[gentoo-commits] gentoo-x86 commit in sci-chemistry/dssp/files: dssp-2.0.4-gcc47.patch dssp-2.0.4-gentoo.patch

[gentoo-commits] gentoo-x86 commit in sci-chemistry/dssp/files: dssp-2.0.4-gcc47.patch dssp-2.0.4-gentoo.patch

[Justin Lecher (jlec)]

jlec        12/06/03 15:06:13

  Added:                dssp-2.0.4-gcc47.patch dssp-2.0.4-gentoo.patch
  Log:
  sci-chemistry/dssp: Version Bump
  
  (Portage version: 2.2.0_alpha109/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch?rev=1.1&content-type=text/plain

Index: dssp-2.0.4-gcc47.patch
===================================================================
 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



1.1                  sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch?rev=1.1&content-type=text/plain

Index: dssp-2.0.4-gentoo.patch
===================================================================
 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