From 50e96887d25c3a6f63dcc8eed90a4618442f277e Mon Sep 17 00:00:00 2001
From: Daichi GOTO <daichi@FreeBSD.org>
Date: Tue, 14 Oct 2003 12:18:51 +0000
Subject: update biology/nab: 4.5.1 -> 4.5.2
PR: 57970
Submitted by: M. L. Dodson <bdodson@scms.utmb.edu> (maintainer)
---
biology/nab/Makefile | 18 ++++++++++++++----
biology/nab/distinfo | 2 +-
biology/nab/files/patch-Makefile | 15 ++++++---------
biology/nab/pkg-descr | 2 +-
biology/nab/pkg-plist | 21 ++++++++++++++++-----
5 files changed, 38 insertions(+), 20 deletions(-)
(limited to 'biology/nab')
diff --git a/biology/nab/Makefile b/biology/nab/Makefile
index e2d701f241a4..406e1323c629 100644
--- a/biology/nab/Makefile
+++ b/biology/nab/Makefile
@@ -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/
@@ -15,8 +15,6 @@ MAINTAINER= bdodson@scms.utmb.edu
COMMENT= \
"This is nab (nucleic acid builder), a language for macromolecules"
-BROKEN= Does not fetch
-
BUILD_DEPENDS= ucpp:${PORTSDIR}/devel/ucpp
ONLY_FOR_ARCHS= i386
@@ -43,7 +41,19 @@ pre-patch:
${WRKSRC}/cifparse/cifparse.c
post-patch:
- @rm -f ${WRKSRC}/examples/program_7.nab.orig
+ @${RM} -f ${WRKSRC}/examples/program_7.nab.orig
+ @${RM} -f ${WRKSRC}/examples/program_1.c \
+ ${WRKSRC}/examples/program_1.exe
+ @${RM} -f ${WRKSRC}/test/1ubq/a.exe
+ @${RM} -f ${WRKSRC}/test/1ubq/rattle_min.c
+ @${RM} -f ${WRKSRC}/test/1ubq/runleap.c
+ @${RM} -f ${WRKSRC}/test/*.exe
+ @${RM} -f ${WRKSRC}/tleap/utilMakeHelp.exe
+ @${RM} -f ${WRKSRC}/fd_data/abdna.dat.old
+ @${RM} -f ${WRKSRC}/reslib/leap/parm94.dat~
+ @(cd ${WRKSRC}/reslib/leap && \
+ ${FIND} . -type f -print | ${GREP} -v '\./[a-zA-Z0-9]' | \
+ ${XARGS} ${RM} -f)
pre-install:
@cd ${WRKSRC}/src && \
diff --git a/biology/nab/distinfo b/biology/nab/distinfo
index 9b854a4b868a..e8a2891bb7c0 100644
--- a/biology/nab/distinfo
+++ b/biology/nab/distinfo
@@ -1 +1 @@
-MD5 (nab-4.5.1.tar.gz) = 650be5581dfe5af1b7edb6da44a221d4
+MD5 (nab-4.5.2.tar.gz) = b5e9053e6ae97f36a55cc2a1317e9ba8
diff --git a/biology/nab/files/patch-Makefile b/biology/nab/files/patch-Makefile
index 039c7d0abffb..9c258367476c 100644
--- a/biology/nab/files/patch-Makefile
+++ b/biology/nab/files/patch-Makefile
@@ -1,12 +1,12 @@
---- Makefile.orig Mon Oct 23 20:33:23 2000
-+++ Makefile Wed Feb 12 16:33:42 2003
+--- Makefile.orig Tue Jul 15 21:11:15 2003
++++ Makefile Sat Aug 9 13:50:34 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 ucpp-1.3; make install )
(cd cifparse; make install )
(cd src; make install )
(cd nss; make install )
@@ -20,21 +20,18 @@
# 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 @@
+@@ -18,14 +18,12 @@
(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 )
- (cd tleap; make uninstall )
- -/bin/rm config.h
--
diff --git a/biology/nab/pkg-descr b/biology/nab/pkg-descr
index b4fcfcb34f6a..2d85d2947733 100644
--- a/biology/nab/pkg-descr
+++ b/biology/nab/pkg-descr
@@ -1,4 +1,4 @@
-This is version 4.5 of nab (nucleic acid builder), a computer
+This is version 4.5.2 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
diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist
index 1d3ca0851424..27719e7d3fcc 100644
--- a/biology/nab/pkg-plist
+++ b/biology/nab/pkg-plist
@@ -78,7 +78,6 @@ share/nab/examples/rna_pseudoknot.pdb
share/nab/examples/test.pdb
share/nab/examples/test.sup.pdb
share/nab/fd_data/abdna.dat
-share/nab/fd_data/abdna.dat.old
share/nab/fd_data/adna.dat
share/nab/fd_data/aprna.dat
share/nab/fd_data/arna.dat
@@ -171,6 +170,7 @@ 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
@@ -270,13 +270,11 @@ share/nab/test/2.pdb
share/nab/test/5pti.obs
share/nab/test/5pti.pdb
share/nab/test/5pti.shifts.check
-share/nab/test/a.exe
share/nab/test/d01.lin.check
share/nab/test/d01.pdb.check
share/nab/test/dg_gyrate.nab
share/nab/test/dg_gyrate.out.check
share/nab/test/dna.circle.nab
-share/nab/test/duplex.exe
share/nab/test/duplex.in
share/nab/test/duplex.nab
share/nab/test/fd.nab
@@ -285,9 +283,8 @@ share/nab/test/gbrna.nab
share/nab/test/gbrna.out.check
share/nab/test/gbrna.pdb
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
@@ -301,9 +298,11 @@ 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/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 +321,18 @@ 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
--
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