Update to 4.6

PR:		ports/68561
Submitted by:	maintainer

7 files changed, 58 insertions, 51 deletions

diff --git a/biology/nab/Makefile b/biology/nab/Makefile
index 45bfd381f1b2..95a223dc4cbb 100644
--- a/biology/nab/Makefile
+++ b/biology/nab/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	nab
-PORTVERSION=	4.5.3
+PORTVERSION=	4.6
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/ \
 		http://www.scripps.edu/case/ \
@@ -60,7 +60,6 @@ post-patch:
 pre-install:
 	@cd ${WRKSRC}/src && \
 		${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall
-	@${CP} ${WRKSRC}/config.h ${WRKSRC}/include/
 
 do-install:
 	@-${MKDIR} ${PREFIX}/share/nab
@@ -79,8 +78,12 @@ do-install:
 		${CHMOD} -R ugo+rX-w nab)
 	@-(cd ${PREFIX}/share/nab && ${LN} -sf ../NDB coords)
 	${INSTALL_PROGRAM} ${WRKSRC}/bin/*     ${PREFIX}/bin
-	${INSTALL_DATA}    ${WRKSRC}/include/* ${PREFIX}/share/nab/include
-	${INSTALL_DATA} ${WRKSRC}/lib/*     ${PREFIX}/lib
+.for f in ${INCS}
+	${INSTALL_DATA}    ${WRKSRC}/include/${f} ${PREFIX}/include
+	@-(cd ${PREFIX}/share/nab/include && ${LN} -sf ${PREFIX}/include/${f} .)
+.endfor
+	${INSTALL_DATA} ${WRKSRC}/config.h ${PREFIX}/share/nab/include
+	${INSTALL_DATA} ${WRKSRC}/lib/* ${PREFIX}/lib
 	@-cd ${WRKSRC}/doc && ${GZIP_CMD} ${MAN1}
 	${INSTALL_MAN} ${WRKSRC}/doc/nab.1.gz ${PREFIX}/man/man1
 .for f in ${BINARIES}
diff --git a/biology/nab/distinfo b/biology/nab/distinfo
index 6f5ed092a61a..be2704233758 100644
--- a/biology/nab/distinfo
+++ b/biology/nab/distinfo
@@ -1,2 +1,2 @@
-MD5 (nab-4.5.3.tar.gz) = 844cc6e4dad076edb4773bd06e1fe126
-SIZE (nab-4.5.3.tar.gz) = 4045456
+MD5 (nab-4.6.tar.gz) = ec1e51b8a9f6d5a46770b952f0e59d26
+SIZE (nab-4.6.tar.gz) = 3794078
diff --git a/biology/nab/files/patch-Makefile b/biology/nab/files/patch-Makefile
index 9c258367476c..493b85bcda86 100644
--- a/biology/nab/files/patch-Makefile
+++ b/biology/nab/files/patch-Makefile
@@ -1,12 +1,13 @@
---- Makefile.orig	Tue Jul 15 21:11:15 2003
-+++ Makefile	Sat Aug  9 13:50:34 2003
-@@ -1,15 +1,15 @@
+--- Makefile.orig	Tue May 18 15:46:55 2004
++++ Makefile	Thu Jul  1 09:03:32 2004
+@@ -1,16 +1,15 @@
  #   top-level Makefile for the NAB suite of programs
  
-+all: compiler test
++all:	compiler test
  compiler:
  	-mkdir bin lib include
 -	(cd ucpp-1.3; make install )
+-	(cd byacc; make install )
  	(cd cifparse; make install )
  	(cd src; make install )
  	(cd nss; make install )
@@ -20,18 +21,24 @@
  
  #   note:  "make test" needs to follow "make", since it is very hard to
  #          tell if the compiler is completely "made" or not.
-@@ -18,14 +18,12 @@
+@@ -19,18 +18,15 @@
  	(cd nss; make test )
  
  clean:
 -	(cd ucpp-1.3; make clean )
+-	(cd byacc; make clean )
  	(cd cifparse; make clean )
  	(cd src; make clean )
  	(cd nss; make clean )
  	(cd tleap; make clean )
- 	
+-	
++
  uninstall:
 -	(cd ucpp-1.3; 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-atom.c b/biology/nab/files/patch-atom.c
deleted file mode 100644
index 61958e20d134..000000000000
--- a/biology/nab/files/patch-atom.c
+++ /dev/null
@@ -1,10 +0,0 @@
---- tleap/atom.c.orig	Sat Apr 20 22:35:09 2002
-+++ tleap/atom.c	Sat Mar  6 08:02:25 2004
-@@ -908,6 +908,7 @@
-     for ( i=0; i<iBonds; i++ ) {
- 	aBond = aaBond[i];
- 	VP1(( "Breaking bond: %s - %s\n",
-+	        sAtom1,
- 		sContainerFullDescriptor( (CONTAINER)aBond, sAtom2 ) ));
- 	AtomRemoveBond( aAtom, aBond );
-     }
diff --git a/biology/nab/files/patch-src:database.c b/biology/nab/files/patch-src:database.c
index 34b3f2851083..14e70c31326a 100644
--- a/biology/nab/files/patch-src:database.c
+++ b/biology/nab/files/patch-src:database.c
@@ -14,3 +14,12 @@
  
  
  
+@@ -71,7 +78,7 @@
+ 
+ #include	<stdio.h>
+ #include	<string.h>
+-#include	<malloc.h>
++#include	<stdlib.h>
+ 
+ #include        "database.h"
+ 
diff --git a/biology/nab/files/patch-src:molio.c b/biology/nab/files/patch-src:molio.c
new file mode 100644
index 000000000000..656042bb2f24
--- /dev/null
+++ b/biology/nab/files/patch-src:molio.c
@@ -0,0 +1,10 @@
+--- src/molio.c.orig	Mon May 10 16:53:34 2004
++++ src/molio.c	Fri Jun 18 23:26:01 2004
+@@ -1,7 +1,6 @@
+ #include	<stdio.h>
+ #include	<ctype.h>
+ #include	<string.h>
+-#include	<malloc.h>
+ #include	<math.h>
+ #include	<stdlib.h>
+ #include	<assert.h>
diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist
index f887aca3aab6..191041c7cab2 100644
--- a/biology/nab/pkg-plist
+++ b/biology/nab/pkg-plist
@@ -9,6 +9,10 @@ bin/transform
 bin/tss_init
 bin/tss_main
 bin/tss_next
+include/defreal.h
+include/nab.h
+include/nabcode.h
+include/nabtypes.h
 lib/cifparse.a
 lib/libnab.a
 lib/libsym.a
@@ -70,9 +74,6 @@ share/nab/dgdb/basepairs/ct.XVII.pdb
 share/nab/dgdb/basepairs/ct.XVIII.pdb
 share/nab/dgdb/basepairs/cu.XVII.pdb
 share/nab/dgdb/basepairs/cu.XVIII.pdb
-share/nab/dgdb/basepairs/CVS/Entries
-share/nab/dgdb/basepairs/CVS/Repository
-share/nab/dgdb/basepairs/CVS/Root
 share/nab/dgdb/basepairs/ga.IX.pdb
 share/nab/dgdb/basepairs/ga.VIII.pdb
 share/nab/dgdb/basepairs/ga.X.pdb
@@ -142,9 +143,6 @@ share/nab/dgdb/stacking/ag.ddna.pdb
 share/nab/dgdb/stacking/ag.tdna.pdb
 share/nab/dgdb/stacking/at.adna.pdb
 share/nab/dgdb/stacking/at.bdna.pdb
-share/nab/dgdb/stacking/CVS/Entries
-share/nab/dgdb/stacking/CVS/Repository
-share/nab/dgdb/stacking/CVS/Root
 share/nab/dgdb/stacking/at.cdna.pdb
 share/nab/dgdb/stacking/at.ddna.pdb
 share/nab/dgdb/stacking/at.tdna.pdb
@@ -244,6 +242,7 @@ share/nab/examples/acgtacgt.pdb
 share/nab/examples/gcg10.pdb
 share/nab/examples/gcg10.pdb.save
 share/nab/examples/getbase.nab
+share/nab/examples/mme_typical_calling_sequence.nab
 share/nab/examples/program_1.nab
 share/nab/examples/program_10.nab
 share/nab/examples/program_11.nab
@@ -299,8 +298,6 @@ share/nab/reslib/bdna.std/bdna.std.chi
 share/nab/reslib/bdna.std/bdna.std.pdb
 share/nab/reslib/bdna.std/dna.qr
 share/nab/reslib/bounds.db
-share/nab/reslib/cdd.mol2
-share/nab/reslib/charlie.star.note
 share/nab/reslib/conf.lib
 share/nab/reslib/dna.amber94.3.rlb
 share/nab/reslib/dna.amber94.5.rlb
@@ -346,7 +343,6 @@ share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd
 share/nab/reslib/hetatm.amber94/hetatm.amber94.chi
 share/nab/reslib/hetatm.amber94/hetatm.amber94.pdb
 share/nab/reslib/hetatm.amber94/hetatm.amber94.qr
-share/nab/reslib/leap.log
 share/nab/reslib/leap/0README
 share/nab/reslib/leap/Notes
 share/nab/reslib/leap/all_amino91.lib
@@ -361,12 +357,15 @@ share/nab/reslib/leap/dna.amberua.lib
 share/nab/reslib/leap/dna.amberua.redch.lib
 share/nab/reslib/leap/ions91.lib
 share/nab/reslib/leap/ions94.lib
-share/nab/reslib/leap/parm94.dat.istvan
-share/nab/reslib/leap/leap.log
 share/nab/reslib/leap/leaprc.dna.amberua
 share/nab/reslib/leap/leaprc.dna.amberua.redch
 share/nab/reslib/leap/leaprc.nmr
 share/nab/reslib/leap/leaprc.protein.amberua
+share/nab/reslib/leap/leaprc.ff03
+share/nab/reslib/leap/solvents.lib
+share/nab/reslib/leap/frcmod.ff03
+share/nab/reslib/leap/all_amino03.lib
+share/nab/reslib/leap/parm99.dat
 share/nab/reslib/leap/leaprc.rna
 share/nab/reslib/leap/leaprc.rna.amberua
 share/nab/reslib/leap/leaprc.std
@@ -446,7 +445,6 @@ share/nab/reslib/rna.amberua/rna.amberua.bnd
 share/nab/reslib/rna.amberua/rna.amberua.chi
 share/nab/reslib/rna.amberua/rna.amberua.pdb
 share/nab/reslib/rna.amberua/rna.amberua.qr
-share/nab/reslib/syblCDD.lib
 share/nab/suppose/Makefile
 share/nab/suppose/PCA_suppose.nab
 share/nab/suppose/ccmath.h
@@ -463,8 +461,13 @@ share/nab/test/5pti.pdb
 share/nab/test/5pti.shifts.check
 share/nab/test/d01.lin.check
 share/nab/test/d01.pdb.check
+share/nab/test/dhfrndpmtx.prmtop
 share/nab/test/dg_gyrate.nab
 share/nab/test/dg_gyrate.out.check
+share/nab/test/dg_gyrate2.nab
+share/nab/test/dhfrndpmtx.ambpdb
+share/nab/test/dhfrndpmtx.nab
+share/nab/test/dhfrndpmtx.out.check
 share/nab/test/dna.circle.nab
 share/nab/test/duplex.in
 share/nab/test/duplex.nab
@@ -475,7 +478,6 @@ share/nab/test/gbrna.out.check
 share/nab/test/gbrna.pdb
 share/nab/test/gbrna.prmtop
 share/nab/test/gbrna_long.nab
-share/nab/test/gbrna_sa.nab
 share/nab/test/gbtrx.nab
 share/nab/test/gbtrx.out.check
 share/nab/test/get_pep_info.nab
@@ -489,11 +491,11 @@ share/nab/test/ico.sym
 share/nab/test/ico.sym.out.check
 share/nab/test/ltest.nab
 share/nab/test/ltest.out.check
-share/nab/test/msurf.nab
+share/nab/test/mm_plus_dg.nab
 share/nab/test/pointplane.nab
 share/nab/test/prmtop
 share/nab/test/prmtop.gb2
-share/nab/test/prmtop.new
+share/nab/test/pseudoknot.nab
 share/nab/test/rattle_md.nab
 share/nab/test/rattle_md.out.check
 share/nab/test/rattle_min.nab
@@ -512,18 +514,6 @@ share/nab/test/tbv.com.pdb
 share/nab/test/trxox.2.4ns.pdb
 share/nab/test/trxox.2.4ns.x
 share/nab/test/write_sander_inp.nab
-share/nab/test/lCmd
-share/nab/test/1ubq/1ubq.pdb
-share/nab/test/1ubq/5pti.pdb
-share/nab/test/1ubq/leap.log
-share/nab/test/1ubq/out.1
-share/nab/test/1ubq/prmtop
-share/nab/test/1ubq/prmtop.1
-share/nab/test/1ubq/rattle_min.nab
-share/nab/test/1ubq/runleap.nab
-share/nab/test/2strand.nab
-share/nab/test/2strand.pdb
-@dirrm share/nab/test/1ubq
 @dirrm share/nab/test
 @dirrm share/nab/suppose
 @dirrm share/nab/reslib/rna.amberua
@@ -546,9 +536,7 @@ share/nab/test/2strand.pdb
 @dirrm share/nab/include
 @dirrm share/nab/fd_data
 @dirrm share/nab/examples
-@dirrm share/nab/dgdb/stacking/CVS
 @dirrm share/nab/dgdb/stacking
-@dirrm share/nab/dgdb/basepairs/CVS
 @dirrm share/nab/dgdb/basepairs
 @dirrm share/nab/dgdb
 @dirrm share/nab/bin