11 files changed, 73 insertions, 215 deletions

diff --git a/biology/nab/files/Makefile b/biology/nab/files/Makefile
deleted file mode 100644
index 79f216e09eb8..000000000000
--- a/biology/nab/files/Makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-# $FreeBSD$
-#SUBDIR=cccp cifparse src
-SUBDIR=src tleap doc
-MAN1=nab.1
-
-.include <bsd.subdir.mk>
diff --git a/biology/nab/files/Makefile.doc b/biology/nab/files/Makefile.doc
deleted file mode 100644
index 279a1dcd4d88..000000000000
--- a/biology/nab/files/Makefile.doc
+++ /dev/null
@@ -1,5 +0,0 @@
-all:
-
-install:
-	gzip -nfc -9 nab.1 > nab.1.gz
-	${INSTALL_MAN} ${WRKSRC}/doc/nab.1.gz   ${PREFIX}/man/man1
diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h
index d79236788f96..8166c22b49ce 100644
--- a/biology/nab/files/config.h
+++ b/biology/nab/files/config.h
@@ -1,7 +1,8 @@
 ###############################################################################
 # Configuration section:  look at sections (1) to (4) below, making
-#      changes that seem necessary.  For most UNIX systems, no changes
-#      should be necessary.
+#      changes that seem necessary.  For many UNIX systems, no changes
+#      should be necessary, but check especially the compiler options in
+#      section (4).
 #
 ###############################################################################
 #
@@ -9,7 +10,7 @@
 #    make command line (e.g. "make ARCH=sun4 NABHOME=/thr/eigen/nab5")
 #    or as environment variables.
 #
-#    NABHOME should be an absolute path to the directory above this one.
+#    NABHOME should be an absolute path to this directory.
 #    ARCH is used to distinguish compilations for various architectures.
 #
 #    Files created by "make install" end up in:
@@ -20,12 +21,8 @@
 #       You can choose ARCH as you wish, but it would generally 
 #       be related to the output of the "uname" command.
 #
-#BINDIR=$(NABHOME)/bin/$(ARCH)
-#LIBDIR=$(NABHOME)/lib/$(ARCH)
-#NABHOME=/usr/local/share/nab
-#ARCH=
-BINDIR=$(NABHOME)/bin
-LIBDIR=$(NABHOME)/lib
+BINDIR=$(NABHOME)/bin/$(ARCH)
+LIBDIR=$(NABHOME)/lib/$(ARCH)
 INCDIR=$(NABHOME)/include
 #
 ###############################################################################
@@ -37,9 +34,8 @@ INCDIR=$(NABHOME)/include
 #      included in FLIBS are always searched.)
 #
 #FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a
-#FLIBS=../cifparse/cifparse.a
 #
-#  following for Sun4, Solaris 2.x
+#  following for linking in fortran subroutines on Sun4, Solaris 2.x
 #
 #FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a -lF77 -lM77 -lsunmath
 #
@@ -69,32 +65,40 @@ SHELL=		/bin/sh
 #
 #  Set the C compiler, etc. 
 #
-#               (For GNU:  cc-->gcc; lex-->flex; yacc-->bison -y -t;
-#                Note: If you lexer is "really" flex, you need to set
-#                LEX=flex below.  For example, on many linux distributions,
-#                /usr/bin/lex is really just a pointer to /usr/bin/flex,
-#                so LEX=flex is necessary.  In general, gcc seems to need
-#                flex.)
+#          For GNU:  cc-->gcc; lex-->flex; yacc-->bison -y -t;
+#          Note: If you lexer is "really" flex, you need to set
+#          LEX=flex below.  For example, on many linux distributions,
+#          /usr/bin/lex is really just a pointer to /usr/bin/flex,
+#          so LEX=flex is necessary.  In general, gcc seems to need
+#          flex.
 #
+#          For 64-bit IRIX, add "-n32" unless 64-bit objects are 
+#          needed; it is also useful to add "-Wl,-dont_warn_unused"
+#          to keep the loader from complaining about libraries that
+#          are not used.
+#
+#          For RedHat Linux 5.1 (and other linuxes?) add -DHAVE_STRERROR
+#
+#	   For FreeBSD 4.2-STABLE, there seems to be a dependency
+#	   on bison.  Berkeley yacc was very problematic.
 CC=		cc
 LEX=    	flex
-YACC=   	yacc
+YACC=   	bison -y -t
 AR=		ar
 #
-#  Set the C-preprocessor.  Code for the preprocessor from gcc is in
-#    ../cccp;  it gets installed as $(NABHOME)/bin/$(ARCH)/cpp;
+#  Set the C-preprocessor.  Code for a small preprocessor is in
+#    uccp-0.7;  it gets installed as $(NABHOME)/bin/$(ARCH)/ucpp;
 #    this should generally *not* be changed.
 #
-#CPP=    $(NABHOME)/bin/$(ARCH)/cpp -lang-c++
-#CPP=    ../cccp/cpp -lang-c++
-CPP=    cc -E -x c++
+#  Again, for FreeBSD 4.2-STABLE, I had problems using the system
+#    C-preprocessor.
+#
+CPP=    ucpp -l
 #
 #  Use these CFLAGS if AVS = 0
-#  Notes: for 64-bit IRIX, add "-n32" to both CFLAGS and OCFLAGS
-#         for RedHat Linux 5.1 (and other linuxes?) add -DHAVE_STRERROR
 #
+CFLAGS= 
 OCFLAGS= -O
-CFLAGS= -DHAVE_STRERROR ${OCFLAGS}
 NABFLAGS=
 #
 #  Use these CFLAGS if AVS = 1
@@ -103,7 +107,7 @@ NABFLAGS=
 #OCFLAGS= 	-O -DAVS=$(AVS) -DAVSDIR='"$(AVSDIR)"' -I$(AVSINCDIR)
 #
 #
-#  For Win95, set SFX to ".exe"; for Unix,NT leave it empty:
+#  For Win95/98, set SFX to ".exe"; for Unix,NT leave it empty:
 #
 #SFX=.exe
 SFX=
diff --git a/biology/nab/files/patch-aa b/biology/nab/files/patch-aa
index c8e736e87ab8..a04b27361f18 100644
--- a/biology/nab/files/patch-aa
+++ b/biology/nab/files/patch-aa
@@ -1,25 +1,32 @@
-*** src/Makefile.orig	Fri Jan  8 16:06:59 1999
---- src/Makefile	Thu Jan 14 16:15:53 1999
+*** Makefile.orig	Mon Oct 23 20:01:09 2000
+--- Makefile	Sun Jan 28 13:36:22 2001
 ***************
-*** 7,15 ****
-  	./nab  -c $(NABFLAGS) $<
-  	@rm -f $*.c
+*** 1,5 ****
+--- 1,6 ----
+  #   top-level Makefile for the NAB suite of programs
   
-- .c.o: $<
-- 	$(CC) -c $(CFLAGS) $<
-- 
-  NAB2COBJS=	\
-  	nab2c.o	\
-  	cgen.o	\
---- 7,12 ----
++ all: compiler test
+  compiler:
+  	-mkdir bin lib include
+  	(cd ucpp-0.7; make install )
 ***************
-*** 77,82 ****
---- 74,81 ----
-  	yammp.o
+*** 7,15 ****
+  	(cd src; make install )
+  	(cd nss; make install )
+  	(cd tleap; make install )
+! 	@echo
+! 	@echo "completed installation of NAB version 4"
+! 	@echo
   
-  #===========================================================================
-+ 
-+ all: system
+  #   note:  "make test" needs to follow "make", since it is very hard to
+  #          tell if the compiler is completely "made" or not.
+--- 8,16 ----
+  	(cd src; make install )
+  	(cd nss; make install )
+  	(cd tleap; make install )
+! #	@echo
+! #	@echo "completed installation of NAB version 4"
+! #	@echo
   
-  system:	nab	\
-  	nab2c	\
+  #   note:  "make test" needs to follow "make", since it is very hard to
+  #          tell if the compiler is completely "made" or not.
diff --git a/biology/nab/files/patch-ac b/biology/nab/files/patch-ac
index 1487c52d9336..e3c6e85535de 100644
--- a/biology/nab/files/patch-ac
+++ b/biology/nab/files/patch-ac
@@ -1,13 +1,18 @@
-*** cccp/Makefile.orig	Thu Jan 14 16:20:38 1999
---- cccp/Makefile	Thu Jan 14 16:21:08 1999
+*** src/Makefile.orig	Mon Nov 13 13:37:07 2000
+--- src/Makefile	Mon Jan 29 12:33:37 2001
 ***************
-*** 4,9 ****
---- 4,11 ----
-  ######### no configuration should be needed beyond this line #################
-  ##############################################################################
+*** 175,180 ****
+--- 175,187 ----
+  	cp defreal.h $(INCDIR)
+  	cp nab.h $(INCDIR)
   
-+ all: cpp$(SFX)
++ beforerealinstall: 
++ 	$(CC) -DBINDIR='"$(PREFIX)/bin"' \
++ 		-DINCDIR='"$(PREFIX)/include"' \
++ 		-DLIBDIR='"$(PREFIX)/lib"' \
++ 		$(CFLAGS) -DCC='"$(CC)"' -DCPP='"$(CPP)"' -DFLIBS='"$(FLIBS)"' \
++ 		-o ../bin/nab nab.c
 + 
-  cpp$(SFX): cppmain.o cpplib.o cpphash.o cppalloc.o cpperror.o cppexp.o version.o \
-  		obstack.o alloca.o
-  	$(CC) $(CFLAGS) -o cpp$(SFX) cppmain.o cpplib.o cpphash.o \
+  uninstall: clean
+  	-rm -f \
+          $(BINDIR)/nab2c$(SFX) $(BINDIR)/nab$(SFX) $(INCDIR)/nabcode.h \
diff --git a/biology/nab/files/patch-ad b/biology/nab/files/patch-ad
deleted file mode 100644
index f498e568a3cf..000000000000
--- a/biology/nab/files/patch-ad
+++ /dev/null
@@ -1,13 +0,0 @@
-*** cifparse/Makefile.orig	Thu Jan 14 16:21:50 1999
---- cifparse/Makefile	Thu Jan 14 16:22:08 1999
-***************
-*** 11,16 ****
---- 11,18 ----
-  	cifp.tab.o \
-  	cifparse.o
-  
-+ all: cifparse.a
-+ 
-  cifparse.a: $(CIFOBS)
-  	-rm cifparse.a
-  	$(AR) rv cifparse.a $(CIFOBS)
diff --git a/biology/nab/files/patch-ae b/biology/nab/files/patch-ae
deleted file mode 100644
index b901073e9ebb..000000000000
--- a/biology/nab/files/patch-ae
+++ /dev/null
@@ -1,19 +0,0 @@
-*** examples/program_7.nab.orig	Thu Jan 14 16:53:07 1999
---- examples/program_7.nab	Thu Jan 14 16:53:24 1999
-***************
-*** 9,15 ****
-  cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" );
-  
-  m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb",
-!          "dna", 2.25, -4.96, 36.0, 4.38, "" );
-  
-  b = newbounds(m, "");
-  allocate xyz[ 4*m.natoms ];
---- 9,15 ----
-  cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" );
-  
-  m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb",
-!          "dna", 2.25, -4.96, 36.0, 3.38, "" );
-  
-  b = newbounds(m, "");
-  allocate xyz[ 4*m.natoms ];
diff --git a/biology/nab/files/patch-af b/biology/nab/files/patch-af
deleted file mode 100644
index bf908f8b23a6..000000000000
--- a/biology/nab/files/patch-af
+++ /dev/null
@@ -1,23 +0,0 @@
-*** src/reslib.c.orig	Tue Apr 21 14:10:50 1998
---- src/reslib.c	Mon Feb  1 09:50:35 1999
-***************
-*** 610,618 ****
-  		fclose( cfp );
-  	}
-  
-! 	fclose( pfp );
-  
-! 	fclose( bfp );
-  
-  	return( rlp );
-  }
---- 610,618 ----
-  		fclose( cfp );
-  	}
-  
-! 	if( pfp ) {fclose( pfp );}
-  
-! 	if( bfp ) {fclose( bfp );}
-  
-  	return( rlp );
-  }
diff --git a/biology/nab/files/patch-ag b/biology/nab/files/patch-ag
deleted file mode 100644
index d902077dd59d..000000000000
--- a/biology/nab/files/patch-ag
+++ /dev/null
@@ -1,32 +0,0 @@
-*** src/database.c.orig	Tue Apr 21 12:17:17 1998
---- src/database.c	Tue Mar  9 09:09:06 1999
-***************
-*** 73,78 ****
---- 73,85 ----
-  
-  #include        "database.h"
-  
-+ #if (defined(__unix__) || defined(unix)) && !defined(USG)
-+ #include <sys/param.h>
-+ #endif
-+ 
-+ #if defined(BSD)
-+ #include <math.h>
-+ #endif
-  
-  #ifndef	TRUE
-  #define	TRUE	1
-***************
-*** 985,991 ****
---- 992,1002 ----
-  
-      sDBRemoveLeadingSpaces( sLine );
-      sDBRemoveFirstString( sLine, sHead );
-+ #if defined(linux) || defined(BSD)
-+     sscanf( sHead, "%lg", dPDbl );
-+ #else
-      sscanf( sHead, "%lG", dPDbl );
-+ #endif
-  
-  }
-  
diff --git a/biology/nab/files/patch-ah b/biology/nab/files/patch-ah
deleted file mode 100644
index 71f8da6baac6..000000000000
--- a/biology/nab/files/patch-ah
+++ /dev/null
@@ -1,19 +0,0 @@
-*** semantics/Makefile.orig	Fri Mar 10 20:08:16 2000
---- semantics/Makefile	Sun Sep 10 18:47:44 2000
-***************
-*** 43,49 ****
-  SYM_UPARROW_ASSIGN.rules
-  
-  checkexpr.c: $(RULES) attribute.tab parse ../src/nab.h ../src/nabgrm.y
-! 	./parse *.rules
-  
-  parse: parse.c
-  	$(CC) -o parse parse.c
---- 43,49 ----
-  SYM_UPARROW_ASSIGN.rules
-  
-  checkexpr.c: $(RULES) attribute.tab parse ../src/nab.h ../src/nabgrm.y
-! 	env NABHOME=.. ./parse *.rules
-  
-  parse: parse.c
-  	$(CC) -o parse parse.c
diff --git a/biology/nab/files/patch-ai b/biology/nab/files/patch-ai
deleted file mode 100644
index 76cf860b0ce6..000000000000
--- a/biology/nab/files/patch-ai
+++ /dev/null
@@ -1,41 +0,0 @@
-*** tleap/Makefile.orig	Tue Jun 20 13:41:55 2000
---- tleap/Makefile	Sun Sep 10 19:38:24 2000
-***************
-*** 5,13 ****
-  .SUFFIXES:
-  .SUFFIXES:  .c .o
-  
-- .c.o: $<
-- 	$(CC) -c $(CFLAGS) -DSYSV $<
-- 
-  #
-  #  Absolutely necessary routines
-  #
---- 5,10 ----
-***************
-*** 76,81 ****
---- 73,79 ----
-  OUL2P= utilLib2Pdb.o
-  
-  TLEAP_OBJ= $(OA) $(OG) $(OO) $(OL) $(OC)
-+ all: teLeap$(SFX)
-  teLeap$(SFX): $(TLEAP_OBJ)
-  	$(CC) -o $@ $(TLEAP_OBJ) -lm
-  
-***************
-*** 409,415 ****
-  zMatrix.o: zMatrix.h
-  
-  install:  teLeap$(SFX)
-! 	mv teLeap$(SFX) $(BINDIR)
-  
-  uninstall: clean
-  	-rm $(BINDIR)/teLeap$(SFX)
---- 407,413 ----
-  zMatrix.o: zMatrix.h
-  
-  install:  teLeap$(SFX)
-! 	mv teLeap$(SFX) $(PREFIX)/bin
-  
-  uninstall: clean
-  	-rm $(BINDIR)/teLeap$(SFX)