ports/68561: maintainer update for biology/nab
M. L. Dodson
bdodson at scms.utmb.edu
Thu Jul 1 16:11:41 UTC 2004
>Number: 68561
>Category: ports
>Synopsis: maintainer update for biology/nab
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Thu Jul 01 16:10:16 GMT 2004
>Closed-Date:
>Last-Modified:
>Originator: M. L. Dodson
>Release: FreeBSD 5.2-CURRENT i386
>Organization:
University of Texas Medical Branch
>Environment:
System: FreeBSD histidine.utmb.edu 5.2-CURRENT FreeBSD 5.2-CURRENT #0: Thu May 27 12:07:35 CDT 2004 bdodson at histidine.utmb.edu:/usr/src/sys/i386/compile/HISTIDINE i386
>Description:
NA
>How-To-Repeat:
NA
>Fix:
file files/patch-atom.c should be deleted and is deleted by the diff
file files/patch-src:molio.c is new and is created by the diff
diff -ruN nab.bak/Makefile nab/Makefile
--- nab.bak/Makefile Mon May 3 10:31:41 2004
+++ nab/Makefile Thu Jul 1 10:31:20 2004
@@ -2,11 +2,11 @@
# Date created: Sept. 10, 2000
# Whom: M. L. Dodson <bdodson at scms.utmb.edu>
#
-# $FreeBSD: ports/biology/nab/Makefile,v 1.14 2004/05/02 03:28:48 petef Exp $
+# $FreeBSD$
#
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 @@
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 @@
${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 -ruN nab.bak/distinfo nab/distinfo
--- nab.bak/distinfo Mon May 3 10:31:41 2004
+++ nab/distinfo Fri Jun 18 23:05:46 2004
@@ -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 -ruN nab.bak/files/patch-Makefile nab/files/patch-Makefile
--- nab.bak/files/patch-Makefile Tue Oct 14 07:18:51 2003
+++ nab/files/patch-Makefile Thu Jul 1 09:03:52 2004
@@ -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 -ruN nab.bak/files/patch-atom.c nab/files/patch-atom.c
--- nab.bak/files/patch-atom.c Sat May 1 22:28:49 2004
+++ nab/files/patch-atom.c Wed Dec 31 18:00:00 1969
@@ -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 -ruN nab.bak/files/patch-src:database.c nab/files/patch-src:database.c
--- nab.bak/files/patch-src:database.c Tue Jul 8 06:50:36 2003
+++ nab/files/patch-src:database.c Fri Jun 18 23:22:19 2004
@@ -14,3 +14,12 @@
+@@ -71,7 +78,7 @@
+
+ #include <stdio.h>
+ #include <string.h>
+-#include <malloc.h>
++#include <stdlib.h>
+
+ #include "database.h"
+
diff -ruN nab.bak/files/patch-src:molio.c nab/files/patch-src:molio.c
--- nab.bak/files/patch-src:molio.c Wed Dec 31 18:00:00 1969
+++ nab/files/patch-src:molio.c Fri Jun 18 23:28:08 2004
@@ -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 -ruN nab.bak/pkg-plist nab/pkg-plist
--- nab.bak/pkg-plist Mon May 3 10:31:42 2004
+++ nab/pkg-plist Thu Jul 1 10:05:20 2004
@@ -9,6 +9,10 @@
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.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.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/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.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.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.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.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.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.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.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/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
- at dirrm share/nab/test/1ubq
@dirrm share/nab/test
@dirrm share/nab/suppose
@dirrm share/nab/reslib/rna.amberua
@@ -546,9 +536,7 @@
@dirrm share/nab/include
@dirrm share/nab/fd_data
@dirrm share/nab/examples
- at dirrm share/nab/dgdb/stacking/CVS
@dirrm share/nab/dgdb/stacking
- at dirrm share/nab/dgdb/basepairs/CVS
@dirrm share/nab/dgdb/basepairs
@dirrm share/nab/dgdb
@dirrm share/nab/bin
>Release-Note:
>Audit-Trail:
>Unformatted:
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