diff options
Diffstat (limited to 'sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch')
| -rw-r--r-- | sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch | 216 |
1 files changed, 216 insertions, 0 deletions
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 new file mode 100644 index 000000000000..e383615cde48 --- /dev/null +++ b/sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch @@ -0,0 +1,216 @@ +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 |