1 files changed, 0 insertions, 207 deletions
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch
deleted file mode 100644
index 7383811b5bfd..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch
+++ /dev/null
@@ -1,207 +0,0 @@
- 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