Drop "CCP4: Software for Macromolecular Crystallography"

obsoletes:
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=160190
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=324059
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=332485
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367771
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367773
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=383227
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=448756
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460502
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460504
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=466936
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467040
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467048
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=476580
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478580
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478586
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478588
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478594
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478604
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521646
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=528512
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=530878
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=540760
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=555614
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=556498
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=557038
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=561196
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=562780

Signed-off-by: Justin Lecher <jlec@gentoo.org>

6 files changed, 0 insertions, 547 deletions

diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch
deleted file mode 100644
index 3a6f5498ffba..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch
+++ /dev/null
@@ -1,46 +0,0 @@
---- Makefile	2008-12-05 14:36:44.000000000 +0100
-+++ Makefile.new	2008-12-05 14:37:21.000000000 +0100
-@@ -19,13 +19,7 @@
- CHECKOUT_SCRIPT_MODULE = util
- CHECKOUT_SCRIPT = checkout.sh
- 
--LIBDIRS =  cifobj-common-v4.1 \
--           tables-v8.0 \
--           regex-v2.2 \
--           cif-file-v1.0 \
--           misclib-v2.2 \
--           cifparse-obj-v7.0 \
--           $(EXTRACT)
-+LIBDIRS =  $(EXTRACT)
- 
- all:	compile
- 
---- pdb-extract-v3.0/Makefile	2008-12-05 14:42:58.000000000 +0100
-+++ pdb-extract-v3.0/Makefile.new	2008-12-05 14:42:15.510315392 +0100
-@@ -6,6 +6,7 @@
- 
- M_INCL_DIR = ../include
- M_LIB_DIR  = ../lib
-+M_LIB_DIR_GENTOO = @GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
- M_BIN_DIR  = ../bin
- 
- PROJ_DIR   = .
-@@ -37,12 +38,12 @@
- include ../etc/Makefile.platform
- 
- # Dependent libraries for the pdbml-parser
--CIF_FILE_LIB      = $(M_LIB_DIR)/cif-file.a
--CIFPARSE_LIB      = $(M_LIB_DIR)/cifparse-obj.a
--CIF_TABLE_LIB     = $(M_LIB_DIR)/cif-table-obj.a
--CIFOBJ_COMMON_LIB = $(M_LIB_DIR)/cifobj-common.a
--REGEX_LIB         = $(M_LIB_DIR)/regex.a
--MISCLIB_LIB       = $(M_LIB_DIR)/misclib.a
-+CIF_FILE_LIB      = $(M_LIB_DIR_GENTOO)/cif-file.a
-+CIFPARSE_LIB      = $(M_LIB_DIR_GENTOO)/cifparse-obj.a
-+CIF_TABLE_LIB     = $(M_LIB_DIR_GENTOO)/tables.a
-+CIFOBJ_COMMON_LIB = $(M_LIB_DIR_GENTOO)/common.a
-+REGEX_LIB         = $(M_LIB_DIR_GENTOO)/regex.a
-+MISCLIB_LIB       = $(M_LIB_DIR_GENTOO)/misclib.a
- 
- ALL_DEP_LIBS = $(CIF_FILE_LIB) $(CIFPARSE_LIB) \
-   $(CIF_TABLE_LIB) $(CIFOBJ_COMMON_LIB) $(REGEX_LIB) $(MISCLIB_LIB)
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
deleted file mode 100644
index cdf48e4784c6..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
+++ /dev/null
@@ -1,199 +0,0 @@
-diff -Naur pdb-extract-v3.004-prod-src/Makefile pdb-extract-v3.004-prod-src.new/Makefile
---- pdb-extract-v3.004-prod-src/Makefile	2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/Makefile	2009-12-03 21:34:10.000000000 -0500
-@@ -52,7 +52,7 @@
- 		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 -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3
---- pdb-extract-v3.004-prod-src/etc/make.platform.darwin3	2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3	2009-12-03 21:34:10.000000000 -0500
-@@ -91,7 +91,7 @@
- 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 @@
- STATIC_LINKING=
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
- 
- # Fortran linker
- F77_LINKER=f77
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4
---- pdb-extract-v3.004-prod-src/etc/make.platform.darwin4	2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4	2009-12-03 21:34:10.000000000 -0500
-@@ -92,7 +92,7 @@
- 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 @@
- STATIC_LINKING=
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
- 
- # Fortran linker
- F77_LINKER=f77
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3
---- pdb-extract-v3.004-prod-src/etc/make.platform.gnu3	2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3	2009-12-03 21:34:10.000000000 -0500
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
- 
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
-+
- #-----Lexer and Parser section-------------------------------------------#
- 
- # Lexer executable
-@@ -89,7 +91,7 @@
- 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 @@
- 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 @@
- 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 @@
- F77=f77
- 
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
- 
- # Additional Fortran libraries
- F77LIBS=
-@@ -154,11 +156,11 @@
- #-----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 -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4
---- pdb-extract-v3.004-prod-src/etc/make.platform.gnu4	2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4	2009-12-03 21:34:10.000000000 -0500
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
- 
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
-+
- #-----Lexer and Parser section-------------------------------------------#
- 
- # Lexer executable
-@@ -34,7 +36,7 @@
- 
- # 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 @@
- 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 @@
- 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
-@@ -129,9 +131,9 @@
- 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
-@@ -145,7 +147,7 @@
- F77=f77
- 
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
- 
- # Additional Fortran libraries
- F77LIBS=
-@@ -155,11 +157,11 @@
- #-----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/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch
deleted file mode 100644
index 6506713742b6..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- pdb-extract-v3.0/src/extract.C	2007-09-11 17:19:48.000000000 +0200
-+++ pdb-extract-v3.0/src/extract.C.new	2008-12-05 17:49:59.000000000 +0100
-@@ -1689,7 +1689,7 @@
-         open_file_error(inpfile, "get_mmcif");
-     }
-     
--    (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT");
-+    (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT_ROOT");
-     if(temp != NULL) {
-         strcpy(pdb_extract, "");
-         strcpy(pdb_extract_sf, "");
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch
deleted file mode 100644
index 6907399c27df..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- cifobj-common-v4.1/src/GenString.C	2008-11-13 10:44:01.000000000 +0100
-+++ cifobj-common-v4.1/src/GenString.C.new	2008-11-13 10:43:54.000000000 +0100
-@@ -144,6 +144,7 @@
- #include <string>
- #include <algorithm>
- #include <sstream>
-+#include <string.h>
- 
- #include "GenString.h"
- 
---- tables-v8.0/src/ISTable.C	2007-09-11 17:19:47.000000000 +0200
-+++ tables-v8.0/src/ISTable.C.new	2008-11-13 10:48:18.000000000 +0100
-@@ -150,6 +150,7 @@
- #include <sstream>
- #include <iostream>
- #include <iomanip>
-+#include <limits.h>
- 
- #include "Exceptions.h"
- #include "GenString.h"
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
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch
deleted file mode 100644
index 5284bd745d53..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch
+++ /dev/null
@@ -1,64 +0,0 @@
- 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));
-         } 
-     }
-