QA and keyworded for linux prefix

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

4 files changed, 96 insertions, 13 deletions

diff --git a/sci-biology/probcons/ChangeLog b/sci-biology/probcons/ChangeLog
index 9aeb9f3e504c..212d6096034a 100644
--- a/sci-biology/probcons/ChangeLog
+++ b/sci-biology/probcons/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/probcons
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/ChangeLog,v 1.9 2009/08/16 18:18:18 dberkholz Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/ChangeLog,v 1.10 2010/06/15 13:27:50 jlec Exp $
+
+*probcons-1.12-r1 (15 Jun 2010)
+
+  15 Jun 2010; Justin Lecher <jlec@gentoo.org> +probcons-1.12-r1.ebuild,
+  files/probcons-1.12-cxxflags.patch:
+  QA and keyworded for linux prefix
 
   16 Aug 2009; Donnie Berkholz <dberkholz@gentoo.org>; probcons-1.12.ebuild:
   Keyword ~amd64.
diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest
index cfd080f7fa92..222cdd2e6a1a 100644
--- a/sci-biology/probcons/Manifest
+++ b/sci-biology/probcons/Manifest
@@ -3,17 +3,18 @@ Hash: SHA1
 
 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 844 RMD160 c5f07264e5ef9d76baa22b676b26f4a51c76fc73 SHA1 a797284ff9a7df4a7b8bff9ee286594109aabdda SHA256 56e30ce88806c520296e0e06230e4020ac341e91738106aa5392d5fad4975502
+AUX probcons-1.12-cxxflags.patch 1957 RMD160 5f9e849c7bdf97077325af9c9713d1de0f08376e SHA1 87e9143f948602e466526a2425c92887eb1ead21 SHA256 5342d2f86fc2d440db1649e0e1f4cf094d8e5a5861c145fb410d014bc9cd8a27
 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 1236 RMD160 b24658a6866f556bab2d9ee041540ed65fba961b SHA1 2302f7a9c2a1ba349b3949546187e34e2c7aeafe SHA256 86a6355ad1d5a3bc7914579262047bde097c3228d5ef88ae6a988beb3577c964
+EBUILD probcons-1.12-r1.ebuild 1338 RMD160 b715074c1abdbfa3198b610c2b084f107327fc40 SHA1 f428a3728420421d0bd1c30687c3be14f82d254b SHA256 fa2cf717c20cccd428b7216b9fa478e4357dcf0f00f2e85023b6a7bbf7eb8732
 EBUILD probcons-1.12.ebuild 1307 RMD160 d964b0cd0787854506dcb065fcfd4b611e86ba53 SHA1 0959b01cc1b82d4f179c7ff3bb40f6e419b07411 SHA256 f715ed901b184bbeeea6969bc76101eecd2c2d9bd94f56479d7b87c83ab024a3
-MISC ChangeLog 1540 RMD160 2ed3cda909d9e4a1a38a1da8d09fca865854f1b0 SHA1 5436a3753f043455d65bd948cf06ed44bea94a9f SHA256 faa301041e459e2deba63e33a80a1d35963e8f4f3a317ed3ce684b7582e5730c
+MISC ChangeLog 1717 RMD160 5b5ee80867ed0f58df93922100456d375e8e7425 SHA1 7096fe510aff2c632bd6edf635d1c6049b49744e SHA256 91c18dd88fc135e44fb1a559092938ad3d170b986c01ef3e913cb868cc91dbeb
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.11 (GNU/Linux)
+Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkqITXQACgkQXVaO67S1rtsu9gCgzTaCzTZCBYtFKoCGaU9MgyqN
-RPEAoJIxFq2YN4UDorQ0uqGu8PxGCCoZ
-=8bJv
+iEYEARECAAYFAkwXf9wACgkQgAnW8HDreRYqjwCg0o9jhCbPAqT2lUAcmD2pb4Z0
+QqQAnA9j/U4QjTVQ/KFoHFWYK63mncKf
+=ZMq2
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/probcons/files/probcons-1.12-cxxflags.patch b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
index a2431c4a0936..e07ebe1a613f 100644
--- a/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
+++ b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
@@ -1,7 +1,8 @@
-diff -Naur probcons/Makefile probcons-new/Makefile
---- probcons/Makefile	2007-04-03 13:39:23.000000000 -0400
-+++ probcons-new/Makefile	2007-10-06 07:07:10.000000000 -0400
-@@ -15,6 +15,8 @@
+diff --git a/Makefile b/Makefile
+index 75fc47a..4a19140 100644
+--- a/Makefile
++++ b/Makefile
+@@ -15,6 +15,8 @@ CXX = g++
  #    c) RELEASE mode
  ################################################################################
  
@@ -10,7 +11,7 @@ diff -Naur probcons/Makefile probcons-new/Makefile
  OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
  
  # debug mode    
-@@ -25,7 +27,7 @@
+@@ -25,7 +27,7 @@ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
  
  # release mode
  #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
@@ -19,3 +20,28 @@ diff -Naur probcons/Makefile probcons-new/Makefile
  
  ################################################################################
  # 3) Dependencies
+@@ -37,19 +39,19 @@ TARGETS = probcons compare project makegnuplot
+ all : $(TARGETS)
+ 
+ probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
+-	$(CXX) $(CXXFLAGS) -lm -o probcons Main.cc 
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o probcons Main.cc -lm
+ 
+ compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+-	$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o compare CompareToRef.cc
+ 
+ fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
+-	$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o fixref FixRef.cc
+ 
+ project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
+-	$(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o project ProjectPairwise.cc
+ 
+ makegnuplot : MakeGnuPlot.cc
+-	$(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
+ 
+ .PHONY : clean
+ clean:
diff --git a/sci-biology/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild
new file mode 100644
index 000000000000..4dbeda112c8e
--- /dev/null
+++ b/sci-biology/probcons/probcons-1.12-r1.ebuild
@@ -0,0 +1,50 @@
+# 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-r1.ebuild,v 1.1 2010/06/15 13:27:50 jlec Exp $
+
+EAPI="3"
+
+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/${MY_P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+# Gnuplot is explicitly runtime-only, it's run using system()
+RDEPEND="sci-visualization/gnuplot"
+DEPEND=""
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	epatch "${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 || die
+}
+
+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"
+}