[pkgsrc/trunk]: pkgsrc/biology/hmmer Update hmmer to 2.3.2. Patch provided b...

[minskim <minskim%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/ca42080f42a8
branches:  trunk
changeset: 484914:ca42080f42a8
user:      minskim <minskim%pkgsrc.org@localhost>
date:      Wed Dec 01 04:01:09 2004 +0000

description:
Update hmmer to 2.3.2.  Patch provided by David Price in PR pkg/28483.
While here, enable pkgviews installation.

Changes:
-:- hmmsearch intermittently failed on Swissprot searches, on some
    platforms (reports on AMD/Linux; Mac OS/X). (#h25)
-:- hmmpfam memory allocation strategy did not guarantee RAMLIMIT,
    and could explode to very large allocations when searching
    with large sequences. (#h26)
-:- technical improvements in handing dsq's (digitized sequences);
    "bug" has no visible effects, except when compiling on
    different platforms. (#h27)
-:- typo fix in P7Forward() recursion; typo may have had minor
    effect on calculated scores. (#h28)
-:- hmmalign now includes --outformat and --oneline option for
    specifying different output alignment formats than the default
    Stockholm.

diffstat:

 biology/hmmer/Makefile |  9 +++++----
 biology/hmmer/distinfo |  6 +++---
 2 files changed, 8 insertions(+), 7 deletions(-)

diffs (36 lines):

diff -r 9af0895858d1 -r ca42080f42a8 biology/hmmer/Makefile
--- a/biology/hmmer/Makefile    Wed Dec 01 03:51:22 2004 +0000
+++ b/biology/hmmer/Makefile    Wed Dec 01 04:01:09 2004 +0000
@@ -1,15 +1,16 @@
-# $NetBSD: Makefile,v 1.5 2004/08/16 02:47:49 ben Exp $
+# $NetBSD: Makefile,v 1.6 2004/12/01 04:01:09 minskim Exp $
 #
 
-DISTNAME=              hmmer-2.3.1
+DISTNAME=              hmmer-2.3.2
 CATEGORIES=            biology
-MASTER_SITES=          ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.1/
+MASTER_SITES=          ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/
 
 MAINTAINER=            hdp%cs.nmsu.edu@localhost
 HOMEPAGE=              http://hmmer.wustl.edu/
 COMMENT=               Implementation of profile HMM software for protein sequence analysis
 
-WRKSRC=                        ${WRKDIR}/hmmer-2.3.1
+PKG_INSTALLATION_TYPES=        overwrite pkgviews
+
 USE_BUILDLINK3=                yes
 GNU_CONFIGURE=         yes
 
diff -r 9af0895858d1 -r ca42080f42a8 biology/hmmer/distinfo
--- a/biology/hmmer/distinfo    Wed Dec 01 03:51:22 2004 +0000
+++ b/biology/hmmer/distinfo    Wed Dec 01 04:01:09 2004 +0000
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.3 2004/08/23 14:37:04 ben Exp $
+$NetBSD: distinfo,v 1.4 2004/12/01 04:01:09 minskim Exp $
 
-SHA1 (hmmer-2.3.1.tar.gz) = bf6a3ec56c24332d7e66d6ce8865de1d72dce01f
-Size (hmmer-2.3.1.tar.gz) = 1023122 bytes
+SHA1 (hmmer-2.3.2.tar.gz) = aa34cb97cbc43ff3bd92dd111ba5677298fe2d40
+Size (hmmer-2.3.2.tar.gz) = 1024933 bytes
 SHA1 (patch-aa) = e443df78be8036bb8e58567ae9e9f734f8b6ae99