Version Bump, #399289

Package-Manager: portage-2.2.0_alpha84/cvs/Linux x86_64

5 files changed, 140 insertions, 15 deletions

diff --git a/sci-chemistry/autodock_vina/ChangeLog b/sci-chemistry/autodock_vina/ChangeLog
index 131dd6268cfe..6c3913f29c50 100644
--- a/sci-chemistry/autodock_vina/ChangeLog
+++ b/sci-chemistry/autodock_vina/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/autodock_vina
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/autodock_vina/ChangeLog,v 1.3 2011/04/06 16:42:37 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/autodock_vina/ChangeLog,v 1.4 2012/01/21 16:50:09 jlec Exp $
+
+*autodock_vina-1.1.2 (21 Jan 2012)
+
+  21 Jan 2012; Justin Lecher <jlec@gentoo.org> +files/1.1.2-gentoo.patch,
+  +autodock_vina-1.1.2.ebuild, metadata.xml:
+  Version Bump, #399289
 
   06 Apr 2011; Justin Lecher <jlec@gentoo.org> autodock_vina-1.1.1-r1.ebuild:
   Fix compilation problem with =dev-libs/boost-1.46, #362243; thanks few and
diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
index 37a280d32b62..43fc0c49f375 100644
--- a/sci-chemistry/autodock_vina/Manifest
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -1,15 +1,18 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
 AUX 1.1.1-gentoo.patch 2377 RMD160 ba9aad38e4e64de9e7c2040593daaadee9b7052c SHA1 785f42d6d6d86bad025fc7a820f14dab49132aeb SHA256 3d6b388b831d1a2eab9025c7881a0bac9b71a8e1a5abbad7a05d4ba4c0fbc6ea
+AUX 1.1.2-gentoo.patch 2448 RMD160 54c1f3b15a25fb4c2b1b53e45143555a82de0752 SHA1 bba2eb51bca3d97178e32bf70d865ed8b9af2567 SHA256 41a0f4091be44dc2a59a7f32fedc18fb6e8266740284c756f5b79f39a5080d57
 DIST autodock_vina_1_1_1.tgz 66972 RMD160 3e65dd8e38f9f726c9200057fc37e0fcafe7d460 SHA1 620b2f5713b7ad2f13cc90ddb837dfd9fd2b4875 SHA256 f9aaf6b2a322775e1be30f22fb69573418610300c0ab2b9345fd6accc1c1b9fd
+DIST autodock_vina_1_1_2.tgz 67366 RMD160 02e5f7b291d62cebae88238e0110c8d2b38abc03 SHA1 e6321035a05897c05039093385ed087af933db1f SHA256 b86412d316960b1e4e319401719daf57ff009229d91654d623c3cf09339f6776
 EBUILD autodock_vina-1.1.1-r1.ebuild 1020 RMD160 7caccdcdb9a96e355c818d3a42f590b9517ad900 SHA1 b869fbef808c6c1ccf2a3ed99664203c33701305 SHA256 3b516413a7f9f41d6cfa00f78f4001f7f0235cb6827b9f3a0d705bab60f59a27
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+EBUILD autodock_vina-1.1.2.ebuild 997 RMD160 5d2415d27bcf622873e03933a1e78f0a48873009 SHA1 d3248c74da0fee426fd8df44297deee5ef085ba7 SHA256 d3e5bb622efedcca4eed5036a3e58b8fb83c02bc3631c1e20395d165639e1c30
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+Version: GnuPG v2.0.18 (GNU/Linux)
 
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-=rf+J
+iEYEAREKAAYFAk8a7MsACgkQgAnW8HDreRY65QCghpNpqPTTWj0FknDusTJVKaBp
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diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
new file mode 100644
index 000000000000..a88aebaa92d5
--- /dev/null
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild,v 1.1 2012/01/21 16:50:09 jlec Exp $
+
+EAPI=4
+
+inherit eutils flag-o-matic versionator
+
+MY_P="${PN}_$(replace_all_version_separators _)"
+
+DESCRIPTION="Program for drug discovery, molecular docking and virtual screening"
+HOMEPAGE="http://vina.scripps.edu/"
+SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+LICENSE="Apache-2.0"
+IUSE="debug"
+
+RDEPEND="dev-libs/boost"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${MY_P}/build/linux/release
+
+src_prepare() {
+	cd "${WORKDIR}"/${MY_P} && epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+	local c_options
+
+	use debug || c_options="-DNDEBUG"
+
+	append-cxxflags -DBOOST_FILESYSTEM_VERSION=2
+
+	emake \
+		BASE="${EPREFIX}"/usr/ \
+		GPP="$(tc-getCXX)" \
+		C_OPTIONS="${c_options}"
+}
+
+src_install() {
+	dobin vina{,_split}
+}
diff --git a/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch
new file mode 100644
index 000000000000..61ae8bec36f5
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch
@@ -0,0 +1,72 @@
+ build/linux/debug/Makefile   |    2 +-
+ build/linux/release/Makefile |    2 +-
+ build/makefile_common        |   14 +++++++-------
+ 3 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/build/linux/debug/Makefile b/build/linux/debug/Makefile
+index 6a41cfc..8097fb9 100644
+--- a/build/linux/debug/Makefile
++++ b/build/linux/debug/Makefile
+@@ -1,7 +1,7 @@
+ BASE=/usr/local
+ BOOST_VERSION=1_41
+ BOOST_INCLUDE = $(BASE)/include
+-C_PLATFORM=-static -pthread
++C_PLATFORM=-pthread
+ GPP=/usr/local/bin/g++
+ C_OPTIONS= -g
+ BOOST_LIB_VERSION=
+diff --git a/build/linux/release/Makefile b/build/linux/release/Makefile
+index 1de1063..ded8133 100644
+--- a/build/linux/release/Makefile
++++ b/build/linux/release/Makefile
+@@ -1,7 +1,7 @@
+ BASE=/usr/local
+ BOOST_VERSION=1_41
+ BOOST_INCLUDE = $(BASE)/include
+-C_PLATFORM=-static -pthread
++C_PLATFORM=-pthread
+ GPP=/usr/local/bin/g++
+ C_OPTIONS= -O3 -DNDEBUG
+ BOOST_LIB_VERSION=
+diff --git a/build/makefile_common b/build/makefile_common
+index a940329..96336e8 100644
+--- a/build/makefile_common
++++ b/build/makefile_common
+@@ -2,29 +2,29 @@ LIBOBJ = cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manif
+ MAINOBJ = main.o
+ SPLITOBJ = split.o
+ 
+-INCFLAGS = -I $(BOOST_INCLUDE)
++INCFLAGS = -I$(BOOST_INCLUDE)
+ 
+ # -pedantic fails on Mac with Boost 1.41 (syntax problems in their headers)
+ #CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
+ CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
+ 
+-LDFLAGS = -L$(BASE)/lib -L.
++LDFLAGS += -L.
+ 
+-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
++LIBS = -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem -lboost_program_options -lpthread
+ 
+ .SUFFIXES: .cpp .o
+ 
+ %.o : ../../../src/lib/%.cpp 
+-	$(CC) $(CFLAGS) -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -o $@ -c $< 
+ 
+ %.o : ../../../src/design/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 	
+ %.o : ../../../src/main/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 
+ %.o : ../../../src/split/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 
+ all: vina vina_split
+ 
diff --git a/sci-chemistry/autodock_vina/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml
index 3663c619b433..8836d2a13a76 100644
--- a/sci-chemistry/autodock_vina/metadata.xml
+++ b/sci-chemistry/autodock_vina/metadata.xml
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-  <email>jlec@gentoo.org</email>
-</maintainer>
-<longdescription>
+	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>jlec@gentoo.org</email>
+	</maintainer>
+	<longdescription>
 AutoDock Vina is a new open-source program for drug discovery, molecular
 docking and virtual screening, offering multi-core capability, high
 performance and enhanced accuracy and ease of use. [1]
@@ -17,7 +17,7 @@ of docking with a new scoring function, efficient optimization and
 multithreading
 Journal of Computational Chemistry 31 (2010) 455-461
 </longdescription>
-<!--
+	<!--
 <use>
   <flag name='flag'>Description of how USE='flag' affects this package</flag>
   <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this