Attachment #26661 for bug #45466

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#

PORTNAME=	seaview
PORTVERSION=	2002.10.18
CATEGORIES=	biology
MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
DISTNAME=	${PORTNAME}
EXTRACT_SUFX=	.tar

MAINTAINER=	ports@FreeBSD.org

LIB_DEPENDS=	fltk.1:${PORTSDIR}/x11-toolkits/fltk

LIB_DEPENDS=	forms.1:${PORTSDIR}/x11-toolkits/xforms

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


Line 1 Link Here

(-)seaview/distinfo (-1 / +1 lines)
1	MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab	1	MD5 (seaview.tar) = 1f9b5157966b98f2724428d3fb1f6b17




--- 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 : $(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
+




--- 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;

Line 1 Link Here

(-)seaview/pkg-comment (-1 / +1 lines)
1	Multiple DNA sequence alignment editor	1	Multiple DNA/protein sequence alignment editor




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:

	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:
*
*   seaview*helpfile:	/usr/X11R6/lib/X11/seaview/seaview.help
*****************************************************************************

Lines 1-3 Link Here

(-)seaview/pkg-plist (+1 lines)
1	bin/seaview	1	bin/seaview
		2	bin/seaview_align.sh
2	lib/X11/seaview/seaview.help	3	lib/X11/seaview/seaview.help
3	@dirrm lib/X11/seaview	4	@dirrm lib/X11/seaview

Return to bug 45466

Lines 6-31 Link Here

(-)seaview/Makefile (-5 / +5 lines)
6	#	6	#
7		7
8	PORTNAME= seaview	8	PORTNAME= seaview
9	PORTVERSION= 1.0	9	PORTVERSION= 2002.10.18
10	CATEGORIES= biology	10	CATEGORIES= biology
11	MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/	11	MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
12	DISTNAME= ${PORTNAME}	12	DISTNAME= ${PORTNAME}
13	EXTRACT_SUFX= .tar	13	EXTRACT_SUFX= .tar
14		14
15	MAINTAINER= frankch@waru.life.nthu.edu.tw	15	MAINTAINER= ports@FreeBSD.org
16		16
17	BROKEN= "Checksum is incorrect"	17	LIB_DEPENDS= fltk.1:${PORTSDIR}/x11-toolkits/fltk
18
19	LIB_DEPENDS= forms.1:${PORTSDIR}/x11-toolkits/xforms
20		18
21	USE_X_PREFIX= YES	19	USE_X_PREFIX= YES
22	NO_WRKSUBDIR= YES	20	NO_WRKSUBDIR= YES
23	EXTRACT_CMD= ${TAR}	21	EXTRACT_CMD= ${TAR}
24	EXTRACT_BEFORE_ARGS= -xf	22	EXTRACT_BEFORE_ARGS= -xf
25	EXTRACT_AFTER_ARGS= # empty	23	EXTRACT_AFTER_ARGS= # empty
		24	MAKEFILE= makefile
26		25
27	do-install:	26	do-install:
28	@ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin	27	@ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin
		28	@ ${INSTALL_SCRIPT} ${WRKSRC}/seaview_align.sh ${PREFIX}/bin
29	@ (${MKDIR} ${PREFIX}/lib/X11/seaview)	29	@ (${MKDIR} ${PREFIX}/lib/X11/seaview)
30	@ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview	30	@ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview
31		31

Lines 1-20 Link Here

(-)seaview/files/patch-aa (-18 / +21 lines)
1	--- Makefile.orig Mon Aug 30 20:54:56 1999	1	--- makefile.orig Wed Sep 25 23:58:15 2002
2	+++ Makefile Mon Aug 30 20:55:48 1999	2	+++ makefile Mon Nov 18 11:26:42 2002
3	@@ -0,0 +1,17 @@	3	@@ -1,13 +1,15 @@
4	+#matpt.h	4	-FLTK = ../fltk-1.1.0
5	+#seaview.h	5	+OPT = -O2
6	+CC ?= gcc	6
7	+CFLAGS+= -I${X11BASE}/include	7	-OBJECTS = seaview.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o old_file_chooser.o
8	+LIBS = -L${X11BASE}/lib -lxforms -lX11 -lm	8	+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
9	+SRCS = align.c comlines.c load_seq.c regions.c seaview.c use_mase_files.c xfmatpt.c	9
10	+OBJS = align.o comlines.o load_seq.o regions.o seaview.o use_mase_files.o xfmatpt.o	10	-CFLAGS = -c $(OPT) -I$(FLTK)
		11	+CFLAGS = -c $(OPT) -I$(PREFIX)/include
		12
		13	-CXX = CC
		14	+CXX = g++
11	+	15	+
12	+all: seaview	16	+all: seaview
13	+	17
14	+seaview: $(OBJS)	18	seaview : $(OBJECTS)
15	+ $(CC) -o seaview $(OBJS) $(LIBS)	19	- $(CXX) -o $@ $(OBJECTS) -L$(FLTK)/lib -lfltk -lX11 -lm
16	+	20	+ $(CXX) -o $@ $(OBJECTS) -L$(PREFIX)/lib -lfltk -lX11 -lMesaGL -lXext -lm
17	+c.o.: $(SRCS)	21
18	+ $(CC) $(CFLAGS) -c $(SRCS)	22
19	+	23	.SUFFIXES: .cxx .h .o
20	+

Line 0 Link Here

(-)seaview/files/patch-ab (+38 lines)
	1	--- align.cxx.orig Tue Oct 8 19:43:40 2002
	2	+++ align.cxx Mon Nov 18 11:40:08 2002
	3	@@ -1,5 +1,6 @@
	4	#include "seaview.h"
	5	#include <stdlib.h>
	6	+#include <unistd.h>
	7	#include <ctype.h>
	8	#ifndef WIN32
	9	#include <FL/x.H>
	10	@@ -155,7 +156,7 @@
	11	#endif
	12	debut = view->active_region->list->debut;
	13	fin = view->active_region->list->fin;
	14	-tmpnam(base_fname);
	15	+mkstemp(base_fname);
	16	/*
	17	convertir en minuscules car clustalw n'accepte pas les majuscules ds filenames
	18	*/
	19	--- chooser_plus.cxx.orig Mon Nov 18 11:14:10 2002
	20	+++ chooser_plus.cxx Mon Nov 18 11:17:52 2002
	21	@@ -442,7 +442,7 @@
	22	strcmp(pat,f->browser.pattern))) {
	23	// if pattern is different, remove name but leave old directory:
	24	const char* p = f->input.value();
	25	- const char* q = fl_filename_name(p);
	26	+ const char* q = filename_name(p);
	27	f->input.value(p, q-p);
	28	}
	29	f->browser.pattern = pat;
	30	@@ -500,7 +500,7 @@
	31	strcmp(pat,f->browser.pattern))) {
	32	// if pattern is different, remove name but leave old directory:
	33	const char* p = f->input.value();
	34	- const char* q = fl_filename_name(p);
	35	+ const char* q = filename_name(p);
	36	f->input.value(p, q-p);
	37	}
	38	f->browser.pattern = pat;

Lines 1-15 Link Here

(-)seaview/pkg-descr (-5 / +5 lines)
1	Seaview is a multiple DNA sequence alignment editor.	1	Seaview is a multiple sequence alignment editor.
2	You can align DNA sequences from several organisms, and find out their	2	You can align DNA/protein sequences from several organisms, and find out their
3	relative postions in phylogenic tree.	3	relative postions in phylogenic tree.
4		4
5	File test.mase can be used as an example file.
6	Open the on-line help window through button 'Help' to learn seaview usage.	5	Open the on-line help window through button 'Help' to learn seaview usage.
		6	Example mase files could be found at:
7		7
8	WWW: http://pbil.univ-lyon1.fr/software/seaview.html	8	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
9		9
10	*****************************************************************************	10	*****************************************************************************
11	* The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ .	11	* The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ .
12	* Add an entry in your Xresources or Xdefaults file with:	12	* Add an entry in your .Xresources or .Xdefaults file with:
13	*	13	*
14	* seaview*helpfile: /usr/X11R6/lib/X11/seaview/seaview.help	14	* seaview*helpfile: /usr/X11R6/lib/X11/seaview/seaview.help
15	*****************************************************************************	15	*****************************************************************************