Attachment 26661 Details for Bug 45466 – file.diff

[patch] file.diff

file.diff (text/plain), 5.60 KB, created by frankch on 2002-11-19 05:10:01 UTC

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Creator: frankch

Created: 2002-11-19 05:10:01 UTC

Size: 5.60 KB

patch

obsolete

>diff -ruN seaview.orig/Makefile seaview/Makefile
>--- seaview.orig/Makefile	Mon Nov 18 10:33:40 2002
>+++ seaview/Makefile	Mon Nov 18 11:42:02 2002
>@@ -6,26 +6,26 @@
> #
> 
> PORTNAME=	seaview
>-PORTVERSION=	1.0
>+PORTVERSION=	2002.10.18
> CATEGORIES=	biology
> MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
> DISTNAME=	${PORTNAME}
> EXTRACT_SUFX=	.tar
> 
>-MAINTAINER=	frankch@waru.life.nthu.edu.tw
>+MAINTAINER=	ports@FreeBSD.org
> 
>-BROKEN=		"Checksum is incorrect"
>-
>-LIB_DEPENDS=	forms.1:${PORTSDIR}/x11-toolkits/xforms
>+LIB_DEPENDS=	fltk.1:${PORTSDIR}/x11-toolkits/fltk
> 
> USE_X_PREFIX=	YES
> NO_WRKSUBDIR=	YES
> EXTRACT_CMD=		${TAR}
> EXTRACT_BEFORE_ARGS=	-xf
> EXTRACT_AFTER_ARGS=	# empty
>+MAKEFILE=	makefile
> 
> 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 ${PREFIX}/lib/X11/seaview
> 
>diff -ruN seaview.orig/distinfo seaview/distinfo
>--- seaview.orig/distinfo	Mon Nov 18 10:33:40 2002
>+++ seaview/distinfo	Mon Nov 18 10:36:54 2002
>@@ -1 +1 @@
>-MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab
>+MD5 (seaview.tar) = 1f9b5157966b98f2724428d3fb1f6b17
>diff -ruN seaview.orig/files/patch-aa seaview/files/patch-aa
>--- seaview.orig/files/patch-aa	Mon Nov 18 10:33:40 2002
>+++ seaview/files/patch-aa	Mon Nov 18 11:26:53 2002
>@@ -1,20 +1,23 @@
>---- Makefile.orig	Mon Aug 30 20:54:56 1999
>-+++ Makefile	Mon Aug 30 20:55:48 1999
>-@@ -0,0 +1,17 @@
>-+#matpt.h
>-+#seaview.h
>-+CC	?= gcc
>-+CFLAGS+= -I${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
>+--- makefile.orig	Wed Sep 25 23:58:15 2002
>++++ makefile	Mon Nov 18 11:26:42 2002
>+@@ -1,13 +1,15 @@
>+-FLTK = ../fltk-1.1.0
>++OPT = -O2
>+ 
>+-OBJECTS = seaview.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o old_file_chooser.o
>++OBJECTS = seaview.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o
>+ 
>+-CFLAGS  = -c $(OPT) -I$(FLTK)
>++CFLAGS  = -c $(OPT) -I$(PREFIX)/include
>+ 
>+-CXX = CC
>++CXX = g++
> +
> +all: seaview
>-+
>-+seaview: $(OBJS)
>-+	$(CC) -o seaview $(OBJS) $(LIBS)
>-+
>-+c.o.: $(SRCS)
>-+	$(CC) $(CFLAGS) -c $(SRCS)
>-+
>-+
>+ 
>+ seaview : $(OBJECTS) 
>+-	$(CXX) -o $@ $(OBJECTS) -L$(FLTK)/lib -lfltk -lX11 -lm
>++	$(CXX) -o $@ $(OBJECTS) -L$(PREFIX)/lib -lfltk -lX11 -lMesaGL -lXext -lm
>+ 
>+ 
>+ .SUFFIXES:	.cxx .h .o
>diff -ruN seaview.orig/files/patch-ab seaview/files/patch-ab
>--- seaview.orig/files/patch-ab	Thu Jan  1 08:00:00 1970
>+++ seaview/files/patch-ab	Mon Nov 18 11:40:50 2002
>@@ -0,0 +1,38 @@
>+--- align.cxx.orig	Tue Oct  8 19:43:40 2002
>++++ align.cxx	Mon Nov 18 11:40:08 2002
>+@@ -1,5 +1,6 @@
>+ #include "seaview.h"
>+ #include <stdlib.h>
>++#include <unistd.h>
>+ #include <ctype.h>
>+ #ifndef WIN32
>+ #include <FL/x.H>
>+@@ -155,7 +156,7 @@
>+ #endif
>+ debut = view->active_region->list->debut;
>+ fin = view->active_region->list->fin;
>+-tmpnam(base_fname);
>++mkstemp(base_fname);
>+ /* 
>+ convertir en minuscules car clustalw n'accepte pas les majuscules ds filenames
>+ */
>+--- chooser_plus.cxx.orig	Mon Nov 18 11:14:10 2002
>++++ chooser_plus.cxx	Mon Nov 18 11:17:52 2002
>+@@ -442,7 +442,7 @@
>+ 					   strcmp(pat,f->browser.pattern))) {
>+     // if pattern is different, remove name but leave old directory:
>+     const char* p = f->input.value();
>+-    const char* q = fl_filename_name(p);
>++    const char* q = filename_name(p);
>+     f->input.value(p, q-p);
>+   }
>+   f->browser.pattern = pat;
>+@@ -500,7 +500,7 @@
>+ 					   strcmp(pat,f->browser.pattern))) {
>+     // if pattern is different, remove name but leave old directory:
>+     const char* p = f->input.value();
>+-    const char* q = fl_filename_name(p);
>++    const char* q = filename_name(p);
>+     f->input.value(p, q-p);
>+   }
>+   f->browser.pattern = pat;
>diff -ruN seaview.orig/pkg-comment seaview/pkg-comment
>--- seaview.orig/pkg-comment	Mon Nov 18 10:33:40 2002
>+++ seaview/pkg-comment	Mon Nov 18 11:34:33 2002
>@@ -1 +1 @@
>-Multiple DNA sequence alignment editor
>+Multiple DNA/protein sequence alignment editor
>diff -ruN seaview.orig/pkg-descr seaview/pkg-descr
>--- seaview.orig/pkg-descr	Mon Nov 18 10:33:40 2002
>+++ seaview/pkg-descr	Mon Nov 18 11:33:38 2002
>@@ -1,15 +1,15 @@
>-Seaview is a multiple DNA sequence alignment editor.
>-You can align DNA sequences from several organisms, and find out their
>+Seaview is a multiple sequence alignment editor.
>+You can align DNA/protein 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.
>+Example mase files could be found at:
> 
>-WWW: http://pbil.univ-lyon1.fr/software/seaview.html
>+	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
> 
> *****************************************************************************
> *   The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ .
>-*   Add an entry in your Xresources or Xdefaults file with:
>+*   Add an entry in your .Xresources or .Xdefaults file with:
> *
> *   seaview*helpfile:	/usr/X11R6/lib/X11/seaview/seaview.help
> *****************************************************************************
>diff -ruN seaview.orig/pkg-plist seaview/pkg-plist
>--- seaview.orig/pkg-plist	Mon Nov 18 10:33:40 2002
>+++ seaview/pkg-plist	Mon Nov 18 11:31:18 2002
>@@ -1,3 +1,4 @@
> bin/seaview
>+bin/seaview_align.sh
> lib/X11/seaview/seaview.help
> @dirrm lib/X11/seaview

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Attachments on bug 45466: 26661