 
-iJwEAQECAAYFAkyNC70ACgkQIiMqcbOVdxTPZwP9FP6dx7iza7elqcnwgv9XP1qC
-2W+UA4X3LYQiYf/4Du+dMf+FSFUHSRz9rkPR9ik3jNymDnxDCn8CWQkOyuEmO63N
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-P6gGKvw4OnPtiVBvXMY=
-=kSYZ
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+wofluSmNxkYJmC1/JBkk
+=q1Wy
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/paml/metadata.xml b/sci-biology/paml/metadata.xml
index 34294c65ca04..f17a827e3101 100644
--- a/sci-biology/paml/metadata.xml
+++ b/sci-biology/paml/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-biology</herd>
+  <herd>sci-biology</herd>
 </pkgmetadata>
diff --git a/sci-biology/paml/paml-4.4c-r1.ebuild b/sci-biology/paml/paml-4.4c-r1.ebuild
new file mode 100644
index 000000000000..da4ad52739e7
--- /dev/null
+++ b/sci-biology/paml/paml-4.4c-r1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/paml-4.4c-r1.ebuild,v 1.1 2015/03/03 15:26:16 jlec Exp $
+
+EAPI=5
+
+inherit toolchain-funcs versionator
+
+MY_P=$(version_format_string '${PN}$1$2')
+
+DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
+HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
+SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
+
+LICENSE="free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+S=${WORKDIR}/${MY_P}
+
+src_prepare() {
+	# Notice send by mail to prof. Ziheng Yang
+	sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608
+}
+
+src_compile() {
+	emake -C src CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	pushd "${S}"/src
+	dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2
+	popd
+	dodoc README.txt doc/*
+	insinto /usr/share/${PN}/control
+	doins *.ctl
+	insinto /usr/share/${PN}/dat
+	doins stewart* *.dat dat/*
+	insinto /usr/share/${PN}
+	doins -r examples/
+}