Version bump. Fixes bug 335608. Thanks to Diego for report.

Package-Manager: portage-2.2_rc72/cvs/Linux x86_64

4 files changed, 22 insertions, 77 deletions

diff --git a/sci-biology/paml/ChangeLog b/sci-biology/paml/ChangeLog
index 96ab6e81ee32..22b05b2c7c9d 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 1.11 2010/02/09 11:17:38 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/ChangeLog,v 1.12 2010/09/02 06:56:14 xarthisius Exp $
+
+*paml-4.4c (02 Sep 2010)
+
+  02 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> -paml-4.1.ebuild,
+  -paml-4.2b-r1.ebuild, +paml-4.4c.ebuild:
+  Version bump. Fixes bug 335608. Thanks to Diego for report.
 
   09 Feb 2010; Pacho Ramos <pacho@gentoo.org> paml-4.3a.ebuild:
   amd64 stable, bug 298772
diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
index 03efee2063d9..25d6c22b53f9 100644
--- a/sci-biology/paml/Manifest
+++ b/sci-biology/paml/Manifest
@@ -1,20 +1,8 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-DIST paml4.1.tar.gz 2865301 RMD160 44e5eb18eb9a168c6d2f090ff45462e07234bc07 SHA1 790c83990a93baec48b55686bb350bed43fdc440 SHA256 64680a56304bb3f5cd61cfc9be253fe1fe37250cb450bceaaf76b99ee08111f1
-DIST paml4.2b.tar.gz 2664576 RMD160 49465de70e9c973bd269c2808f96ce7cccc4c2ad SHA1 db9e7ce2623049665b7e3a38e14c6f69ad15ac66 SHA256 2ee29961b4e7f07983e01c3587ff5a345ba7dfefaa85352f0c9e71190f8187f8
 DIST paml4.3a.tar.gz 2940883 RMD160 0427e2398c1e7983becb20cc6ddce5ba915823b9 SHA1 e1d85c1719c6428b7858944be6b4d9ecb53f5e4a SHA256 5f33f5a4bc6823381161a9abd1082c30e96dc167ebe90d8329e0006068f8d1ab
 DIST paml4.3b.tar.gz 2967249 RMD160 e55d06d7cc8a0a3b204e4c8d1555697efbd2b618 SHA1 897afd1f67ebbc5daab53f617d2079796d2e2347 SHA256 98b02155c1cc2eda4045abd56f151495df8bc8f799c666e51257dcb4b09f1787
-EBUILD paml-4.1.ebuild 1159 RMD160 e92d3c17407d5362b4438749c3d0d21eaad34337 SHA1 c848a2aee7e7fd0bfbde46b95899a5f84c7e58d6 SHA256 552630b699f130fa154eb719eecccc3a5ec58bfc398344aa3d54ca270fee4aa7
-EBUILD paml-4.2b-r1.ebuild 1170 RMD160 9a03b6e6eb277919a2f0a9f9c2c938911085fd33 SHA1 7bbb6e8f26f83b61ebd9bf5ecdebc721c83c53af SHA256 036f85b9125c04211d599b0de85a15ffab0218a4138d22717d883d4bb2b95d14
+DIST paml4.4c.tar.gz 2891715 RMD160 9a9307b1d32d60ac2b02d76c62d522e49ef50da2 SHA1 4e9cfa207fa08e4eb39efa99091b22bb46c22563 SHA256 08aad25b6b06a359d4f2f12a60ea601c95694864d5f29f7028f67b80890974d6
 EBUILD paml-4.3a.ebuild 1164 RMD160 472b1d8f01adbacdd1b29e75c65e4a9ff270ee5b SHA1 3d4ecea0396d0b2b435c2e5375c9eca3bce2daa5 SHA256 323cd6d4e760a33df5d8dbb6d495275270c329fbbe96394d8ad4b62036cfb023
 EBUILD paml-4.3b.ebuild 1167 RMD160 cc455c55875e6996e58e79683c0bc84e003cf409 SHA1 fe3785b3d8db64fbc5882523ebd97dff73d2b336 SHA256 0192e82059ec0bd10906a9968145d5bc8f05b85883d6bb8d0b96f0561edee573
-MISC ChangeLog 1588 RMD160 f4be5478ed52352e1b270cb40ed040ae887542af SHA1 fe1c7fd13bdb36ee91bcfe70888a2d9af7ddfac0 SHA256 86dc942fbf11a044ce80b0d50d24ea7a1cd8d241db55a00ed0c6319a884df93d
+EBUILD paml-4.4c.ebuild 1213 RMD160 2aadd75740cb5f59fca5cb2c08b2f9fe3773b02a SHA1 aad5862ca9f9dd20535156582510b5a537c8f808 SHA256 b45f320402706b1577a64aaf20582bde3a4e2e4e725710df74076216c565211e
+MISC ChangeLog 1797 RMD160 c6c733d7072ebeaaac668be041aeb6e003c159c6 SHA1 ff158a885c8f5de5ad517f9f8ce6de9a349c6787 SHA256 37bc439a4c1420d9f044c7b0a76fcdd7202f4fed4ba742567eedc20ed79e91e7
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.14 (GNU/Linux)
-
-iEYEARECAAYFAktxRFgACgkQCaWpQKGI+9S0tQCfbsj+3EnUuGShZvjzzTLEki16
-vkQAnjk8AHWklOgI5t4yVRoEpwyJPuAB
-=CIcg
------END PGP SIGNATURE-----
diff --git a/sci-biology/paml/paml-4.1.ebuild b/sci-biology/paml/paml-4.1.ebuild
deleted file mode 100644
index f2ea1263ca95..000000000000
--- a/sci-biology/paml/paml-4.1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/paml-4.1.ebuild,v 1.1 2008/09/07 12:02:02 markusle Exp $
-
-inherit toolchain-funcs
-
-MY_PV="${PV/./}"
-DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
-HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
-SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}"
-S="${WORKDIR}/${PN}${MY_PV}"
-
-src_compile() {
-	cd src
-	emake \
-		-f Makefile.UNIX \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	pushd "${S}"/src
-	dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2 \
-		|| die "Failed to install binaries"
-	popd
-
-	dodoc README.txt doc/* || die "Failed to install docs"
-
-	insinto /usr/share/${PN}/control
-	doins *.ctl || die "Failed to install control files"
-
-	insinto /usr/share/${PN}/dat
-	doins stewart* *.dat dat/* || die "Failed to install data files"
-
-	insinto /usr/share/${PN}
-	doins -r examples/ || die "Failed to install examples"
-}
diff --git a/sci-biology/paml/paml-4.2b-r1.ebuild b/sci-biology/paml/paml-4.4c.ebuild
index 5159fee6c399..c828da151cae 100644
--- a/sci-biology/paml/paml-4.2b-r1.ebuild
+++ b/sci-biology/paml/paml-4.4c.ebuild
@@ -1,44 +1,39 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/paml-4.2b-r1.ebuild,v 1.1 2009/07/21 08:44:44 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/paml-4.4c.ebuild,v 1.1 2010/09/02 06:56:14 xarthisius Exp $
 
 EAPI="2"
 
-inherit toolchain-funcs
+inherit toolchain-funcs versionator
+
+MY_P=$(version_format_string '${PN}$1$2')
 
-MY_P="${PN}42"
 DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
 HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
 SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
 
 LICENSE="free-noncomm"
 SLOT="0"
-KEYWORDS="~x86 ~amd64"
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
+S=${WORKDIR}/${MY_P}
 
 src_prepare() {
-	sed -i 's/-static//' "${S}/src/Makefile.UNIX" || die
+	# Notice send by mail to prof. Ziheng Yang
+	sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608
 }
 
 src_compile() {
-	cd src
-	emake \
-		-f Makefile.UNIX \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}" \
-		|| die "make failed"
+	emake -C src CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" || die
 }
 
 src_install() {
 	pushd "${S}"/src
 	dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2 || die
 	popd
-	dodoc README.txt doc/*
+	dodoc README.txt doc/* || die
 	insinto /usr/share/${PN}/control
 	doins *.ctl || die "Failed to install control files"
 	insinto /usr/share/${PN}/dat