Drop old

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

7 files changed, 44 insertions, 137 deletions

diff --git a/sci-biology/probcons/ChangeLog b/sci-biology/probcons/ChangeLog
index 88f28e5ade22..418fdd76c1a1 100644
--- a/sci-biology/probcons/ChangeLog
+++ b/sci-biology/probcons/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/probcons
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/ChangeLog,v 1.14 2011/06/13 11:17:41 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/ChangeLog,v 1.15 2015/03/29 14:58:53 jlec Exp $
+
+  29 Mar 2015; Justin Lecher <jlec@gentoo.org> -files/1.10-fix-cxxflags.patch,
+  -probcons-1.10.ebuild, -probcons-1.12.ebuild, metadata.xml,
+  probcons-1.12-r1.ebuild:
+  Drop old
 
   13 Jun 2011; Justin Lecher <jlec@gentoo.org> probcons-1.12-r1.ebuild,
   +files/probcons-1.12-gcc-4.6.patch:
@@ -58,4 +63,3 @@
   New multiple sequence alignment package. Probably the best global aligner,
   although it runs slower. Takes 5-10 times longer than clustalw, but about
   half as long as t-coffee.
-
diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest
index 06b33f37f04c..44a60c6177a9 100644
--- a/sci-biology/probcons/Manifest
+++ b/sci-biology/probcons/Manifest
@@ -1,11 +1,29 @@
-AUX 1.10-fix-cxxflags.patch 845 RMD160 1e04c84b35c245623619c6d5a7128a8ab1c880af SHA1 9d3ecd0da754d899cd4b4016bf2dbffe5e9d87b6 SHA256 73a298114996b5d879b9ec3253d104464cb456d19382668cdf75bfe9f93f11de
-AUX gcc-4.3.patch 1300 RMD160 c0865d3158f7517154d0084edea3e9d50f11f79b SHA1 909160de3fee66ca4c1489f963aed78a870d0a9a SHA256 e9669d83770557834b54268f0b4e404981b91084587d69f6492c7160c1659d6b
-AUX probcons-1.12-cxxflags.patch 1957 RMD160 5f9e849c7bdf97077325af9c9713d1de0f08376e SHA1 87e9143f948602e466526a2425c92887eb1ead21 SHA256 5342d2f86fc2d440db1649e0e1f4cf094d8e5a5861c145fb410d014bc9cd8a27
-AUX probcons-1.12-gcc-4.6.patch 306 RMD160 cc9a8000bc1529837d28524492bac22ce8c3cb45 SHA1 0a8abc5dd5428d18b3e9154a2ef0962eaa8484cf SHA256 75bff1b697a732e183f1d4e20153b7b37afb4d3242f43305651c044809a02761
-DIST probcons_v1_10.tar.gz 43004 RMD160 ba7caa3cadd702c3dc00c20f01bfb22416435784 SHA1 773d82f6883202ec41e5dee39713b5db649ef5b0 SHA256 f7a775ac4ba3b3261c0bbe5d2c203c96fc2551e67448aefbac83b461c931b518
-DIST probcons_v1_12.tar.gz 43200 RMD160 4d7d9a89c2c95f22056719c8349216ca1ba635c9 SHA1 ee6ce81777c9ce366f575ab4096ff07f39af9829 SHA256 ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383
-EBUILD probcons-1.10.ebuild 1255 RMD160 49e26aae7838e14072b99e658e0497fdf48e3305 SHA1 97ee5cb12c869ff4c5c0669bdb1f7a9c8e8b7c0c SHA256 4f0d18095845561c68d69a40de2a5b4433b2d0d61ad110b2c1d1b1c599bb53e1
-EBUILD probcons-1.12-r1.ebuild 1395 RMD160 dd6d372e43e4df8703262ca42396ad0d6f966995 SHA1 865c1b3e1fb9765fd30a344d86c77e7b30482f06 SHA256 363bcce12e3484b292a48c71c5df51a01e9a369dc7c10d81da1e8fe11cbdd565
-EBUILD probcons-1.12.ebuild 1326 RMD160 5925f8df5fff2dc25f8112f2dda4f8877743267c SHA1 ac50b96c0203bcf0ad8c5a38a733fe59eaa73317 SHA256 c9cddf715df24fee17bf77d9ca7da71b1490664d651baf0f114d68626e1bc14b
-MISC ChangeLog 2258 RMD160 0311dc14add713148e5878500ad4ef8d14a38696 SHA1 a4a3d20325ce33f046ccfbb2d72d655d9413a555 SHA256 4dff3d237b115ad3d79fb142d6d15125e4b9c865e00f4e1182eb7d12a1536c2c
-MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
+AUX gcc-4.3.patch 1300 SHA256 e9669d83770557834b54268f0b4e404981b91084587d69f6492c7160c1659d6b SHA512 a1839f844cd9ce0cd7a9542c0e4abaa859ed8f4f42de1dfae01af72ceb0326019379ba17ae56d4756bbb7d649da0b5deeb624cbcd5176de8a5ab34123fb689bd WHIRLPOOL 87c1ab62d7ead97f5dfe5ad01826eca1bd80887ff86efba50935419095156fff338350923ff21ec9673924a430760144e0ef364178daeb7e13340087a07eac40
+AUX probcons-1.12-cxxflags.patch 1957 SHA256 5342d2f86fc2d440db1649e0e1f4cf094d8e5a5861c145fb410d014bc9cd8a27 SHA512 033e92e414d3e2d1db867aec980d82759a662cf46692e3cc908bb7b3428d5eca105fb81cbdd8764c54dd3d759d29e713ef085fc48aac183426d26fe68a48a38e WHIRLPOOL 42c13cf76077bcaccf7eeea31f8defbbc82108b4314ba2cf494a8220d57dbf89a2cdb943fec36a21c46fcda7ad7c4abfc4eecfe8280ea2679d5b740c56150431
+AUX probcons-1.12-gcc-4.6.patch 306 SHA256 75bff1b697a732e183f1d4e20153b7b37afb4d3242f43305651c044809a02761 SHA512 f8a393cce2a860ea54aa18add7ba236aa43e21893925e4484b272190e29aa2dc27bf20b11edc5694446f027c6d8d6ff3c3f92383f0b0c8958b1b1d5b7564f828 WHIRLPOOL 5bc8ae7d4d35e6989fe2606b86ea236e3baaf72ecba15bd4ec15d10bad09eef47c3a7cb508329a38607c403d75906183f8381f0cda11b4b835067434694146b4
+DIST probcons_v1_12.tar.gz 43200 SHA256 ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383
+EBUILD probcons-1.12-r1.ebuild 1301 SHA256 c808d3d04f8a71fcb97ee271273481be8058076d765d762e0243d5a30bf51fe5 SHA512 a40b8d70e7ed48e63016a1fe0b1ecdbfd2622974cc4726dda0053419341e56e7f45b880d0c1a7bd21d9eb3b9b8ccf6d30813c0089f0d1bc09d0582ececbc13b3 WHIRLPOOL 052c07fd0000cf4e7e79eaa77ce02a711d17dae09255440d81c072f6e9748736317842cfdeca9c39b5d3d5f2a1a162c54c53a4d9023166912ed19ba03d9b7c1a
+MISC ChangeLog 2437 SHA256 7d9d0fb934a1fc4e86dd6341350c939b45f9836b2ecb6a275d3712626c3ca4b1 SHA512 8d48e29d79fcf12a7ddb5396f1706f782e80471e50d07950c5f61fc5b3e2f0314676fc84424df5b64dda0dab15a55b97205ebb728afbfdf4aca53404665983ea WHIRLPOOL 6d99fce52c6fa9115cbd8dc50a95a1e6f564e1514b88dd72fc0e9ed027aac8e5dc84e1c6dd46e382770a4eca387f96fc376bafde4743d5ab261f180c91900479
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0
+
+iQJ8BAEBCgBmBQJVGBM2XxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w
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+3sCfv24UeRjBp1TuqzMQ
+=fKol
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/probcons/files/1.10-fix-cxxflags.patch b/sci-biology/probcons/files/1.10-fix-cxxflags.patch
deleted file mode 100644
index bf76e77b36c1..000000000000
--- a/sci-biology/probcons/files/1.10-fix-cxxflags.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff -urN probcons.orig/Makefile probcons/Makefile
---- probcons.orig/Makefile	2006-02-21 12:14:37.000000000 -0800
-+++ probcons/Makefile	2006-02-21 12:15:15.000000000 -0800
-@@ -15,6 +15,8 @@
- #    c) RELEASE mode
- ################################################################################
- 
-+OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
-+
- OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.10"
- 
- # debug mode    
-@@ -25,7 +27,7 @@
- 
- # release mode
- #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
--CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
-+CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS)
- 
- ################################################################################
- # 3) Dependencies
diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml
index 34294c65ca04..f17a827e3101 100644
--- a/sci-biology/probcons/metadata.xml
+++ b/sci-biology/probcons/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/probcons/probcons-1.10.ebuild b/sci-biology/probcons/probcons-1.10.ebuild
deleted file mode 100644
index e648de636d28..000000000000
--- a/sci-biology/probcons/probcons-1.10.ebuild
+++ /dev/null
@@ -1,46 +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/probcons/probcons-1.10.ebuild,v 1.3 2010/06/17 09:46:52 jlec Exp $
-
-inherit eutils toolchain-funcs
-
-MY_P="${PN}_v${PV/./_}"
-DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences"
-HOMEPAGE="http://probcons.stanford.edu/"
-SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz"
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="x86"
-IUSE=""
-# Gnuplot is explicitly runtime-only, it's run using system()
-RDEPEND="
-	!sci-geosciences/gmt
-	sci-visualization/gnuplot"
-DEPEND=""
-S="${WORKDIR}/${PN}"
-
-src_unpack() {
-	unpack ${A}
-	epatch ${FILESDIR}/${PV}-fix-cxxflags.patch
-}
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		OPT_CXXFLAGS="${CXXFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	DESTTREE="/usr" dobin probcons project makegnuplot
-	# Overlap with imagemagick
-	DESTTREE="/usr" newbin compare compare-probcons
-	dodoc README
-}
-
-pkg_postinst() {
-	ewarn "The 'compare' binary is installed as 'compare-probcons'"
-	ewarn "to avoid overlap with other packages."
-	einfo "You may also want to download the user manual"
-	einfo "from http://probcons.stanford.edu/manual.pdf"
-}
diff --git a/sci-biology/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild
index 6acfffefbe43..b8ba7173c1bf 100644
--- a/sci-biology/probcons/probcons-1.12-r1.ebuild
+++ b/sci-biology/probcons/probcons-1.12-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/probcons-1.12-r1.ebuild,v 1.5 2011/06/13 11:17:41 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/probcons-1.12-r1.ebuild,v 1.6 2015/03/29 14:58:53 jlec Exp $
 
-EAPI=3
+EAPI=5
 
 inherit eutils toolchain-funcs
 
@@ -35,15 +35,14 @@ src_prepare() {
 src_compile() {
 	emake \
 		CXX="$(tc-getCXX)" \
-		OPT_CXXFLAGS="${CXXFLAGS}" \
-		|| die "make failed"
+		OPT_CXXFLAGS="${CXXFLAGS}"
 }
 
 src_install() {
-	dobin probcons project makegnuplot || die "failed to install"
+	dobin probcons project makegnuplot
 	# Overlap with imagemagick
-	newbin compare compare-probcons || die "failed to install compare"
-	dodoc README || die
+	newbin compare compare-probcons
+	dodoc README
 }
 
 pkg_postinst() {
diff --git a/sci-biology/probcons/probcons-1.12.ebuild b/sci-biology/probcons/probcons-1.12.ebuild
deleted file mode 100644
index a636ebf5e0cb..000000000000
--- a/sci-biology/probcons/probcons-1.12.ebuild
+++ /dev/null
@@ -1,47 +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/probcons/probcons-1.12.ebuild,v 1.5 2010/06/17 09:46:52 jlec Exp $
-
-inherit eutils toolchain-funcs
-
-MY_P="${PN}_v${PV/./_}"
-DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences"
-HOMEPAGE="http://probcons.stanford.edu/"
-SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz"
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-# Gnuplot is explicitly runtime-only, it's run using system()
-RDEPEND="
-	!sci-geosciences/gmt
-	sci-visualization/gnuplot"
-DEPEND=""
-S="${WORKDIR}/${PN}"
-
-src_unpack() {
-	unpack ${A}
-	epatch "${FILESDIR}"/${P}-cxxflags.patch
-	epatch "${FILESDIR}"/gcc-4.3.patch
-}
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		OPT_CXXFLAGS="${CXXFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	dobin probcons project makegnuplot || die "failed to install"
-	# Overlap with imagemagick
-	newbin compare compare-probcons || die "failed to install compare"
-	dodoc README
-}
-
-pkg_postinst() {
-	ewarn "The 'compare' binary is installed as 'compare-probcons'"
-	ewarn "to avoid overlap with other packages."
-	einfo "You may also want to download the user manual"
-	einfo "from http://probcons.stanford.edu/manual.pdf"
-}