ports/54990: [patch][non-maintainer] fix fetch and plist for biology/nab

[Mark Linimon]

>Number:         54990
>Category:       ports
>Synopsis:       [patch][non-maintainer] fix fetch and plist for biology/nab
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Jul 28 13:10:10 PDT 2003
>Closed-Date:
>Last-Modified:
>Originator:     Mark Linimon
>Release:        FreeBSD-
>Organization:
FreeBSD
>Environment:
System: FreeBSD lonesome.lonesome.com 4.8-STABLE FreeBSD 4.8-STABLE #1: Sun Jul 13 23:03:01 CDT 2003 root at lonesome.lonesome.com:/usr/src/sys/compile/MULTIMEDIA i386
>Description:
	Per the mastersite, the distfile has been upgraded: "Version 4.5.2 has
	some fix-ups to the manual and a faster implementation of the
	generalized Born algorithm."  Also, the plist was incomplete
>How-To-Repeat:
	per bento logs
>Fix:
	The following fixes everything except one file in plist that
	clearly should not be installed, "/usr/local/share/nab/leap/?????".
	I'll leave that to the port maintainer to fix and send to the
	original authors.  (There are other questionable files that are
	installed as well: *.dat~, *.exe).

--- nab/Makefile.dist	Tue Jul  8 06:50:36 2003
+++ nab/Makefile	Sun Jul 27 14:07:44 2003
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	nab
-PORTVERSION=	4.5.1
+PORTVERSION=	4.5.2
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/ \
 		http://www.scripps.edu/case/
--- nab/distinfo.dist	Tue Jul  8 06:50:36 2003
+++ nab/distinfo	Sun Jul 27 14:08:18 2003
@@ -1 +1 @@
-MD5 (nab-4.5.1.tar.gz) = 650be5581dfe5af1b7edb6da44a221d4
+MD5 (nab-4.5.2.tar.gz) = b5e9053e6ae97f36a55cc2a1317e9ba8
--- nab/pkg-plist.dist	Tue Jul  8 06:50:36 2003
+++ nab/pkg-plist	Sun Jul 27 14:27:40 2003
@@ -54,6 +54,8 @@
 share/nab/examples/gcg10.pdb
 share/nab/examples/gcg10.pdb.save
 share/nab/examples/getbase.nab
+share/nab/examples/program_1.c
+share/nab/examples/program_1.exe
 share/nab/examples/program_1.nab
 share/nab/examples/program_10.nab
 share/nab/examples/program_11.nab
@@ -186,6 +188,8 @@
 share/nab/reslib/leap/parm91X.dat
 share/nab/reslib/leap/parm91X.ua.dat
 share/nab/reslib/leap/parm94.dat
+share/nab/reslib/leap/parm94.dat.istvan
+share/nab/reslib/leap/parm94.dat~
 share/nab/reslib/leap/parm94X.dat
 share/nab/reslib/leap/pro-dna91.nmr.lib
 share/nab/reslib/leap/pro-dna91.nmr.prepin
@@ -266,7 +270,21 @@
 share/nab/suppose/suppose.1
 share/nab/suppose/suppose.nab
 share/nab/suppose/trnm.c
+share/nab/test/1ubq/1ubq.pdb
+share/nab/test/1ubq/5pti.pdb
+share/nab/test/1ubq/a.exe
+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.c
+share/nab/test/1ubq/rattle_min.nab
+share/nab/test/1ubq/runleap.c
+share/nab/test/1ubq/runleap.nab
 share/nab/test/2.pdb
+share/nab/test/2strand.exe
+share/nab/test/2strand.nab
+share/nab/test/2strand.pdb
 share/nab/test/5pti.obs
 share/nab/test/5pti.pdb
 share/nab/test/5pti.shifts.check
@@ -287,7 +305,7 @@
 share/nab/test/gbrna.prmtop
 share/nab/test/gbrna_long.exe
 share/nab/test/gbrna_long.nab
-share/nab/test/gbrna_long.out
+share/nab/test/gbrna_sa.nab
 share/nab/test/gbtrx.nab
 share/nab/test/gbtrx.out.check
 share/nab/test/get_pep_info.nab
@@ -299,11 +317,14 @@
 share/nab/test/hash.out.check
 share/nab/test/ico.sym
 share/nab/test/ico.sym.out.check
+share/nab/test/lCmd
 share/nab/test/ltest.nab
 share/nab/test/ltest.out.check
+share/nab/test/msurf.nab
 share/nab/test/pointplane.nab
 share/nab/test/prmtop
 share/nab/test/prmtop.gb2
+share/nab/test/prmtop.new
 share/nab/test/rattle_md.nab
 share/nab/test/rattle_md.out.check
 share/nab/test/rattle_min.nab
@@ -322,6 +343,7 @@
 share/nab/test/trxox.2.4ns.pdb
 share/nab/test/trxox.2.4ns.x
 share/nab/test/write_sander_inp.nab
+ at dirrm share/nab/test/1ubq
 @dirrm share/nab/test
 @dirrm share/nab/suppose
 @dirrm share/nab/reslib/rna.amberua
--- nab/files/patch-Makefile.dist	Sun Jul 27 14:10:14 2003
+++ nab/files/patch-Makefile	Sun Jul 27 14:15:24 2003
@@ -6,7 +6,7 @@
 +all: compiler test
  compiler:
  	-mkdir bin lib include
--	(cd ucpp-0.7; make install )
+-	(cd ucpp-1.3; make install )
  	(cd cifparse; make install )
  	(cd src; make install )
  	(cd nss; make install )
@@ -24,14 +24,14 @@
  	(cd nss; make test )
  
  clean:
--	(cd ucpp-0.7; make clean )
+-	(cd ucpp-1.3; 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 ucpp-1.3; make uninstall )
  	(cd cifparse; make uninstall )
  	(cd src; make uninstall )
  	(cd nss; make uninstall )
>Release-Note:
>Audit-Trail:
>Unformatted: