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author | Justin Lecher <jlec@gentoo.org> | 2012-06-03 15:06:13 +0000 |
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committer | Justin Lecher <jlec@gentoo.org> | 2012-06-03 15:06:13 +0000 |
commit | 2e19930399581c3baf7ab38420de67ea059ae683 (patch) | |
tree | 7c2d860f94408c1abb6cbc32248d003368f00b2f /sci-chemistry | |
parent | Fix libpolymake.so.0 symlink (diff) | |
download | gentoo-2-2e19930399581c3baf7ab38420de67ea059ae683.tar.gz gentoo-2-2e19930399581c3baf7ab38420de67ea059ae683.tar.bz2 gentoo-2-2e19930399581c3baf7ab38420de67ea059ae683.zip |
sci-chemistry/dssp: Version Bump
(Portage version: 2.2.0_alpha109/cvs/Linux x86_64)
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/dssp/ChangeLog | 10 | ||||
-rw-r--r-- | sci-chemistry/dssp/dssp-2.0.4.ebuild | 37 | ||||
-rw-r--r-- | sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch | 46 | ||||
-rw-r--r-- | sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch | 70 | ||||
-rw-r--r-- | sci-chemistry/dssp/metadata.xml | 8 |
5 files changed, 165 insertions, 6 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/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> |