Date: Sun, 16 Jun 2002 17:20:03 -0700 (PDT) From: Tony Maher <tonym@biolateral.com.au> To: freebsd-ports@FreeBSD.org Subject: Re: ports/39357: Maintainer update: biology/ncbi-toolkit Message-ID: <200206170020.g5H0K3n81701@freefall.freebsd.org>
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The following reply was made to PR ports/39357; it has been noted by GNATS. From: Tony Maher <tonym@biolateral.com.au> To: freebsd-gnats-submit@FreeBSD.ORG, pat@FreeBSD.ORG Cc: Subject: Re: ports/39357: Maintainer update: biology/ncbi-toolkit Date: Mon, 17 Jun 2002 10:13:47 +1000 (EST) Sorry, updated a single file and regenerated the patch just before sending but used -u instread of -ruN. Here is patch generated correctly this time (I hope!) thanks -- tonym diff -ruN seaview.orig/Makefile seaview/Makefile --- seaview.orig/Makefile Sat May 18 12:36:56 2002 +++ seaview/Makefile Mon Jun 17 10:05:18 2002 @@ -2,34 +2,61 @@ # Date created: Dec 5 1997 # Whom: frankch@waru.life.nthu.edu.tw # -# $FreeBSD: ports/biology/seaview/Makefile,v 1.18 2002/05/18 02:36:56 kris Exp $ +# $FreeBSD: ports/biology/seaview/Makefile,v 1.17 2000/10/08 10:19:17 asami Exp $ # PORTNAME= seaview -PORTVERSION= 1.0 +PORTVERSION= 2002.04.09 CATEGORIES= biology MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/ DISTNAME= ${PORTNAME} EXTRACT_SUFX= .tar -MAINTAINER= frankch@waru.life.nthu.edu.tw +MAINTAINER= tonym@biolateral.com.au -BROKEN= "Checksum is incorrect" - -LIB_DEPENDS= xforms.0:${PORTSDIR}/x11-toolkits/xforms +LIB_DEPENDS= fltk.1:${PORTSDIR}/x11-toolkits/fltk USE_X_PREFIX= YES +USE_MESA= YES NO_WRKSUBDIR= YES -EXTRACT_CMD= ${TAR} +MAKEFILE= makefile +ALL_TARGET= seaview +EXTRACT_CMD= ${TAR} EXTRACT_BEFORE_ARGS= -xf EXTRACT_AFTER_ARGS= # empty +DOCDIR= ${PREFIX}/share/doc/${PORTNAME} + +pre-extract: +.if !defined(BATCH) && !defined(PACKAGE_BUILDING) && !defined(HAVE_UTAH) + @(/usr/bin/dialog --textbox ${MASTERDIR}/pkg-warning 8 70 || ${TRUE}) +.endif + +pre-patch: +.if defined(HAVE_UTAH) +P_CFLAGS= ${PTHREAD_CFLAGS} +P_LIBS= ${PTHREAD_LIBS} +.endif + +post-patch: + @ ${REINPLACE_CMD} -e 's|../fltk|${X11BASE}|;' \ + -e "s|I(.*)$$|I\\1/include|;" \ + -e 's|-lfltk|-lfltk -lGL -lXext|;' \ + -e 's|^CFLAGS =|CFLAGS += ${P_CFLAGS} |;' \ + -e 's|-lm|-lm ${P_LIBS}|;' \ + ${WRKSRC}/${MAKEFILE} + @ ${REINPLACE_CMD} -e "s|tmpnam|mkstemp|;" \ + -e "s|(<stdlib.h>)|\1\n#include <unistd.h>|;" \ + ${WRKSRC}/align.cxx do-install: @ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin - @ (${MKDIR} ${PREFIX}/lib/X11/seaview) - @ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview + @ ${INSTALL_SCRIPT} ${WRKSRC}/seaview_align.sh ${PREFIX}/bin +.if !defined(NOPORTDOCS) + @ ${MKDIR} ${DOCDIR} + @ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${DOCDIR} +.endif post-install: - @ ${CAT} ${DESCR} + @ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${PKGMESSAGE} .include <bsd.port.mk> diff -ruN seaview.orig/distinfo seaview/distinfo --- seaview.orig/distinfo Mon Apr 24 19:45:46 2000 +++ seaview/distinfo Sun Jun 16 16:12:24 2002 @@ -1 +1 @@ -MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab +MD5 (seaview.tar) = 28b96855e50986b7e6ff6a0249b062b7 diff -ruN seaview.orig/files/patch-aa seaview/files/patch-aa --- seaview.orig/files/patch-aa Tue Aug 31 13:57:56 1999 +++ seaview/files/patch-aa Thu Jan 1 10:00:00 1970 @@ -1,20 +0,0 @@ ---- Makefile.orig Mon Aug 30 20:54:56 1999 -+++ Makefile Mon Aug 30 20:55:48 1999 -@@ -0,0 +1,17 @@ -+#matpt.h -+#seaview.h -+CC ?= gcc -+CFLAGS+= -I${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 Sun Jun 16 18:27:38 2002 @@ -2,14 +2,6 @@ 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 - -***************************************************************************** -* The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ . -* Add an entry in your Xresources or Xdefaults file with: -* -* seaview*helpfile: /usr/X11R6/lib/X11/seaview/seaview.help -***************************************************************************** +WWW: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/ diff -ruN seaview.orig/pkg-message seaview/pkg-message --- seaview.orig/pkg-message Thu Jan 1 10:00:00 1970 +++ seaview/pkg-message Sun Jun 16 18:31:49 2002 @@ -0,0 +1,6 @@ +***************************************************************************** +* The help file (seaview.help) is located in %%PREFIX%%/share/doc/seaview/ * +* Add an entry in your Xresources or Xdefaults file with: * +* * +* seaview*helpfile: %%PREFIX%%/share/doc/seaview/seaview.help * +***************************************************************************** diff -ruN seaview.orig/pkg-plist seaview/pkg-plist --- seaview.orig/pkg-plist Mon Dec 22 09:04:39 1997 +++ seaview/pkg-plist Sun Jun 16 18:26:13 2002 @@ -1,3 +1,4 @@ bin/seaview -lib/X11/seaview/seaview.help -@dirrm lib/X11/seaview +bin/seaview_align.sh +%%PORTDOCS%%share/doc/seaview/seaview.help +%%PORTDOCS%%@dirrm share/doc/seaview/ diff -ruN seaview.orig/pkg-warning seaview/pkg-warning --- seaview.orig/pkg-warning Thu Jan 1 10:00:00 1970 +++ seaview/pkg-warning Mon Jun 17 08:53:42 2002 @@ -0,0 +1,3 @@ +If you are using XFree86 version 3 with utah-glx hit Ctrl-C now +and use 'make -DHAVE_UTAH' +Otherwise hit OK and continue. 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