upgrade to 4.4

PR:		40612
Submitted by:	maintainer

8 files changed, 97 insertions, 16 deletions

diff --git a/biology/nab/Makefile b/biology/nab/Makefile
index 669b522af9c7..d87e52a8103f 100644
--- a/biology/nab/Makefile
+++ b/biology/nab/Makefile
@@ -4,7 +4,7 @@
 # $FreeBSD$
 
 PORTNAME=	nab
-PORTVERSION=	4.3.2
+PORTVERSION=	4.4
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/
 
@@ -31,6 +31,9 @@ pre-patch:
 	@${PERL} -pi -e 's,<malloc.h>,<stdlib.h>,' \
 		${WRKSRC}/cifparse/cifparse.c
 
+post-patch:
+	@rm -f ${WRKSRC}/examples/program_7.nab.orig
+
 pre-install:
 	@cd ${WRKSRC}/src && \
 		${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall
diff --git a/biology/nab/distinfo b/biology/nab/distinfo
index c32c9718676d..00bddf409b0e 100644
--- a/biology/nab/distinfo
+++ b/biology/nab/distinfo
@@ -1 +1 @@
-MD5 (nab-4.3.2.tar.gz) = 35a706bd124a212cc8310ca1327be227
+MD5 (nab-4.4.tar.gz) = c1fe516ab9aebff74fcadd61f874d474
diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h
index 8166c22b49ce..1d2f9ebab0a8 100644
--- a/biology/nab/files/config.h
+++ b/biology/nab/files/config.h
@@ -97,8 +97,8 @@ CPP=    ucpp -l
 #
 #  Use these CFLAGS if AVS = 0
 #
-CFLAGS= 
-OCFLAGS= -O
+CFLAGS= -O -pipe
+OCFLAGS= -O -pipe
 NABFLAGS=
 #
 #  Use these CFLAGS if AVS = 1
diff --git a/biology/nab/files/patch-examples:program_7.nab b/biology/nab/files/patch-examples:program_7.nab
new file mode 100644
index 000000000000..4e6455533df4
--- /dev/null
+++ b/biology/nab/files/patch-examples:program_7.nab
@@ -0,0 +1,19 @@
+*** examples/program_7.nab	Wed Mar 10 18:57:51 1999
+--- examples/program_7.nab	Sun Jun  2 13:40:36 2002
+***************
+*** 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-src:database.c b/biology/nab/files/patch-src:database.c
new file mode 100644
index 000000000000..fc36828b3bfd
--- /dev/null
+++ b/biology/nab/files/patch-src:database.c
@@ -0,0 +1,32 @@
+*** 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
+  
+  }
+  
diff --git a/biology/nab/files/patch-tleap:database.c b/biology/nab/files/patch-tleap:database.c
new file mode 100644
index 000000000000..bdb35b202fa7
--- /dev/null
+++ b/biology/nab/files/patch-tleap:database.c
@@ -0,0 +1,35 @@
+*** 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 );
diff --git a/biology/nab/pkg-descr b/biology/nab/pkg-descr
index 782bbe66c6a0..6b5bb0463a4b 100644
--- a/biology/nab/pkg-descr
+++ b/biology/nab/pkg-descr
@@ -1,4 +1,4 @@
-This is version 4.2 of nab (nucleic acid builder), a computer language that
+This is version 4.4 of nab (nucleic acid builder), a computer language that
 is intended for use in creating, describing and modifying macromolecules,
 especially nucleic acids. Programs written in nab are translated into C,
 which in turn is compiled into machine code.
diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist
index f79f228b8b52..ba96f8b296ca 100644
--- a/biology/nab/pkg-plist
+++ b/biology/nab/pkg-plist
@@ -101,17 +101,6 @@ share/nab/test/write_sander_inp.nab
 share/nab/test/duplex.nab
 share/nab/test/ltest.out.check
 share/nab/test/dg_gyrate.out.check
-share/nab/peptide/COPYING
-share/nab/peptide/aaaa.pdb
-share/nab/peptide/lprot.nab
-share/nab/peptide/write_pdb.nab
-share/nab/peptide/README
-share/nab/peptide/Makefile
-share/nab/peptide/conf.lib
-share/nab/peptide/peptide.nab
-share/nab/peptide/match_template.nab
-share/nab/peptide/peptide.c
-share/nab/peptide/fix_angles.nab
 share/nab/suppose/suppose.1
 share/nab/suppose/suppose.nab
 share/nab/dgdb/adna.basepair.db
@@ -131,6 +120,8 @@ share/nab/dgdb/trna.stack.db
 share/nab/dgdb/zdna.basepair.db
 share/nab/dgdb/zdna.nucleotide.db
 share/nab/dgdb/zdna.stack.db
+share/nab/peptide/peptide.nab
+share/nab/peptide/README
 share/nab/reslib/leap.log
 share/nab/reslib/hetatm.amber94/hetatm.amber94.chi
 share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd
@@ -301,6 +292,7 @@ share/nab/fd_data/sbdna.dat
 share/nab/fd_data/abdna.dat
 share/nab/fd_data/aprna.dat
 share/nab/fd_data/lbdna.dat
+share/nab/fd_data/abdna.dat.old
 share/nab/coords
 share/nab/lib/cifparse.a
 share/nab/lib/libnab.a