diff options
Diffstat (limited to 'sci-chemistry/pdb-extract')
| -rw-r--r-- | sci-chemistry/pdb-extract/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-chemistry/pdb-extract/Manifest | 9 | ||||
| -rw-r--r-- | sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch | 216 |
3 files changed, 9 insertions, 222 deletions
diff --git a/sci-chemistry/pdb-extract/ChangeLog b/sci-chemistry/pdb-extract/ChangeLog index 42082a236dc8..8ab5774be2b3 100644 --- a/sci-chemistry/pdb-extract/ChangeLog +++ b/sci-chemistry/pdb-extract/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-chemistry/pdb-extract # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.19 2012/04/24 06:20:06 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.20 2012/04/24 06:55:49 jlec Exp $ + + 24 Apr 2012; Justin Lecher <jlec@gentoo.org> + -files/respect-cflags-and-fix-install.patch: + Drop old patch 24 Apr 2012; Justin Lecher <jlec@gentoo.org> -pdb-extract-1.700.ebuild, -pdb-extract-3.004-r1.ebuild: diff --git a/sci-chemistry/pdb-extract/Manifest b/sci-chemistry/pdb-extract/Manifest index e5ec0c03f375..9d592768c072 100644 --- a/sci-chemistry/pdb-extract/Manifest +++ b/sci-chemistry/pdb-extract/Manifest @@ -5,15 +5,14 @@ AUX pdb-extract-3.004-Makefile.patch 1530 RMD160 ba4b642e37c26643dd682288f16db6f AUX pdb-extract-3.004-cflags-install.patch 7218 RMD160 c596e67b38f4058d69fd0e9626450a57dcef629d SHA1 f6a86b03ed9797d60278ba9466f66d4b255c6789 SHA256 cac3cf50b6fbf21dd03e096a9c02f9b4280e46818307c9452c6b4f4e988ed206 AUX pdb-extract-3.004-env.patch 501 RMD160 6698680915a9e585f7a8c4d266f5c644e3229ce0 SHA1 ccc2371360fb6da39a6370132764ee97952387b1 SHA256 ccba5db2e3e6eb18465c62b795635ea4ecfbd6695f36376bc298132f986dd8ff AUX pdb-extract-3.004-gcc-4.3.patch 573 RMD160 a9d563b1834bf6293568793a1895026f5b5b9d39 SHA1 bc726c4461ead9faae1694eff53603726d53d91a SHA256 e92f42fb84198e8b543edc364565804f61fbb440da03103506bcb6e6848750ed -AUX respect-cflags-and-fix-install.patch 8415 RMD160 b1418278385f197db26a49be4bf1ad2bbed4b4c0 SHA1 93bd785a4683542716309d917335de7a9c3573d4 SHA256 ab44177b9a9e34573331aafeb112efa86154a0c1ee706930aa05c32c0eb1e58b DIST pdb-extract-v3.004-prod-src.tar.gz 942450 RMD160 3d5d46e668a52109678fdf59afbe664dac1643f9 SHA1 7b5d7ce200d33e68fa352cd3658e382bc37e9768 SHA256 58bef2aba4869cdd16a79ddc588da5596a2ccd1f5c925f300b63b6d8299bb953 EBUILD pdb-extract-3.004-r2.ebuild 2102 RMD160 1417b0c56a0d5bf18fb21fb8bc35beebfc6a74cf SHA1 c40ef4f41464cb8bc18355112b9a8514c70763b8 SHA256 da31319913debf0ee0fb6604e8ab4c392a4f9f9c0a8e8a7657f0dfd44017f423 -MISC ChangeLog 3098 RMD160 d602f26d1d0812920c173ce44180ff9314a2940e SHA1 ec3838b16d45d8f8953eda9e1eed4515d5b486ed SHA256 2dc10b4abbac08f53e6e91dd33f607faa21829646c8f4b2214c2ed313d1ef9b2 +MISC ChangeLog 3210 RMD160 c49db44d04bc8131391309f2f7e3fbebcd7aeefb SHA1 a7cb606533d6e06fb16f57ce06116930ff2c4353 SHA256 48358cc3b2090174d912073d70c5a8941808c60e9f6d1046eb56451a74fb0eac MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.19 (GNU/Linux) -iEYEAREKAAYFAk+WRjMACgkQgAnW8HDreRaz7gCgu4PfVUsgD7fZ886ZLgR5rjtN -ERgAnjO/HPp79H1KQW7iXsUtDqmvR3Az -=0Khz +iEYEAREKAAYFAk+WTpAACgkQgAnW8HDreRbAiACdF3uQHLYLv0GrDYWuXSt3Il9Y +m4UAninmn0pbO8jhkYNJRdOU33Qx0q7R +=KQQG -----END PGP SIGNATURE----- diff --git a/sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch b/sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch deleted file mode 100644 index e383615cde48..000000000000 --- a/sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch +++ /dev/null @@ -1,216 +0,0 @@ -diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/connect-v2.2/Makefile pdb-extract-v1.700-prod-src/connect-v2.2/Makefile ---- pdb-extract-v1.700-prod-src.orig/connect-v2.2/Makefile 2005-07-13 06:22:23.000000000 -0700 -+++ pdb-extract-v1.700-prod-src/connect-v2.2/Makefile 2005-12-18 23:34:56.000000000 -0800 -@@ -31,22 +31,22 @@ - #---------------------------------------------------------------------------- - include ../etc/Makefile.platform - --LIBS = $(LIBINSTDIR)/libciffileobj.a \ -- $(LIBINSTDIR)/libtblindex.a \ -- $(LIBINSTDIR)/libcifobj.a \ -- $(LIBINSTDIR)/libistable.a \ -- $(LIBINSTDIR)/libregex.a \ -- $(LIBINSTDIR)/libcifstr.a \ -- $(LIBINSTDIR)/libndbmisc.a -+LIBS = $(LIBDIR)/libciffileobj.a \ -+ $(LIBDIR)/libtblindex.a \ -+ $(LIBDIR)/libcifobj.a \ -+ $(LIBDIR)/libistable.a \ -+ $(LIBDIR)/libregex.a \ -+ $(LIBDIR)/libcifstr.a \ -+ $(LIBDIR)/libndbmisc.a - - LIBSH = $(LIBINSTDIR)/libndbhtml.a \ -- $(LIBINSTDIR)/libciffileobj.a \ -- $(LIBINSTDIR)/libtblindex.a \ -- $(LIBINSTDIR)/libcifobj.a \ -- $(LIBINSTDIR)/libistable.a \ -- $(LIBINSTDIR)/libregex.a \ -- $(LIBINSTDIR)/libcifstr.a \ -- $(LIBINSTDIR)/libndbmisc.a -+ $(LIBDIR)/libciffileobj.a \ -+ $(LIBDIR)/libtblindex.a \ -+ $(LIBDIR)/libcifobj.a \ -+ $(LIBDIR)/libistable.a \ -+ $(LIBDIR)/libregex.a \ -+ $(LIBDIR)/libcifstr.a \ -+ $(LIBDIR)/libndbmisc.a - - #---------------------------------------------------------------------------- - # Target definitions. -@@ -261,10 +261,10 @@ - $(CCC) $(C++FLAGS) -o $@ $(OBJ7) $(OBJS4) $(LIBS) $(LDFLAGS) -lm - - $(TARGET8): $(OBJ8) -- $(CCC) $(C++FLAGS) -o $@ $(OBJ8) $(LIBINSTDIR)/libndbmisc.a $(LDFLAGS) -lm -+ $(CCC) $(C++FLAGS) -o $@ $(OBJ8) $(LIBDIR)/libndbmisc.a $(LDFLAGS) -lm - - $(TARGET9): $(OBJ9) -- $(CCC) $(C++FLAGS) -o $@ $(OBJ9) $(LIBINSTDIR)/libndbmisc.a $(LDFLAGS) -lm -+ $(CCC) $(C++FLAGS) -o $@ $(OBJ9) $(LIBDIR)/libndbmisc.a $(LDFLAGS) -lm - - $(TARGET10): $(LIBSH) $(HFILES) $(NDBLIB) $(OBJ10) $(OBJS6) - $(CCC) $(C++FLAGS) -o $@ $(OBJ10) $(OBJS6) $(NDBLIB) $(LIBSH) $(LDFLAGS) -lm -diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu3 pdb-extract-v1.700-prod-src/etc/make.platform.gnu3 ---- pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu3 2005-07-13 06:22:18.000000000 -0700 -+++ pdb-extract-v1.700-prod-src/etc/make.platform.gnu3 2005-12-18 23:42:06.000000000 -0800 -@@ -6,6 +6,8 @@ - ## - ########################################################################## - -+LIBDIR= /usr/lib -+ - #-----Lexer and Parser section-------------------------------------------# - - # Lexer executable -@@ -89,7 +91,7 @@ - DEFINES=$(GDEFINES) $(LDEFINES) - - ## Global include directories --GINCLUDES= -+GINCLUDES= -I/usr/include/rcsb - - # Collect all include directories from global include directories and - # include directories specified in module makefile -@@ -107,8 +109,8 @@ - C_WARNINGS=$(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= -diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu4 pdb-extract-v1.700-prod-src/etc/make.platform.gnu4 ---- pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu4 2005-07-13 06:22:18.000000000 -0700 -+++ pdb-extract-v1.700-prod-src/etc/make.platform.gnu4 2005-12-18 23:33:50.000000000 -0800 -@@ -6,6 +6,8 @@ - ## - ########################################################################## - -+LIBDIR= /usr/lib -+ - #-----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) $(LDEFINES) - - ## Global include directories --GINCLUDES= -+GINCLUDES= -I/usr/include/rcsb - - # Collect all include directories from global include directories and - # include directories specified in module makefile -@@ -108,8 +110,8 @@ - C_WARNINGS=$(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= -diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/Makefile pdb-extract-v1.700-prod-src/Makefile ---- pdb-extract-v1.700-prod-src.orig/Makefile 2005-07-13 06:22:16.000000000 -0700 -+++ pdb-extract-v1.700-prod-src/Makefile 2005-12-18 23:39:23.000000000 -0800 -@@ -22,10 +22,7 @@ - - DATADIRS = data pdb-extract-data - --LIBDIRS = misclib-v2.1 regex-v2.1 ciflib-common-v3.02 cifobj-common-v4.04 \ -- btree-obj-v3.1 cif-table-obj-v6.1 cifparse-obj-v6.3 \ -- htmllib-v3.1 connect-v2.2 filterlib-v8.2 $(EXTRACT) \ -- validation-v6.2 maxit-v8.2 -+LIBDIRS = htmllib-v3.1 connect-v2.2 filterlib-v8.2 $(EXTRACT) - - all: compile - -@@ -60,7 +57,7 @@ - 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}" install) || exit 1; \ - done - - binary: -diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/pdb-extract-v1.7/Makefile pdb-extract-v1.700-prod-src/pdb-extract-v1.7/Makefile ---- pdb-extract-v1.700-prod-src.orig/pdb-extract-v1.7/Makefile 2005-07-13 06:22:24.000000000 -0700 -+++ pdb-extract-v1.700-prod-src/pdb-extract-v1.7/Makefile 2005-12-18 23:37:16.000000000 -0800 -@@ -27,13 +27,13 @@ - #---------------------------------------------------------------------------- - include ../etc/Makefile.platform - --CIFLIBS = $(LIBINSTDIR)/libciffileobj.a \ -- $(LIBINSTDIR)/libcifobj.a \ -- $(LIBINSTDIR)/libcifstr.a \ -- $(LIBINSTDIR)/libistable.a \ -- $(LIBINSTDIR)/libregex.a \ -- $(LIBINSTDIR)/libtblindex.a \ -- $(LIBINSTDIR)/libndbmisc.a -+CIFLIBS = $(LIBDIR)/libciffileobj.a \ -+ $(LIBDIR)/libcifobj.a \ -+ $(LIBDIR)/libcifstr.a \ -+ $(LIBDIR)/libistable.a \ -+ $(LIBDIR)/libregex.a \ -+ $(LIBDIR)/libtblindex.a \ -+ $(LIBDIR)/libndbmisc.a - - # TARGET1, 2 is only for test - TARGET1 = $(BIN)/FOtest1 |