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authorJustin Lecher <jlec@gentoo.org>2015-10-26 08:29:56 +0100
committerJustin Lecher <jlec@gentoo.org>2015-10-26 08:32:25 +0100
commit7d62034735e700ca67e977470d79f5571b15b221 (patch)
tree78d45bafd1284caf0c06b4b98131677301303cbb /sci-chemistry/pdb-extract
parentadd co-maintainer Coacher to metadata (diff)
downloadgentoo-7d62034735e700ca67e977470d79f5571b15b221.tar.gz
gentoo-7d62034735e700ca67e977470d79f5571b15b221.tar.bz2
gentoo-7d62034735e700ca67e977470d79f5571b15b221.zip
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>
Diffstat (limited to 'sci-chemistry/pdb-extract')
-rw-r--r--sci-chemistry/pdb-extract/Manifest2
-rw-r--r--sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch46
-rw-r--r--sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch199
-rw-r--r--sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch11
-rw-r--r--sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch20
-rw-r--r--sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch207
-rw-r--r--sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch64
-rw-r--r--sci-chemistry/pdb-extract/metadata.xml5
-rw-r--r--sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild71
-rw-r--r--sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild60
10 files changed, 0 insertions, 685 deletions
diff --git a/sci-chemistry/pdb-extract/Manifest b/sci-chemistry/pdb-extract/Manifest
deleted file mode 100644
index 9036c79e3e7c..000000000000
--- a/sci-chemistry/pdb-extract/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pdb-extract-v3.004-prod-src.tar.gz 942450 SHA256 58bef2aba4869cdd16a79ddc588da5596a2ccd1f5c925f300b63b6d8299bb953 SHA512 4505fd615324982e741a3656d8a36ffc2cd6524c825d254e0a1ff44b3464aaf63cbdbe4f614a6ace6c0e56af8f452634152edadd0ed5305f0148856affa8cb60 WHIRLPOOL b7077431d75a31a9ac4ea41f7cb76874aa49626a19c1290126405a8cdac4d210f56929f9213512ae4f542286be5cbedc972642b9ef07a4e461ac969c6c0d965f
-DIST pdb-extract-v3.11-prod-src.tar.gz 1016140 SHA256 cc56ab58e4b4f0914dcd61834cae673ade5b12688861ea5f0197a33f5939d131 SHA512 06ef4110f873d23bcf878877a8b9f714b895a5b269f8d33312387c0bcb569adb2b1d1577eebc30200d5f0d3648959450912911609dab3749e7d5eb4c84d7e12f WHIRLPOOL ea0e643e1d64f344fdd643348b0ce35143e29f27a64b9153d6645c8dbf914e193f700217c0caecb30ea300ae10f47ea09bed61811c3bb293ef63d9e45acf74d3
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));
- }
- }
-
diff --git a/sci-chemistry/pdb-extract/metadata.xml b/sci-chemistry/pdb-extract/metadata.xml
deleted file mode 100644
index e42d0af60f42..000000000000
--- a/sci-chemistry/pdb-extract/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild
deleted file mode 100644
index 836d76f5c007..000000000000
--- a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-inherit eutils toolchain-funcs multilib prefix
-
-MY_P="${PN}-v${PV}-prod-src"
-
-DESCRIPTION="Tools for extracting mmCIF data from structure determination applications"
-HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html"
-SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
-
-LICENSE="PDB"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="!<app-text/html-xml-utils-5.3"
-DEPEND="${RDEPEND}
- >=sci-libs/cifparse-obj-7.025"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${P}-cflags-install.patch \
- "${FILESDIR}"/${P}-gcc-4.3.patch \
- "${FILESDIR}"/${P}-Makefile.patch \
- "${FILESDIR}"/${P}-env.patch
-
- sed -i "s:GENTOOLIBDIR:$(get_libdir):g" \
- pdb-extract-v3.0/Makefile \
- || die "Failed to fix libdir"
-
- # Get rid of unneeded directories, to make sure we use system files
- ebegin "Deleting redundant directories"
- rm -rf cif-file-v1.0 cifobj-common-v4.1 cifparse-obj-v7.0 \
- misclib-v2.2 regex-v2.2 tables-v8.0
- eend
-
- sed -i \
- -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
- -e "s:^\(CC=\).*:\1$(tc-getCC):g" \
- -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \
- -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
- "${S}"/etc/make.* \
- || die "Failed to fix makefiles"
-
- eprefixify pdb-extract-v3.0/Makefile etc/*
-}
-
-src_install() {
- exeinto /usr/libexec/ccp4/bin
- doexe bin/pdb_extract{,_sf} bin/extract \
- || die "failed to install binaries"
- insinto /usr/include/rcsb
- doins include/* || die "failed to install include files"
- dodoc README* || die "failed to install docs"
- insinto /usr/share/rcsb/
- doins -r pdb-extract-data || die "failed to install data files"
-
- cat >> "${T}"/envd <<- EOF
- PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/"
- PDB_EXTRACT_ROOT="${EPREFIX}/usr/"
- EOF
-
- newenvd "${T}"/envd 20pdb-extract \
- || die "failed to install env files"
-}
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild
deleted file mode 100644
index 04351c8a125a..000000000000
--- a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils toolchain-funcs multilib prefix
-
-MY_P="${PN}-v${PV}-prod-src"
-
-DESCRIPTION="Tools for extracting mmCIF data from structure determination applications"
-HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html"
-SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
-
-LICENSE="PDB"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="!<app-text/html-xml-utils-5.3"
-DEPEND="${RDEPEND}
- >=sci-libs/cifparse-obj-7.025"
-
-S="${WORKDIR}/${MY_P}"
-
-MAKEOPTS+=" -j1"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${P}-cflags-install.patch \
- "${FILESDIR}"/${P}-gcc-4.7.patch \
- "${FILESDIR}"/${PN}-3.004-env.patch
-
- sed -i \
- -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
- -e "s:^\(CC=\).*:\1$(tc-getCC):g" \
- -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \
- -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
- "${S}"/etc/make.* \
- || die "Failed to fix makefiles"
-
- eprefixify pdb-extract-v3.0/Makefile etc/*
-}
-
-src_install() {
- exeinto /usr/libexec/ccp4/bin
- doexe bin/pdb_extract{,_sf} bin/extract
- insinto /usr/include/rcsb
- doins include/*
- dodoc README*
- insinto /usr/share/rcsb/
- doins -r pdb-extract-data
-
- cat >> "${T}"/envd <<- EOF
- PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/"
- PDB_EXTRACT_ROOT="${EPREFIX}/usr/"
- EOF
-
- newenvd "${T}"/envd 20pdb-extract
-}