ports/90140: update biology/seaview: fix help file, remove uneccessary patches

[Fernan Aguero]

>Number:         90140
>Category:       ports
>Synopsis:       update biology/seaview: fix help file, remove uneccessary patches
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Fri Dec 09 14:10:02 GMT 2005
>Closed-Date:
>Last-Modified:
>Originator:     Fernan Aguero
>Release:        FreeBSD 4.10-RELEASE i386
>Organization:
IIB-UNSAM
>Environment:

FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan at pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI  i386

	
>Description:
	
	
	The author of seaview has incorporated two of our patches into
	the upstream sources. So we remove these from the port.

	Also, the CFLAGS defined by the port are now being added
	to seaview's own CFLAGS. As a result the help file is now
	found by seaview as it should be.
	
>How-To-Repeat:
	
	
>Fix:

	



--- seaview.diff begins here ---
diff -ruN /usr/ports/biology/seaview/Makefile seaview/Makefile
--- /usr/ports/biology/seaview/Makefile	Tue Dec  6 14:44:00 2005
+++ seaview/Makefile	Fri Dec  9 07:46:41 2005
@@ -7,7 +7,7 @@
 #
 
 PORTNAME=	seaview
-PORTVERSION=	2005.13.07
+PORTVERSION=	2005.12.07
 CATEGORIES=	biology
 MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
 DISTNAME=	${PORTNAME}
@@ -27,12 +27,12 @@
 ALL_TARGET=	${PORTNAME}
 
 CFLAGS+=	-D HAVE_DIRENT_H \
-		-D DEFAULT_HELPFILE=${PREFIX}/lib/X11/seaview/seaview.help
+		-D DEFAULT_HELPFILE=${PREFIX}/lib/X11/${PORTNAME}/seaview.help
 
 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 ${PREFIX}/lib/X11/seaview
+	@${MKDIR} ${PREFIX}/lib/X11/${PORTNAME}
+	@${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/${PORTNAME}
 
 .include <bsd.port.mk>
diff -ruN /usr/ports/biology/seaview/distinfo seaview/distinfo
--- /usr/ports/biology/seaview/distinfo	Tue Dec  6 14:44:00 2005
+++ seaview/distinfo	Wed Dec  7 12:08:24 2005
@@ -1,3 +1,3 @@
-MD5 (seaview-2005.13.07/seaview.tar) = 0971b3485351f6a1f56a7b56ead2359c
-SHA256 (seaview-2005.13.07/seaview.tar) = 7f48c494e5bee5dacef28bab2a52eab8aff6b66ceff8fab47fe77a18de376fc5
-SIZE (seaview-2005.13.07/seaview.tar) = 595968
+MD5 (seaview-2005.12.07/seaview.tar) = 4d1d1406f5d9ae0a0edad7144742143b
+SHA256 (seaview-2005.12.07/seaview.tar) = ced1844ca3fc8181a9c811079dbc8e2ee67242ef49be113f761abad034ba8ba3
+SIZE (seaview-2005.12.07/seaview.tar) = 595968
diff -ruN /usr/ports/biology/seaview/files/patch-Makefile seaview/files/patch-Makefile
--- /usr/ports/biology/seaview/files/patch-Makefile	Tue Dec  6 12:13:17 2005
+++ seaview/files/patch-Makefile	Fri Dec  9 07:41:35 2005
@@ -1,5 +1,5 @@
 --- Makefile.orig	Wed Apr  6 05:54:30 2005
-+++ Makefile	Mon Dec  5 08:31:05 2005
++++ Makefile	Fri Dec  9 07:41:26 2005
 @@ -1,18 +1,15 @@
 -FLTK = ../fltk
 -PDF = ../PDFlib-Lite-6.0.1/libs/pdflib
@@ -7,7 +7,7 @@
  CXX = g++
  
 -CFLAGS  = -Dunix  -U__APPLE__  -c $(OPT) -I$(FLTK) -I$(PDF) -I$(X11)/include 
-+CFLAGS  = -Dunix -c $(OPT) -I$(X11BASE)/include -I$(LOCALBASE)/include
++CFLAGS+= -Dunix -c $(OPT) -I$(X11BASE)/include -I$(LOCALBASE)/include
  
  
  OBJECTS = seaview.o pdf.o custom.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
diff -ruN /usr/ports/biology/seaview/files/patch-align.cxx seaview/files/patch-align.cxx
--- /usr/ports/biology/seaview/files/patch-align.cxx	Sat Nov 22 01:05:03 2003
+++ seaview/files/patch-align.cxx	Wed Dec 31 21:00:00 1969
@@ -1,19 +0,0 @@
---- align.cxx.orig	Mon Nov 17 14:15:01 2003
-+++ align.cxx	Mon Nov 17 14:15:26 2003
-@@ -1,6 +1,7 @@
- #include "seaview.h"
- #include <stdlib.h>
- #include <ctype.h>
-+#include <unistd.h>
- #ifndef WIN32
- #include <FL/x.H>
- #endif
-@@ -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
- */
diff -ruN /usr/ports/biology/seaview/files/patch-seaview.cxx seaview/files/patch-seaview.cxx
--- /usr/ports/biology/seaview/files/patch-seaview.cxx	Sat Nov 22 01:05:03 2003
+++ seaview/files/patch-seaview.cxx	Wed Dec 31 21:00:00 1969
@@ -1,11 +0,0 @@
---- seaview.cxx.orig	Mon Nov 17 14:16:39 2003
-+++ seaview.cxx	Mon Nov 17 14:17:13 2003
-@@ -164,6 +164,8 @@
- 	"seaview.hlp", 
- #elif defined(__APPLE__)
- 	NULL,
-+#elif defined(DEFAULT_HELPFILE)
-+       __XSTRING(DEFAULT_HELPFILE),
- #else
- 	"seaview.help", 
- #endif
--- seaview.diff ends here ---

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