diff options
Diffstat (limited to 'sci-chemistry/pdb-extract')
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 -} |