Date: Fri, 29 Mar 2002 02:50:02 -0800 (PST) From: Tony Maher <tonym@biolateral.com.au> To: freebsd-ports@FreeBSD.org Subject: Re: ports/36466: please remove biology/seaview Message-ID: <200203291050.g2TAo2G78407@freefall.freebsd.org>
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The following reply was made to PR ports/36466; it has been noted by GNATS. From: Tony Maher <tonym@biolateral.com.au> To: freebsd-gnats-submit@FreeBSD.org Cc: Subject: Re: ports/36466: please remove biology/seaview Date: Fri, 29 Mar 2002 21:42:39 +1100 This is a multi-part message in MIME format. --------------292820DA3D9875C171851A8A Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Attached is a patch to update seaview to a working state. -- tonym --------------292820DA3D9875C171851A8A Content-Type: text/plain; charset=us-ascii; name="seaview.patch" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="seaview.patch" diff -ruN seaview.orig/Makefile seaview/Makefile --- seaview.orig/Makefile Sun Oct 8 21:19:17 2000 +++ seaview/Makefile Fri Mar 29 21:36:56 2002 @@ -6,7 +6,7 @@ # PORTNAME= seaview -PORTVERSION= 1.0 +PORTVERSION= 2002.01.16 CATEGORIES= biology MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/ DISTNAME= ${PORTNAME} @@ -14,7 +14,7 @@ MAINTAINER= frankch@waru.life.nthu.edu.tw -LIB_DEPENDS= xforms.0:${PORTSDIR}/x11-toolkits/xforms +LIB_DEPENDS= fltk.1:${PORTSDIR}/x11-toolkits/fltk USE_X_PREFIX= YES NO_WRKSUBDIR= YES @@ -22,8 +22,14 @@ EXTRACT_BEFORE_ARGS= -xf EXTRACT_AFTER_ARGS= # empty +# The distribution does not come with its own Makefile. + +pre-build: + @ ${CP} ${FILESDIR}/Makefile ${WRKSRC} + do-install: @ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin + @ ${INSTALL_SCRIPT} ${WRKSRC}/seaview_align.sh ${PREFIX}/bin @ (${MKDIR} ${PREFIX}/lib/X11/seaview) @ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview diff -ruN seaview.orig/distinfo seaview/distinfo --- seaview.orig/distinfo Mon Apr 24 19:45:46 2000 +++ seaview/distinfo Fri Mar 29 21:12:52 2002 @@ -1 +1 @@ -MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab +MD5 (seaview.tar) = 05ae4baeacdd00e01ce415bc5acfca13 diff -ruN seaview.orig/files/Makefile seaview/files/Makefile --- seaview.orig/files/Makefile Thu Jan 1 10:00:00 1970 +++ seaview/files/Makefile Fri Mar 29 21:27:08 2002 @@ -0,0 +1,16 @@ +CC = c++ +CFLAGS += -I${X11BASE}/include +LIBS = -L${X11BASE}/lib -lfltk -lGL -lXext -lX11 -lm +SRCS = align.c seaview.c chooser_plus.c nexus.c use_mase_files.c \ + comlines.c regions.c xfmatpt.c load_seq.c resource.c +OBJS = ${SRCS:.c=.o} + +all: seaview + +seaview: $(OBJS) + $(CC) -o seaview $(OBJS) $(LIBS) + +c.o.: $(SRCS) + $(CC) $(CFLAGS) -c $(SRCS) + + diff -ruN seaview.orig/files/patch-aa seaview/files/patch-aa --- seaview.orig/files/patch-aa Tue Aug 31 13:57:56 1999 +++ seaview/files/patch-aa Thu Jan 1 10:00:00 1970 @@ -1,20 +0,0 @@ ---- Makefile.orig Mon Aug 30 20:54:56 1999 -+++ Makefile Mon Aug 30 20:55:48 1999 -@@ -0,0 +1,17 @@ -+#matpt.h -+#seaview.h -+CC ?= gcc -+CFLAGS+= -I${X11BASE}/include -+LIBS = -L${X11BASE}/lib -lxforms -lX11 -lm -+SRCS = align.c comlines.c load_seq.c regions.c seaview.c use_mase_files.c xfmatpt.c -+OBJS = align.o comlines.o load_seq.o regions.o seaview.o use_mase_files.o xfmatpt.o -+ -+all: seaview -+ -+seaview: $(OBJS) -+ $(CC) -o seaview $(OBJS) $(LIBS) -+ -+c.o.: $(SRCS) -+ $(CC) $(CFLAGS) -c $(SRCS) -+ -+ diff -ruN seaview.orig/pkg-descr seaview/pkg-descr --- seaview.orig/pkg-descr Mon May 3 07:37:59 1999 +++ seaview/pkg-descr Fri Mar 29 21:39:24 2002 @@ -2,10 +2,9 @@ You can align DNA sequences from several organisms, and find out their relative postions in phylogenic tree. -File test.mase can be used as an example file. -Open the on-line help window through button 'Help' to learn seaview usage. +An example file test.mase can be obtained from the ftp site. -WWW: http://acnuc.univ-lyon1.fr/phylogeny/seaview.html +WWW: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/ ***************************************************************************** * The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ . diff -ruN seaview.orig/pkg-plist seaview/pkg-plist --- seaview.orig/pkg-plist Mon Dec 22 09:04:39 1997 +++ seaview/pkg-plist Fri Mar 29 21:29:19 2002 @@ -1,3 +1,4 @@ bin/seaview +bin/seaview_align.sh lib/X11/seaview/seaview.help @dirrm lib/X11/seaview --------------292820DA3D9875C171851A8A-- To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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