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authorminskim <minskim@pkgsrc.org>2004-12-01 04:01:09 +0000
committerminskim <minskim@pkgsrc.org>2004-12-01 04:01:09 +0000
commit15e9128d894332d65aa6cd713922ab7f2a34fd09 (patch)
treefbdf402073064d4caa45d5f747b25f389c9b3745 /biology/hmmer
parentcff4149cea431ed6600f7f4eb7682d45d6260c46 (diff)
downloadpkgsrc-15e9128d894332d65aa6cd713922ab7f2a34fd09.tar.gz
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 (limited to 'biology/hmmer')
-rw-r--r--biology/hmmer/Makefile9
-rw-r--r--biology/hmmer/distinfo6
2 files changed, 8 insertions, 7 deletions
diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
index 0205a9f3e31..04536081268 100644
--- a/biology/hmmer/Makefile
+++ b/biology/hmmer/Makefile
@@ -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
HOMEPAGE= http://hmmer.wustl.edu/
COMMENT= Implementation of profile HMM software for protein sequence analysis
-WRKSRC= ${WRKDIR}/hmmer-2.3.1
+PKG_INSTALLATION_TYPES= overwrite pkgviews
+
USE_BUILDLINK3= yes
GNU_CONFIGURE= yes
diff --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo
index 0ea4ec8505f..7b0f7f43c6b 100644
--- a/biology/hmmer/distinfo
+++ b/biology/hmmer/distinfo
@@ -1,5 +1,5 @@
-$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