sci-chemistry/dssp: Version Bump

Package-Manager: portage-2.2.0_alpha109/cvs/Linux x86_64

6 files changed, 177 insertions, 13 deletions

diff --git a/sci-chemistry/dssp/ChangeLog b/sci-chemistry/dssp/ChangeLog
index 999dbd11ba28..ad610fc75a66 100644
--- a/sci-chemistry/dssp/ChangeLog
+++ b/sci-chemistry/dssp/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/dssp
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/dssp/ChangeLog,v 1.5 2011/04/13 09:25:37 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/dssp/ChangeLog,v 1.6 2012/06/03 15:06:13 jlec Exp $
+
+*dssp-2.0.4 (03 Jun 2012)
+
+  03 Jun 2012; Justin Lecher <jlec@gentoo.org> +dssp-2.0.4.ebuild,
+  +files/dssp-2.0.4-gcc47.patch, +files/dssp-2.0.4-gentoo.patch, metadata.xml:
+  Version Bump
 
   13 Apr 2011; Justin Lecher <jlec@gentoo.org> dssp-101007.ebuild:
   Fixed URL for download, #363175
diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
index ace8597a64a3..8c8453bcaeac 100644
--- a/sci-chemistry/dssp/Manifest
+++ b/sci-chemistry/dssp/Manifest
@@ -1,17 +1,22 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
 AUX Makefile 237 RMD160 e7c5528bcf5d5d514c0ff2a58019d1570c3ba932 SHA1 497481dac448abe16e73517d6c25ab760b992bea SHA256 4caa74d9736641485b2e977f0b810f692b8afde933d80947da338c56a6f53510
+AUX dssp-2.0.4-gcc47.patch 1518 RMD160 e711b2e8bfac33ba3ff64dab0c9927d109325e2e SHA1 8ce1c3b93da2c5e204a7e07a7390b0d64183f381 SHA256 869deac0af501fae6588ef2f8223d22af987ad7e7035b61d4d3bf94175221638
+AUX dssp-2.0.4-gentoo.patch 1931 RMD160 ce0c3a11f48132021dcc571e82bc12a4de9d96cc SHA1 d9b24b73e3d6eb27032bff332b0fa78990327bb9 SHA256 5eb675b623aecd9fd6574a2dfcec4c70e71b7aa56815426067bcd6e6a9af3e78
 DIST dssp-070831cmbi.tar.gz 451919 RMD160 656e1be2c5db6150a3db2785bcaf874632b3cf27 SHA1 40ffc8fcd1400eb4675285995f1c366ff6612004 SHA256 bf5cdd970f92fd80268b87a468d4efe891d3227fd15136147889605299f75661
 DIST dssp-101007.tar.gz 541779 RMD160 aac7fb41de73b011fcbe3358c35e27e0272257af SHA1 1809b8128b4aafe77de8f2e8d68cf1ab835d4051 SHA256 2678aa0914df970c79862bf04f854eff97a23d2b6710a1b82ddcf8dec41ef37c
+DIST dssp-2.0.4.tgz 33515 RMD160 4aef95c7921c1fc7e17b831e1ad08c6eaf8033d0 SHA1 af7e15f16a732bed4f6631557d6c84bffbb934bc SHA256 9444f36a26c003c5578aa863c3725ff23b0511abe7d7fc873dbd8294dcb2b66b
 EBUILD dssp-070831.ebuild 1142 RMD160 d2d236533b5a400e0460a90d16e1b8f048631a11 SHA1 40333b34be248dd935aba37d6eeed6bef7903f3a SHA256 c9ea78cecb6a2695236e27c2f0681d900fb59053093388058a6e965398ef3e71
 EBUILD dssp-101007.ebuild 1111 RMD160 e74409c66f5d3c4f5b7c8b651ed685eefc9c93e7 SHA1 8aa6bd5ff667003ade3dfe8a55cd73612429a170 SHA256 c0fbd6addd2e2ea160dd26a50dcc6d54e2dca72eefdf1205cd7bf2a69c486bf3
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-MISC metadata.xml 216 RMD160 04a6fc4e2160b439296b52aa97d5b7d83af75508 SHA1 9561c9e6eada6aac9b503407917900529ce703e9 SHA256 24f5c205c2655ef27138c8aa087701626f5b4c666229c9ef7fe814e63ea2e776
+EBUILD dssp-2.0.4.ebuild 894 RMD160 8ba31475c92da3d9e721cb8316476dc742769081 SHA1 7b936deb7c889874cb6c3f8ccbee3c308ac17b81 SHA256 932433966d50312f8637951d832a328e7c159d12594ad07c0b0016432d547f1b
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diff --git a/sci-chemistry/dssp/dssp-2.0.4.ebuild b/sci-chemistry/dssp/dssp-2.0.4.ebuild
new file mode 100644
index 000000000000..7b8f77bda909
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-2.0.4.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/dssp/dssp-2.0.4.ebuild,v 1.1 2012/06/03 15:06:13 jlec Exp $
+
+EAPI=4
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/"
+SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/dssp-2.0.4.tgz"
+
+LICENSE="Boost-1.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+src_prepare() {
+	tc-export CXX
+
+	cat >> make.config <<- EOF
+	BOOST_LIB_SUFFIX = -mt
+	BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)"
+	BOOST_INC_DIR = "${EPREFIX}/usr/include"
+	EOF
+
+	epatch \
+		"${FILESDIR}"/${P}-gcc47.patch \
+		"${FILESDIR}"/${P}-gentoo.patch
+}
+
+src_install() {
+	dobin mkdssp
+	dosym mkdssp /usr/bin/dssp
+	doman doc/mkdssp.1
+	dodoc README.txt changelog
+}
diff --git a/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch b/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch
new file mode 100644
index 000000000000..5db1437beb1f
--- /dev/null
+++ b/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch
@@ -0,0 +1,46 @@
+ src/matrix.h          |    5 +++--
+ src/primitives-3d.cpp |    1 +
+ 2 files changed, 4 insertions(+), 2 deletions(-)
+
+diff --git a/src/matrix.h b/src/matrix.h
+index 1053ad9..d7dae5f 100644
+--- a/src/matrix.h
++++ b/src/matrix.h
+@@ -14,6 +14,7 @@
+ #include <istream>
+ #include <cassert>
+ #include <stdexcept>
++#include <unistd.h>
+ 
+ // --------------------------------------------------------------------
+ // uBlas compatible matrix types
+@@ -284,7 +285,7 @@ class identity_matrix : public matrix_base<T>
+ template<typename T>
+ matrix<T> operator*(const matrix_base<T>& lhs, const matrix_base<T>& rhs)
+ {
+-	matrix<T> result(min(lhs.dim_m(), rhs.dim_m()), min(lhs.dim_n(), rhs.dim_n()));
++	matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n()));
+ 	
+ 	for (uint32 i = 0; i < result.dim_m(); ++i)
+ 	{
+@@ -310,7 +311,7 @@ matrix<T> operator*(const matrix_base<T>& lhs, T rhs)
+ template<typename T>
+ matrix<T> operator-(const matrix_base<T>& lhs, const matrix_base<T>& rhs)
+ {
+-	matrix<T> result(min(lhs.dim_m(), rhs.dim_m()), min(lhs.dim_n(), rhs.dim_n()));
++	matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n()));
+ 	
+ 	for (uint32 i = 0; i < result.dim_m(); ++i)
+ 	{
+diff --git a/src/primitives-3d.cpp b/src/primitives-3d.cpp
+index b04e7c4..4532ecd 100644
+--- a/src/primitives-3d.cpp
++++ b/src/primitives-3d.cpp
+@@ -9,6 +9,7 @@
+ 
+ #include <valarray>
+ #include <cmath>
++#include <unistd.h>
+ 
+ #include <boost/foreach.hpp>
+ #define foreach BOOST_FOREACH
diff --git a/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch b/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch
new file mode 100644
index 000000000000..3db40f640ccd
--- /dev/null
+++ b/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch
@@ -0,0 +1,70 @@
+ makefile |   24 ++++++++++++++----------
+ 1 files changed, 14 insertions(+), 10 deletions(-)
+
+diff --git a/makefile b/makefile
+index df699b7..9d2167b 100644
+--- a/makefile
++++ b/makefile
+@@ -2,7 +2,7 @@
+ #
+ #  Copyright Maarten L. Hekkelman, Radboud University 2008-2011.
+ # Distributed under the Boost Software License, Version 1.0.
+-#    (See accompanying file LICENSE_1_0.txt or copy at
++#    (See aCXXompanying file LICENSE_1_0.txt or copy at
+ #          http://www.boost.org/LICENSE_1_0.txt)
+ #
+ # This makefile includes a file called make.config. It will create a
+@@ -24,22 +24,23 @@ BOOST_LIBS			= thread regex filesystem program_options date_time iostreams math_
+ LIBS				= $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2
+ 
+ DEFINES				= USE_COMPRESSION LINUX VERSION='"$(VERSION)"'
+-CC					= c++
++CXX					?= c++
+ 
+-CFLAGS				= $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread
+-LDOPTS				= $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g -pthread
++CPPFLAGS				+= $(INC_DIR:%=-I%) -iquote src
++CXXFLAGS          += -Wall -Wno-multichar -pthread
++LDOPTS				= $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -pthread
+ 
+ OBJ_DIR				= obj
+ 
+ ifeq ($(DEBUG),1)
+ OBJ_DIR				:= $(OBJ_DIR).dbg
+-CFLAGS				+= -g3
++CFLAGS				+= 
+ else
+ DEFINES				+= NDEBUG
+-CFLAGS				+= -O3
++CFLAGS				+= 
+ endif
+ 
+-CFLAGS				+= $(DEFINES:%=-D%)
++CPPFLAGS				+= $(DEFINES:%=-D%)
+ 
+ DIST_NAME			= dssp-$(VERSION)
+ 
+@@ -49,17 +50,20 @@ OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ
+ 
+ mkdssp: $(OBJECTS)
+ 	@ echo linking $@
+-	@ $(CC) -static -o $@ $^ $(LDOPTS)
++	$(CXX) $(LDFLAGS) -o $@ $^ $(LDOPTS)
+ 	@ echo OK
+ 
+ include $(OBJECTS:%.o=%.d)
+ 
+ $(OBJECTS:.o=.d):
+ 
+-$(OBJ_DIR)/%.o: %.cpp
++OBJ_DIR:
+ 	@ if [ ! -d $(OBJ_DIR) ]; then mkdir $(OBJ_DIR); fi
++
++
++$(OBJ_DIR)/%.o: %.cpp OBJ_DIR
+ 	@ echo compiling $@
+-	@ $(CC) -MD -c -o $@ $< $(CFLAGS)
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -MD -c -o $@ $<
+ 
+ clean:
+ 	rm -rf $(OBJ_DIR)/* mkdssp
diff --git a/sci-chemistry/dssp/metadata.xml b/sci-chemistry/dssp/metadata.xml
index c6856dc7f2cf..210ad0db014c 100644
--- a/sci-chemistry/dssp/metadata.xml
+++ b/sci-chemistry/dssp/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-  <email>jlec@gentoo.org</email>
-</maintainer>
+	<herd>sci</herd>
+	<maintainer>
+		<email>jlec@gentoo.org</email>
+	</maintainer>
 </pkgmetadata>