pkg/43395: [biology/clustalw] Update to 2.0.12

[wenheping%gmail.com@localhost]

>Number:         43395
>Category:       pkg
>Synopsis:       [biology/clustalw] Update to 2.0.12
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    pkg-manager
>State:          open
>Class:          sw-bug
>Submitter-Id:   net
>Arrival-Date:   Mon May 31 13:55:00 +0000 2010
>Originator:     Wen Heping
>Release:        NetBSD-5.0.2
>Organization:
Private
>Environment:
NetBSD nb502.wenjing.com 5.0.2 NetBSD 5.0.2 (GENERIC) #0: Sat Feb  6 17:53:27 
UTC 2010  
builds%b7.netbsd.org@localhost:/home/builds/ab/netbsd-5-0-2-RELEASE/i386/201002061851Z-obj/home/builds/ab/netbsd-5-0-2-RELEASE/src/sys/arch/i386/compile/GENERIC
 i386

>Description:
Please visit http://www.clustal.org/download/2.0.12/CHANGELOG
It seems the changelog of 1.x could not be found.
>How-To-Repeat:

>Fix:
diff -urN clustalw/Makefile clustalw.new/Makefile
--- clustalw/Makefile   2008-03-03 09:10:05.000000000 +0800
+++ clustalw.new/Makefile       2010-06-01 05:39:47.000000000 +0800
@@ -1,10 +1,9 @@
 # $NetBSD: Makefile,v 1.11 2008/03/03 01:10:05 jlam Exp $

-DISTNAME=      clustalw1.83.UNIX
-PKGNAME=       clustalw-1.83
+DISTNAME=      clustalw-2.0.12
 CATEGORIES=    biology
-MASTER_SITES=  ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ \
-               ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
+MASTER_SITES=  http://www.clustal.org/download/current/ \
+               ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.12/

 MAINTAINER=    babafou%babafou.eu.org@localhost
 HOMEPAGE=      http://bips.u-strasbg.fr/fr/Documentation/ClustalW/
@@ -13,25 +12,9 @@
 PKG_INSTALLATION_TYPES=        overwrite pkgviews
 PKG_DESTDIR_SUPPORT=   user-destdir

-MAKE_FILE=     makefile
-BUILD_TARGET=  clustalw
-WRKSRC=                ${WRKDIR}/clustalw1.83
-
-MAKE_FLAGS+=   CC=${CC:Q}
+GNU_CONFIGURE= yes
+USE_LANGUAGES= c c++

 INSTALLATION_DIRS=     bin

-post-patch:
-       @${SED} -e 's:@PREFIX@:${PREFIX}:' < ${WRKSRC}/clustalw.c \
-               > ${WRKSRC}/clustalw.c.tmp \
-               && ${MV} ${WRKSRC}/clustalw.c.tmp ${WRKSRC}/clustalw.c
-
-do-install:
-       ${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${DESTDIR}${PREFIX}/bin
-       ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/clustalw
-       for f in clustalv.doc clustalw.doc clustalw.ms clustalw_help; do \
-               ${INSTALL_DATA} ${WRKSRC}/$$f \
-                       ${DESTDIR}${PREFIX}/share/doc/clustalw; \
-       done
-
 .include "../../mk/bsd.pkg.mk"
diff -urN clustalw/PLIST clustalw.new/PLIST
--- clustalw/PLIST      2009-06-15 01:34:33.000000000 +0800
+++ clustalw.new/PLIST  2010-06-01 05:36:12.000000000 +0800
@@ -1,6 +1,2 @@
-@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $
-bin/clustalw
-share/doc/clustalw/clustalv.doc
-share/doc/clustalw/clustalw.doc
-share/doc/clustalw/clustalw.ms
-share/doc/clustalw/clustalw_help
+@comment $NetBSD$
+bin/clustalw2
diff -urN clustalw/distinfo clustalw.new/distinfo
--- clustalw/distinfo   2005-02-23 05:28:55.000000000 +0800
+++ clustalw.new/distinfo       2010-06-01 05:39:04.000000000 +0800
@@ -1,7 +1,5 @@
 $NetBSD: distinfo,v 1.4 2005/02/22 21:28:55 agc Exp $

-SHA1 (clustalw1.83.UNIX.tar.gz) = 801ce911749171471b7964a1cff93c53c876c282
-RMD160 (clustalw1.83.UNIX.tar.gz) = 20c0ec7739be6747ae08220e5abf2bae412f039e
-Size (clustalw1.83.UNIX.tar.gz) = 166863 bytes
-SHA1 (patch-aa) = 96f95acb4a312c96440275ca65f7f908c9b9032f
-SHA1 (patch-ab) = 75fb21b88132bdf18e7f6bc13d1d35051a1babea
+SHA1 (clustalw-2.0.12.tar.gz) = 28290a97377be2a970de4bb2d208898848e819fa
+RMD160 (clustalw-2.0.12.tar.gz) = a9bb0deb812bfa7777c86e0835d292430c188fd9
+Size (clustalw-2.0.12.tar.gz) = 328025 bytes
diff -urN clustalw/patches/CVS/Entries clustalw.new/patches/CVS/Entries
--- clustalw/patches/CVS/Entries        2010-05-29 20:52:12.000000000 +0800
+++ clustalw.new/patches/CVS/Entries    1970-01-01 07:00:00.000000000 +0700
@@ -1,3 +0,0 @@
-/patch-aa/1.1.1.1/Wed Jul 28 20:07:01 1999//
-/patch-ab/1.1.1.1/Wed Jul 28 20:07:01 1999//
-D
diff -urN clustalw/patches/CVS/Repository clustalw.new/patches/CVS/Repository
--- clustalw/patches/CVS/Repository     2010-05-29 20:52:12.000000000 +0800
+++ clustalw.new/patches/CVS/Repository 1970-01-01 07:00:00.000000000 +0700
@@ -1 +0,0 @@
-pkgsrc/biology/clustalw/patches
diff -urN clustalw/patches/CVS/Root clustalw.new/patches/CVS/Root
--- clustalw/patches/CVS/Root   2010-05-29 20:52:12.000000000 +0800
+++ clustalw.new/patches/CVS/Root       1970-01-01 07:00:00.000000000 +0700
@@ -1 +0,0 @@
-anoncvs%anoncvs.NetBSD.org@localhost:/cvsroot
diff -urN clustalw/patches/patch-aa clustalw.new/patches/patch-aa
--- clustalw/patches/patch-aa   1999-07-29 04:07:01.000000000 +0800
+++ clustalw.new/patches/patch-aa       1970-01-01 07:00:00.000000000 +0700
@@ -1,13 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 1999/07/28 20:07:01 rh Exp $
-
---- clustalw.c.orig    Fri Jan 16 04:44:05 1998
-+++ clustalw.c Tue Feb 16 11:58:13 1999
-@@ -33,7 +33,7 @@
- #ifdef MSDOS
-         char *help_file_name = "clustalw.hlp";
- #else
--        char *help_file_name = "clustalw_help";
-+        char *help_file_name = "@PREFIX@/share/doc/clustalw/clustalw_help";
- #endif
-
- sint max_names; /* maximum length of names in current alignment file */
diff -urN clustalw/patches/patch-ab clustalw.new/patches/patch-ab
--- clustalw/patches/patch-ab   1999-07-29 04:07:01.000000000 +0800
+++ clustalw.new/patches/patch-ab       1970-01-01 07:00:00.000000000 +0700
@@ -1,14 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 1999/07/28 20:07:01 rh Exp $
-
---- amenu.c.orig       Mon Dec  8 08:49:12 1997
-+++ amenu.c    Sat Apr 10 22:07:58 1999
-@@ -13,7 +13,9 @@
- static jmp_buf jmpbuf;
- #ifndef VMS
- #ifndef AIX
-+#ifndef BADSIG
- #define BADSIG (void (*)())-1
-+#endif
- #endif
- #endif
-