Dropped old, respect LDFLAGS, don't mix CFLAGS and CXXFLAGS, move KEYWORDS and fixes from ver-1 to 2

Package-Manager: portage-2.2.0_alpha77/cvs/Linux x86_64

6 files changed, 38 insertions, 64 deletions

diff --git a/sci-biology/primer3/ChangeLog b/sci-biology/primer3/ChangeLog
index 728ed0631d51..58d276b0cbfc 100644
--- a/sci-biology/primer3/ChangeLog
+++ b/sci-biology/primer3/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/primer3
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.25 2011/03/09 11:25:06 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.26 2011/11/23 08:10:50 jlec Exp $
+
+  23 Nov 2011; Justin Lecher <jlec@gentoo.org> -primer3-1.0.0.ebuild,
+  primer3-1.1.4.ebuild, primer3-1.1.4-r2.ebuild, primer3-2.2.3.ebuild:
+  Dropped old, respect LDFLAGS, don't mix CFLAGS and CXXFLAGS, move KEYWORDS
+  and fixes from ver-1 to 2
 
   09 Mar 2011; Justin Lecher <jlec@gentoo.org> +primer3-1.0.0.ebuild:
   Reanimate last stable version for ppc/ppc64
diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
index d3eb8da15026..54ebaf7d8d00 100644
--- a/sci-biology/primer3/Manifest
+++ b/sci-biology/primer3/Manifest
@@ -1,20 +1,18 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
 AUX primer3-1.1.4-ldflags.patch 882 RMD160 c67d4e03fc68155d2a74276bbc7e409bc8e8096b SHA1 5346c976c80b6a474e352f3a27c6153648d58a2b SHA256 10ef0f1491df83c60f5919fcc461a0864e12a0303d8242f4e3ea1c2f8963c436
 DIST primer3-1.1.4.tar.gz 974628 RMD160 87535d123d4c00b64eb763e4e567c5c83fde6b54 SHA1 fcabf7d8aa31c5568bd130b318c3ead4a1b9aa3a SHA256 1cb045791afd3c4033956a65687ca0c1b1a6607ac84705bf4ed7d7151691980b
 DIST primer3-2.2.3.tar.gz 2284282 RMD160 040b41649f5bfc17214502b2ba5e98d1a5afd73f SHA1 20c6a00455b86a5712c1e297930f2624fca45881 SHA256 2e68d638119bfcac12571da351cf261e28a3dd4b32c89074ce17065931a98774
-DIST primer3_1.0.0.tar.gz 936696 RMD160 c08329cafcb8bf702a1654b4348a418b20e55c88 SHA1 0227f1f26c8b45dff9033543bee4387ade173c73 SHA256 fcbcf2e540e0062f3fa0d723b443b04a1c31e3e03e3aa5d97e3b2f910499f34b
-EBUILD primer3-1.0.0.ebuild 733 RMD160 67993b346b6f9a30d5191ff8f37004e87fe98dfb SHA1 1042b17bc4441dfb3a264d3c02622d57827e2242 SHA256 9d93f9fca59a7e60f1e26423058092c3c2a60e762a93a5a19555633c1db409d4
-EBUILD primer3-1.1.4-r2.ebuild 973 RMD160 1ad7270638ba327822f85e884d2d6ad1b5f45edd SHA1 0b6d49ca6506919e27d3706eee65d9a17cc1ff47 SHA256 0d256c50aaf34f381b82e4793220a3c846c1b95a74fd3133b2c8145499688e25
-EBUILD primer3-1.1.4.ebuild 784 RMD160 bac03e8b11917a1143deff34626dae8efdc0cd44 SHA1 5a1d7ff14dd1350960b570eb8d0f18946a570cf9 SHA256 dc43587ef1b94b22632f4307120b52fea1b3bad7d94bdc68ae083f1ffc8443fb
-EBUILD primer3-2.2.3.ebuild 1010 RMD160 13edabc9d289d994ab7b6554c1998b2b0acada50 SHA1 972116704387bf8037caf4ed630995e076c329bd SHA256 76327ce256e5cc1a939ca14e02e49c5ad298cadb8766274e73104203a1952a18
-MISC ChangeLog 3956 RMD160 7341bf0bec4f34adda9ec00d76ac331d749dcf63 SHA1 66dee8af63952bdb7e3ddd9635e548e12fb618e4 SHA256 3f7f2088a93b47b9b9e79f46623910ce3e8b239f55d3839a17cf3afd18c805a5
+EBUILD primer3-1.1.4-r2.ebuild 966 RMD160 36ddb7a39f54ee2650bcb2300ee7d14f594f7ae0 SHA1 2fe782c9bac2232e286439728ac1d55bffdf0c97 SHA256 fb2ea764406931476ae46e9878aa3591b8a23f972be52b57a76ae4fa2085347a
+EBUILD primer3-1.1.4.ebuild 777 RMD160 a7f7d260c80b4899568b11ec28a0431b215db2d1 SHA1 45485dafce00b8500267350041bc66c7c480b4e2 SHA256 cab7435d84362f2dd3b56d85db348662baa22e8ec5757acdffe45ecb08be7a74
+EBUILD primer3-2.2.3.ebuild 1318 RMD160 5ed13ef1a26076e4324328312b1e8da912629c0f SHA1 d68074391682e9fd6210f9025fc9b9a7c5f9b49d SHA256 c8b9364852bdbeafd89e8f4a2924b6bc2e5e2e2528be4b5a7c7852ff1b244d45
+MISC ChangeLog 4203 RMD160 f5f1631e06990bcd5ca7d22437af5ae5b9bafb9a SHA1 d836451298c0bdb139d954a88be9e0da8fbfff0a SHA256 04ba07fd28ce465df42db3a4ccbd7ca988110d42f2dd08fe0b9eaac33460d8df
 MISC metadata.xml 624 RMD160 b9c9f7ed6eb37504dbe39d7fd2c12ea7c0e2b557 SHA1 ecbd008512496eeefae63e1d36bdbe66e71e63fc SHA256 f612edc94f6538c9acf99caadc2a7d6e33cac6f933db9deafae777c7a45505bb
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.17 (GNU/Linux)
+Version: GnuPG v2.0.18 (GNU/Linux)
 
-iEYEARECAAYFAk13Y5gACgkQgAnW8HDreRbNpQCcDKjJWvklHaixdmoFDOHNBnov
-7PMAnR3FZQUR3kkhQOf/29gX7UtyMcrE
-=Wrln
+iEYEAREKAAYFAk7Mqo8ACgkQgAnW8HDreRZI5QCfdn07auGOjPcbglldMQQuIhj8
+HEYAn0IptRb3FAJWYhTI1vuTNPMJ8oSQ
+=2Rvc
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/primer3/primer3-1.0.0.ebuild b/sci-biology/primer3/primer3-1.0.0.ebuild
deleted file mode 100644
index 1d88849c9358..000000000000
--- a/sci-biology/primer3/primer3-1.0.0.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-1.0.0.ebuild,v 1.16 2011/03/09 11:25:06 jlec Exp $
-
-DESCRIPTION="Design primers for PCR reactions."
-HOMEPAGE="http://primer3.sourceforge.net/"
-SRC_URI="http://frodo.wi.mit.edu/${PN}/${PN}_${PV}.tar.gz"
-LICENSE="whitehead"
-
-SLOT="0"
-KEYWORDS="amd64 ppc ppc64 ~sparc x86"
-IUSE=""
-
-RDEPEND=""
-
-DEPEND="dev-lang/perl"
-
-S=${WORKDIR}/${PN}_${PV}/src
-
-src_unpack() {
-	unpack ${A}
-}
-
-src_compile() {
-	emake -e || die
-}
-
-src_test () {
-	cd ../test
-	perl primer_test.pl primer3_core || die
-}
-
-src_install () {
-	dobin primer3_core
-	dodoc release_notes ../README ../example
-}
diff --git a/sci-biology/primer3/primer3-1.1.4-r2.ebuild b/sci-biology/primer3/primer3-1.1.4-r2.ebuild
index b12de1503ef0..0076c5ed19fb 100644
--- a/sci-biology/primer3/primer3-1.1.4-r2.ebuild
+++ b/sci-biology/primer3/primer3-1.1.4-r2.ebuild
@@ -1,19 +1,19 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-1.1.4-r2.ebuild,v 1.1 2010/08/31 12:16:41 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-1.1.4-r2.ebuild,v 1.2 2011/11/23 08:10:50 jlec Exp $
 
 EAPI="3"
 
 inherit eutils toolchain-funcs
 
-DESCRIPTION="Design primers for PCR reactions."
+DESCRIPTION="Primer Design for PCR reactions"
 HOMEPAGE="http://primer3.sourceforge.net/"
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-LICENSE="whitehead"
 
 SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+LICENSE="whitehead"
 IUSE=""
+KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 
 DEPEND="dev-lang/perl"
 RDEPEND=""
@@ -21,6 +21,7 @@ RDEPEND=""
 S=${WORKDIR}/src
 
 src_prepare() {
+
 	[[ ${CHOST} == *-darwin* ]] && \
 		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile
 	epatch "${FILESDIR}"/${P}-ldflags.patch
diff --git a/sci-biology/primer3/primer3-1.1.4.ebuild b/sci-biology/primer3/primer3-1.1.4.ebuild
index 437c3dcf75f8..441d554cd21a 100644
--- a/sci-biology/primer3/primer3-1.1.4.ebuild
+++ b/sci-biology/primer3/primer3-1.1.4.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-1.1.4.ebuild,v 1.2 2009/09/01 16:07:03 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-1.1.4.ebuild,v 1.3 2011/11/23 08:10:50 jlec Exp $
 
-DESCRIPTION="Design primers for PCR reactions."
+DESCRIPTION="Primer Design for PCR reactions"
 HOMEPAGE="http://primer3.sourceforge.net/"
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-LICENSE="whitehead"
 
 SLOT="0"
-KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86"
+LICENSE="whitehead"
 IUSE=""
+KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86"
 
 DEPEND="dev-lang/perl"
-
 RDEPEND=""
 
 S="${WORKDIR}/src"
diff --git a/sci-biology/primer3/primer3-2.2.3.ebuild b/sci-biology/primer3/primer3-2.2.3.ebuild
index dd74e89a4c60..3f10d84c1dde 100644
--- a/sci-biology/primer3/primer3-2.2.3.ebuild
+++ b/sci-biology/primer3/primer3-2.2.3.ebuild
@@ -1,25 +1,32 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-2.2.3.ebuild,v 1.1 2011/02/03 17:08:52 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-2.2.3.ebuild,v 1.2 2011/11/23 08:10:50 jlec Exp $
 
 EAPI="3"
 
 inherit toolchain-funcs
 
-DESCRIPTION="Design primers for PCR reactions."
+DESCRIPTION="Primer Design for PCR reactions"
 HOMEPAGE="http://primer3.sourceforge.net/"
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-LICENSE="GPL-2"
 
 SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86"
+LICENSE="GPL-2"
 IUSE=""
+KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 
-DEPEND=""
+DEPEND="dev-lang/perl"
 RDEPEND=""
 
 src_prepare() {
+	[[ ${CHOST} == *-darwin* ]] && \
+		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile
 	perl -i -ne 's/\$\(CPP\)/'$(tc-getCXX)'/; print unless /^(CC|CPP|CFLAGS|LDFLAGS)\s*=/' src/Makefile || die
+	sed \
+		-e '/oligotm/s:-o $@:$(LDFLAGS) -o $@:g' \
+		-e '/long_seq_tm_test/s:-o $@:$(LDFLAGS) -o $@:g' \
+		-e 's:CFLAGS:CXXFLAGS:g' \
+		-i src/Makefile || die
 }
 
 src_compile() {