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