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authorJustin Lecher <jlec@gentoo.org>2015-08-15 15:56:05 +0200
committerJustin Lecher <jlec@gentoo.org>2015-08-15 16:41:52 +0200
commit11ee21569f870e70f3e8ff45d9b87210b224ac76 (patch)
treef646d2797d9f7bbbd106cf057274ecdc29e57812 /sci-chemistry
parentsci-astronomy/wcslib: Version Bump (diff)
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sci-chemistry/dssp: Add missing USE dep, bug #557840 drop old patches
Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/dssp/dssp-2.2.1-r1.ebuild2
-rw-r--r--sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch46
-rw-r--r--sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch70
3 files changed, 1 insertions, 117 deletions
diff --git a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
index 5e8b800f948..28f8aced15f 100644
--- a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
+++ b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
@@ -15,7 +15,7 @@ SLOT="0"
KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
IUSE=""
-RDEPEND="dev-libs/boost:="
+RDEPEND="dev-libs/boost:=[threads]"
DEPEND="${RDEPEND}"
src_prepare() {
diff --git a/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch b/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch
deleted file mode 100644
index 5db1437beb1..00000000000
--- a/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch
+++ /dev/null
@@ -1,46 +0,0 @@
- 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
deleted file mode 100644
index 3db40f640cc..00000000000
--- a/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch
+++ /dev/null
@@ -1,70 +0,0 @@
- 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