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To: gentoo-commits@g.o
From: "Justin Lecher (jlec)" <jlec@g.o>
Subject: gentoo-x86 commit in sci-chemistry/pdb-extract/files: pdb-extract-3.11-cflags-install.patch pdb-extract-3.11-gcc-4.7.patch
Date: Sat, 23 Jun 2012 18:57:05 +0000 (UTC)
jlec        12/06/23 18:57:05

  Added:                pdb-extract-3.11-cflags-install.patch
                        pdb-extract-3.11-gcc-4.7.patch
  Log:
  sci-chemistry/pdb-extract: Version Bump, #379159
  
  (Portage version: 2.2.0_alpha111/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch?rev=1.1&content-type=text/plain

Index: pdb-extract-3.11-cflags-install.patch
===================================================================
 Makefile                  |    2 +-
 etc/make.platform.darwin3 |    4 ++--
 etc/make.platform.darwin4 |    4 ++--
 etc/make.platform.gnu3    |   20 +++++++++++---------
 etc/make.platform.gnu4    |   20 +++++++++++---------
 5 files changed, 27 insertions(+), 23 deletions(-)

diff --git a/Makefile b/Makefile
index 627d256..72c7e59 100644
--- a/Makefile
+++ b/Makefile
@@ -52,7 +52,7 @@ compile:
 		echo "------------------------------------------------------------"; \
 		echo "**** Making $$libdir ****"; \
 		echo "------------------------------------------------------------"; \
-		(cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
+		(cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \
 	done
 
 beta:
diff --git a/etc/make.platform.darwin3 b/etc/make.platform.darwin3
index c5f7b06..4c1c97c 100644
--- a/etc/make.platform.darwin3
+++ b/etc/make.platform.darwin3
@@ -91,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
 DEFINES=$(GDEFINES) $(LDEFINES)
 
 ## Global include directories
-GINCLUDES= 
+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
 
 # Collect all include directories from global include directories and
 # include directories specified in module makefile
@@ -159,7 +159,7 @@ F77LIBS=
 STATIC_LINKING=
 
 # Linker flags
-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
 
 # Fortran linker
 F77_LINKER=f77
diff --git a/etc/make.platform.darwin4 b/etc/make.platform.darwin4
index 4619b34..f481fdb 100644
--- a/etc/make.platform.darwin4
+++ b/etc/make.platform.darwin4
@@ -92,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
 DEFINES=$(GDEFINES) $(LDEFINES)
 
 ## Global include directories
-GINCLUDES= 
+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
 
 # Collect all include directories from global include directories and
 # include directories specified in module makefile
@@ -160,7 +160,7 @@ F77LIBS=
 STATIC_LINKING=
 
 # Linker flags
-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
 
 # Fortran linker
 F77_LINKER=f77
diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3
index 7fd442e..9bec4dc 100644
--- a/etc/make.platform.gnu3
+++ b/etc/make.platform.gnu3
@@ -6,6 +6,8 @@
 ##
 ##########################################################################
 
+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
+
 #-----Lexer and Parser section-------------------------------------------#
 
 # Lexer executable
@@ -89,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
 DEFINES=$(GDEFINES) $(LDEFINES)
 
 ## Global include directories
-GINCLUDES= 
+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
 
 # Collect all include directories from global include directories and
 # include directories specified in module makefile
@@ -107,8 +109,8 @@ NON_ANSI_C_FLAG=
 C_WARNINGS=$(WARNINGS)
 
 # C compiler flags
-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
                $(INCLUDES) 
 
 ## C++ compiler
@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
 EXT=C
 
 # C++ compiler flags
-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
         $(INCLUDES)
-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
                  $(DEFINES) $(INCLUDES)
 # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
 # source code that is not maintained by PDB
@@ -144,7 +146,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
 F77=f77
 
 # Fortran compiler flags
-FFLAGS=-O -u
+FFLAGS=$(F_OPT)
 
 # Additional Fortran libraries
 F77LIBS=
@@ -154,11 +156,11 @@ F77LIBS=
 #-----Linkers section----------------------------------------------------#
 
 # Static linking option. If not defined, dynamic linking is used.
-STATIC_LINKING=-static
+STATIC_LINKING= 
 
 # Linker flags
-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-LDFLAGS_NO_STATIC=$(ABI) -w
+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
 
 # Fortran linker
 F77_LINKER=f77
diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4
index 78a0007..bc85308 100644
--- a/etc/make.platform.gnu4
+++ b/etc/make.platform.gnu4
@@ -6,6 +6,8 @@
 ##
 ##########################################################################
 
+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
+
 #-----Lexer and Parser section-------------------------------------------#
 
 # Lexer executable
@@ -34,7 +36,7 @@ ABI=
 
 # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
 # warnings as errors.
-WARNINGS_AS_ERRORS=-Werror
+WARNINGS_AS_ERRORS=
 
 # ALL_WARNINGS defines flags to instruct all compilers to report all
 # warnings.
@@ -90,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
 DEFINES=$(GDEFINES) $(LDEFINES)
 
 ## Global include directories
-GINCLUDES= 
+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
 
 # Collect all include directories from global include directories and
 # include directories specified in module makefile
@@ -108,8 +110,8 @@ NON_ANSI_C_FLAG=
 C_WARNINGS=$(WARNINGS)
 
 # C compiler flags
-CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
+CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
 
 ## C++ compiler
 ## This part defines C++ compiler information
@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
 EXT=C
 
 # C++ compiler flags
-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+C++FLAGS=$(CCC_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
   $(DEFINES) $(INCLUDES)
-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
   $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES)
 
 # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
@@ -145,7 +147,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
 F77=f77
 
 # Fortran compiler flags
-FFLAGS=-O -u
+FFLAGS=$(F_OPT)
 
 # Additional Fortran libraries
 F77LIBS=
@@ -158,8 +160,8 @@ F77LIBS=
 STATIC_LINKING=
 
 # Linker flags
-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-LDFLAGS_NO_STATIC=$(ABI) -w
+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
 
 # Fortran linker
 F77_LINKER=f77



1.1                  sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch?rev=1.1&content-type=text/plain

Index: pdb-extract-3.11-gcc-4.7.patch
===================================================================
 common-v4.5/src/mapped_ptr_vector.C |   14 +++++++-------
 1 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/common-v4.5/src/mapped_ptr_vector.C b/common-v4.5/src/mapped_ptr_vector.C
index d7c61f3..e20a236 100644
--- a/common-v4.5/src/mapped_ptr_vector.C
+++ b/common-v4.5/src/mapped_ptr_vector.C
@@ -263,12 +263,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(T* inP,
     _vector.push_back(inP);
 
     typename tIndex::value_type valuePair(inP->GetName(),
-      make_pair(_vector.size() - 1, fileIndex));
+      std::make_pair(_vector.size() - 1, fileIndex));
 
     _index.insert(valuePair);
 
     _currentName = inP->GetName();
-    _currentIndices = make_pair(_vector.size() - 1, fileIndex);
+    _currentIndices = std::make_pair(_vector.size() - 1, fileIndex);
 
 }
 
@@ -281,12 +281,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(const string& name,
     _vector.push_back(NULL);
 
     typename tIndex::value_type valuePair(name,
-      make_pair(_vector.size() - 1, fileIndex));
+      std::make_pair(_vector.size() - 1, fileIndex));
 
     _index.insert(valuePair);
 
     _currentName = name;
-    _currentIndices = make_pair(_vector.size() - 1, fileIndex);
+    _currentIndices = std::make_pair(_vector.size() - 1, fileIndex);
 }
 
 
@@ -454,7 +454,7 @@ void mapped_ptr_vector<T, StringCompareT>::erase(const string& name)
     if (is_equal(_currentName, name, keyComp))
     {
         _currentName.clear();
-        _currentIndices = make_pair(_vector.size(), (unsigned int)0);
+        _currentIndices = std::make_pair(_vector.size(), (unsigned int)0);
     }
 
 }
@@ -539,7 +539,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic
     if (_vector.empty())
     {
         // Empty container. Return invalid index.
-        return(make_pair(_vector.size(), (unsigned int)0));
+        return(std::make_pair(_vector.size(), (unsigned int)0));
     }
 
     typename tIndex::key_compare keyComp = _index.key_comp();
@@ -563,7 +563,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic
         else
         {
             // Not found. Return invalid index.
-            return(make_pair(_vector.size(), (unsigned int)0));
+            return(std::make_pair(_vector.size(), (unsigned int)0));
         } 
     }
     





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Updated Jun 26, 2012

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