update biology/nab: 4.4 -> 4.5.1

PR:		52786
Submitted by:	M. L. Dodson <bdodson@scms.utmb.EDU> (maintainer)

8 files changed, 90 insertions, 128 deletions

diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h
index 1d2f9ebab0a8..51a3556506c5 100644
--- a/biology/nab/files/config.h
+++ b/biology/nab/files/config.h
@@ -79,26 +79,26 @@ SHELL=		/bin/sh
 #
 #          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
+#CC=
 LEX=    	flex
-YACC=   	bison -y -t
+YACC=   	yacc
 AR=		ar
 #
 #  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.
+#  Changed 14 Feb 2003 to use the ucpp port (FreeBSD). MLD
 #
-#  Again, for FreeBSD 4.2-STABLE, I had problems using the system
-#    C-preprocessor.
+#  For FreeBSD 4.x, I had problems using the system C-preprocessor. MLD
 #
 CPP=    ucpp -l
 #
 #  Use these CFLAGS if AVS = 0
 #
-CFLAGS= -O -pipe
-OCFLAGS= -O -pipe
+# Pick up initial CFLAGS from /etc/make.conf instead of here
+# This is a Berkeley make- (pmake-)specific construct
+CFLAGS+=
+OCFLAGS= ${CFLAGS}
 NABFLAGS=
 #
 #  Use these CFLAGS if AVS = 1
diff --git a/biology/nab/files/patch-Makefile b/biology/nab/files/patch-Makefile
new file mode 100644
index 000000000000..039c7d0abffb
--- /dev/null
+++ b/biology/nab/files/patch-Makefile
@@ -0,0 +1,40 @@
+--- Makefile.orig	Mon Oct 23 20:33:23 2000
++++ Makefile	Wed Feb 12 16:33:42 2003
+@@ -1,15 +1,15 @@
+ #   top-level Makefile for the NAB suite of programs
+ 
++all: compiler test
+ compiler:
+ 	-mkdir bin lib include
+-	(cd ucpp-0.7; make install )
+ 	(cd cifparse; make install )
+ 	(cd src; make install )
+ 	(cd nss; make install )
+ 	(cd tleap; make install )
+-	@echo
+-	@echo "completed installation of NAB version 4"
+-	@echo
++#	@echo
++#	@echo "completed installation of NAB version 4"
++#	@echo
+ 
+ #   note:  "make test" needs to follow "make", since it is very hard to
+ #          tell if the compiler is completely "made" or not.
+@@ -18,17 +18,14 @@
+ 	(cd nss; make test )
+ 
+ clean:
+-	(cd ucpp-0.7; make clean )
+ 	(cd cifparse; make clean )
+ 	(cd src; make clean )
+ 	(cd nss; make clean )
+ 	(cd tleap; make clean )
+ 	
+ uninstall:
+-	(cd ucpp-0.7; make uninstall )
+ 	(cd cifparse; make uninstall )
+ 	(cd src; make uninstall )
+ 	(cd nss; make uninstall )
+ 	(cd tleap; make uninstall )
+ 	-/bin/rm config.h
+-	
diff --git a/biology/nab/files/patch-aa b/biology/nab/files/patch-aa
deleted file mode 100644
index a04b27361f18..000000000000
--- a/biology/nab/files/patch-aa
+++ /dev/null
@@ -1,32 +0,0 @@
-*** Makefile.orig	Mon Oct 23 20:01:09 2000
---- Makefile	Sun Jan 28 13:36:22 2001
-***************
-*** 1,5 ****
---- 1,6 ----
-  #   top-level Makefile for the NAB suite of programs
-  
-+ all: compiler test
-  compiler:
-  	-mkdir bin lib include
-  	(cd ucpp-0.7; make install )
-***************
-*** 7,15 ****
-  	(cd src; make install )
-  	(cd nss; make install )
-  	(cd tleap; make install )
-! 	@echo
-! 	@echo "completed installation of NAB version 4"
-! 	@echo
-  
-  #   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
-  
-  #   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-nabgrm.y b/biology/nab/files/patch-nabgrm.y
deleted file mode 100644
index 78ff31d21884..000000000000
--- a/biology/nab/files/patch-nabgrm.y
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/nabgrm.y.orig	Tue Oct 29 13:04:56 2002
-+++ src/nabgrm.y	Tue Oct 29 13:40:29 2002
-@@ -244,7 +244,7 @@
- expr_stmt	: expr SYM_SEMICOLON
- 				{ CG_genmain(); CG_genexpr( $1 );
- 				  CG_genop( NULL, SYM_SEMICOLON ); } ;
--if_stmt		: if_hdr stmt ;
-+if_stmt		: if_hdr stmt
- 		| if_hdr stmt SYM_ELSE
- 				{ CG_genrword( SYM_ELSE ); } stmt ;
- for_stmt	: for_hdr stmt ;
diff --git a/biology/nab/files/patch-parser.y b/biology/nab/files/patch-parser.y
deleted file mode 100644
index bdf23a785552..000000000000
--- a/biology/nab/files/patch-parser.y
+++ /dev/null
@@ -1,10 +0,0 @@
---- tleap/parser.y.orig	Tue Oct 29 13:46:35 2002
-+++ tleap/parser.y	Tue Oct 29 13:48:18 2002
-@@ -220,6 +220,7 @@
- 		{
- 			return;
- 		}
-+	;
- 
- line    :       LENDOFCOMMAND
- 	|	instruct
diff --git a/biology/nab/files/patch-src:database.c b/biology/nab/files/patch-src:database.c
index fc36828b3bfd..34b3f2851083 100644
--- a/biology/nab/files/patch-src:database.c
+++ b/biology/nab/files/patch-src:database.c
@@ -1,32 +1,16 @@
-*** src/database.c.orig	Wed Nov 15 19:46:50 2000
---- src/database.c	Sun Jun  2 12:57:50 2002
-***************
-*** 67,72 ****
---- 67,79 ----
-  
-  
-  
-+ #if (defined(__unix__) || defined(unix)) && !defined(USG)
-+ #include <sys/param.h>
-+ #endif
-+ 
-+ #if defined(BSD)
-+ #include <math.h>
-+ #endif
-  
-  
-  #include	"stdio.h"
-***************
-*** 979,985 ****
---- 986,996 ----
-  
-      sDBRemoveLeadingSpaces( sLine );
-      sDBRemoveFirstString( sLine, sHead );
-+ #if defined (linux) || defined(BSD)
-+     sscanf( sHead, "%lg", dPDbl );
-+ #else
-      sscanf( sHead, "%lG", dPDbl );
-+ #endif
-  
-  }
-  
+--- src/database.c.orig	Thu Nov 16 15:37:11 2000
++++ src/database.c	Fri Feb 14 12:15:53 2003
+@@ -64,6 +64,13 @@
+  *              The TOTAL database name MUST NEVER be longer than
+  *              can be contained in the String object.
+  */
++#if (defined(__unix__) || defined(unix)) && !defined(USG)
++#include <sys/param.h>
++#endif
++
++#if defined(BSD)
++#include <math.h>
++#endif
+ 
+ 
+ 
diff --git a/biology/nab/files/patch-tleap:database.c b/biology/nab/files/patch-tleap:database.c
index bdb35b202fa7..c6004d1d9a24 100644
--- a/biology/nab/files/patch-tleap:database.c
+++ b/biology/nab/files/patch-tleap:database.c
@@ -1,35 +1,16 @@
-*** tleap/database.c.orig	Wed Mar 27 15:41:01 2002
---- tleap/database.c	Sun Jun  2 12:59:14 2002
-***************
-*** 97,102 ****
---- 97,109 ----
-  
-  
-  
-+ #if (defined(__unix__) || defined(unix)) && !defined(USG)
-+ #include <sys/param.h>
-+ #endif
-+ 
-+ #if defined(BSD)
-+ #include <math.h>
-+ #endif
-  
-  
-  #include	"basics.h"
-***************
-*** 563,569 ****
-  
-      sRemoveLeadingSpaces( sLine );
-      sRemoveFirstString( sLine, sHead );
-! #ifdef linux
-      sscanf( sHead, "%lg", dPDbl );
-  #else
-      sscanf( sHead, "%lG", dPDbl );
---- 570,576 ----
-  
-      sRemoveLeadingSpaces( sLine );
-      sRemoveFirstString( sLine, sHead );
-! #if defined(linux) || defined(BSD)
-      sscanf( sHead, "%lg", dPDbl );
-  #else
-      sscanf( sHead, "%lG", dPDbl );
+--- tleap/database.c.orig	Sat Nov  9 18:36:58 2002
++++ tleap/database.c	Wed Jan 29 09:56:46 2003
+@@ -185,6 +185,13 @@
+ }
+ 
+ 
++#if (defined(__unix__) || defined(unix)) && !defined(USG)
++#include <sys/param.h>
++#endif
++
++#if defined(BSD)
++#include <math.h>
++#endif
+ 
+ 
+ 
diff --git a/biology/nab/files/patch-unitio.c b/biology/nab/files/patch-unitio.c
new file mode 100644
index 000000000000..8b3048548a01
--- /dev/null
+++ b/biology/nab/files/patch-unitio.c
@@ -0,0 +1,10 @@
+--- tleap/unitio.c.orig	Sat Nov  9 18:37:02 2002
++++ tleap/unitio.c	Fri Feb 14 12:20:38 2003
+@@ -5958,6 +5958,7 @@
+  *TODO: Add CAP information
+  */
+ #define AMBERINDEX(i)   3*(i-1)
++#undef  INTFORMAT
+ #define INTFORMAT       "%6d"
+ #define DBLFORMAT       "%16.8lE"
+ #define LBLFORMAT       "%-4s"