head 1.10; access; symbols pkgsrc-2023Q4:1.10.0.18 pkgsrc-2023Q4-base:1.10 pkgsrc-2023Q3:1.10.0.16 pkgsrc-2023Q3-base:1.10 pkgsrc-2023Q2:1.10.0.14 pkgsrc-2023Q2-base:1.10 pkgsrc-2023Q1:1.10.0.12 pkgsrc-2023Q1-base:1.10 pkgsrc-2022Q4:1.10.0.10 pkgsrc-2022Q4-base:1.10 pkgsrc-2022Q3:1.10.0.8 pkgsrc-2022Q3-base:1.10 pkgsrc-2022Q2:1.10.0.6 pkgsrc-2022Q2-base:1.10 pkgsrc-2022Q1:1.10.0.4 pkgsrc-2022Q1-base:1.10 pkgsrc-2021Q4:1.10.0.2 pkgsrc-2021Q4-base:1.10 pkgsrc-2021Q3:1.8.0.48 pkgsrc-2021Q3-base:1.8 pkgsrc-2021Q2:1.8.0.46 pkgsrc-2021Q2-base:1.8 pkgsrc-2021Q1:1.8.0.44 pkgsrc-2021Q1-base:1.8 pkgsrc-2020Q4:1.8.0.42 pkgsrc-2020Q4-base:1.8 pkgsrc-2020Q3:1.8.0.40 pkgsrc-2020Q3-base:1.8 pkgsrc-2020Q2:1.8.0.36 pkgsrc-2020Q2-base:1.8 pkgsrc-2020Q1:1.8.0.16 pkgsrc-2020Q1-base:1.8 pkgsrc-2019Q4:1.8.0.38 pkgsrc-2019Q4-base:1.8 pkgsrc-2019Q3:1.8.0.34 pkgsrc-2019Q3-base:1.8 pkgsrc-2019Q2:1.8.0.32 pkgsrc-2019Q2-base:1.8 pkgsrc-2019Q1:1.8.0.30 pkgsrc-2019Q1-base:1.8 pkgsrc-2018Q4:1.8.0.28 pkgsrc-2018Q4-base:1.8 pkgsrc-2018Q3:1.8.0.26 pkgsrc-2018Q3-base:1.8 pkgsrc-2018Q2:1.8.0.24 pkgsrc-2018Q2-base:1.8 pkgsrc-2018Q1:1.8.0.22 pkgsrc-2018Q1-base:1.8 pkgsrc-2017Q4:1.8.0.20 pkgsrc-2017Q4-base:1.8 pkgsrc-2017Q3:1.8.0.18 pkgsrc-2017Q3-base:1.8 pkgsrc-2017Q2:1.8.0.14 pkgsrc-2017Q2-base:1.8 pkgsrc-2017Q1:1.8.0.12 pkgsrc-2017Q1-base:1.8 pkgsrc-2016Q4:1.8.0.10 pkgsrc-2016Q4-base:1.8 pkgsrc-2016Q3:1.8.0.8 pkgsrc-2016Q3-base:1.8 pkgsrc-2016Q2:1.8.0.6 pkgsrc-2016Q2-base:1.8 pkgsrc-2016Q1:1.8.0.4 pkgsrc-2016Q1-base:1.8 pkgsrc-2015Q4:1.8.0.2 pkgsrc-2015Q4-base:1.8 pkgsrc-2015Q3:1.7.0.18 pkgsrc-2015Q3-base:1.7 pkgsrc-2015Q2:1.7.0.16 pkgsrc-2015Q2-base:1.7 pkgsrc-2015Q1:1.7.0.14 pkgsrc-2015Q1-base:1.7 pkgsrc-2014Q4:1.7.0.12 pkgsrc-2014Q4-base:1.7 pkgsrc-2014Q3:1.7.0.10 pkgsrc-2014Q3-base:1.7 pkgsrc-2014Q2:1.7.0.8 pkgsrc-2014Q2-base:1.7 pkgsrc-2014Q1:1.7.0.6 pkgsrc-2014Q1-base:1.7 pkgsrc-2013Q4:1.7.0.4 pkgsrc-2013Q4-base:1.7 pkgsrc-2013Q3:1.7.0.2 pkgsrc-2013Q3-base:1.7 pkgsrc-2013Q2:1.6.0.32 pkgsrc-2013Q2-base:1.6 pkgsrc-2013Q1:1.6.0.30 pkgsrc-2013Q1-base:1.6 pkgsrc-2012Q4:1.6.0.28 pkgsrc-2012Q4-base:1.6 pkgsrc-2012Q3:1.6.0.26 pkgsrc-2012Q3-base:1.6 pkgsrc-2012Q2:1.6.0.24 pkgsrc-2012Q2-base:1.6 pkgsrc-2012Q1:1.6.0.22 pkgsrc-2012Q1-base:1.6 pkgsrc-2011Q4:1.6.0.20 pkgsrc-2011Q4-base:1.6 pkgsrc-2011Q3:1.6.0.18 pkgsrc-2011Q3-base:1.6 pkgsrc-2011Q2:1.6.0.16 pkgsrc-2011Q2-base:1.6 pkgsrc-2011Q1:1.6.0.14 pkgsrc-2011Q1-base:1.6 pkgsrc-2010Q4:1.6.0.12 pkgsrc-2010Q4-base:1.6 pkgsrc-2010Q3:1.6.0.10 pkgsrc-2010Q3-base:1.6 pkgsrc-2010Q2:1.6.0.8 pkgsrc-2010Q2-base:1.6 pkgsrc-2010Q1:1.6.0.6 pkgsrc-2010Q1-base:1.6 pkgsrc-2009Q4:1.6.0.4 pkgsrc-2009Q4-base:1.6 pkgsrc-2009Q3:1.6.0.2 pkgsrc-2009Q3-base:1.6 pkgsrc-2009Q2:1.5.0.40 pkgsrc-2009Q2-base:1.5 pkgsrc-2009Q1:1.5.0.38 pkgsrc-2009Q1-base:1.5 pkgsrc-2008Q4:1.5.0.36 pkgsrc-2008Q4-base:1.5 pkgsrc-2008Q3:1.5.0.34 pkgsrc-2008Q3-base:1.5 cube-native-xorg:1.5.0.32 cube-native-xorg-base:1.5 pkgsrc-2008Q2:1.5.0.30 pkgsrc-2008Q2-base:1.5 cwrapper:1.5.0.28 pkgsrc-2008Q1:1.5.0.26 pkgsrc-2008Q1-base:1.5 pkgsrc-2007Q4:1.5.0.24 pkgsrc-2007Q4-base:1.5 pkgsrc-2007Q3:1.5.0.22 pkgsrc-2007Q3-base:1.5 pkgsrc-2007Q2:1.5.0.20 pkgsrc-2007Q2-base:1.5 pkgsrc-2007Q1:1.5.0.18 pkgsrc-2007Q1-base:1.5 pkgsrc-2006Q4:1.5.0.16 pkgsrc-2006Q4-base:1.5 pkgsrc-2006Q3:1.5.0.14 pkgsrc-2006Q3-base:1.5 pkgsrc-2006Q2:1.5.0.12 pkgsrc-2006Q2-base:1.5 pkgsrc-2006Q1:1.5.0.10 pkgsrc-2006Q1-base:1.5 pkgsrc-2005Q4:1.5.0.8 pkgsrc-2005Q4-base:1.5 pkgsrc-2005Q3:1.5.0.6 pkgsrc-2005Q3-base:1.5 pkgsrc-2005Q2:1.5.0.4 pkgsrc-2005Q2-base:1.5 pkgsrc-2005Q1:1.5.0.2 pkgsrc-2005Q1-base:1.5 pkgsrc-2004Q4:1.4.0.2 pkgsrc-2004Q4-base:1.4 pkgsrc-2004Q3:1.3.0.2 pkgsrc-2004Q3-base:1.3 pkgsrc-2004Q2:1.1.1.1.0.6 pkgsrc-2004Q2-base:1.1.1.1 pkgsrc-2004Q1:1.1.1.1.0.4 pkgsrc-2004Q1-base:1.1.1.1 pkgsrc-2003Q4:1.1.1.1.0.2 pkgsrc-2003Q4-base:1.1.1.1 pkgsrc-base:1.1.1.1 TNF:1.1.1; locks; strict; comment @# @; 1.10 date 2021.10.26.10.03.40; author nia; state Exp; branches; next 1.9; commitid R64ULQLy8JYkZieD; 1.9 date 2021.10.07.13.19.39; author nia; state Exp; branches; next 1.8; commitid CQ422EVgQgYxGSbD; 1.8 date 2015.11.02.18.42.21; author agc; state Exp; branches; next 1.7; commitid QWWynLrDLYuI4yHy; 1.7 date 2013.07.21.15.58.51; author wen; state Exp; branches; next 1.6; commitid xOIugSq8ytGVYlYw; 1.6 date 2009.07.16.14.53.19; author joerg; state Exp; branches; next 1.5; 1.5 date 2005.02.22.21.28.55; author agc; state Exp; branches; next 1.4; 1.4 date 2004.12.01.04.01.09; author minskim; state Exp; branches; next 1.3; 1.3 date 2004.08.23.14.37.04; author ben; state Exp; branches; next 1.2; 1.2 date 2004.08.16.02.47.49; author ben; state Exp; branches; next 1.1; 1.1 date 2003.09.26.03.52.47; author jschauma; state Exp; branches 1.1.1.1; next ; 1.1.1.1 date 2003.09.26.03.52.47; author jschauma; state Exp; branches; next ; desc @@ 1.10 log @biology: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes @ text @$NetBSD: distinfo,v 1.9 2021/10/07 13:19:39 nia Exp $ BLAKE2s (hmmer-3.0.tar.gz) = 3c1f4bc23fbf62069bb6eb137db0cd61123b38a9010aba5cf487ea47ad92acaf SHA512 (hmmer-3.0.tar.gz) = 752f06b0494a87ccd2cf6aa93e622fd02173eaa0df60df0527b3361dcaa2baf2b45a2daf0123217c0029bc9d95e505a92f1e97039eb8b7218b4c4b65ddad1db5 Size (hmmer-3.0.tar.gz) = 3952015 bytes SHA1 (patch-aa) = 8d0d3be4401590c20d102b7e0ebadcb1b6c03066 @ 1.9 log @biology: Remove SHA1 hashes for distfiles @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.8 2015/11/02 18:42:21 agc Exp $ d3 1 a3 1 RMD160 (hmmer-3.0.tar.gz) = 681967fd0d2c0104ca9e080688d9652a187a8b45 @ 1.8 log @Add SHA512 digests for distfiles for biology category. Existing SHA1 digests verified, all found to be the same on the machine holding the existing distfiles (morden). Existing SHA1 digests retained for now as an audit trail. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.7 2013/07/21 15:58:51 wen Exp $ a2 1 SHA1 (hmmer-3.0.tar.gz) = 77803c0bdb3ab07b7051a4c68c0564de31940c6d @ 1.7 log @Update to 3.0 Add LICENSE Add more distfile mirrors Upstream changelog please visit: http://selab.janelia.org/software/hmmer3/3.0/RELEASE-NOTES @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.6 2009/07/16 14:53:19 joerg Exp $ d5 1 @ 1.6 log @Fix patch-aa sum. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.5 2005/02/22 21:28:55 agc Exp $ d3 4 a6 4 SHA1 (hmmer-2.3.2.tar.gz) = aa34cb97cbc43ff3bd92dd111ba5677298fe2d40 RMD160 (hmmer-2.3.2.tar.gz) = 4bf25fc71f332849c76b0a05bca24e88241cee67 Size (hmmer-2.3.2.tar.gz) = 1024933 bytes SHA1 (patch-aa) = 1d5eae739096ec6398e7cd71b92019d76a677d50 @ 1.5 log @Add RMD160 digests in addition to the SHA1 ones. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.4 2004/12/01 04:01:09 minskim Exp $ d6 1 a6 1 SHA1 (patch-aa) = e443df78be8036bb8e58567ae9e9f734f8b6ae99 @ 1.4 log @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. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.3 2004/08/23 14:37:04 ben Exp $ d4 1 @ 1.3 log @Remove unnecessary -p following MKDIR commands. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.2 2004/08/16 02:47:49 ben Exp $ d3 2 a4 2 SHA1 (hmmer-2.3.1.tar.gz) = bf6a3ec56c24332d7e66d6ce8865de1d72dce01f Size (hmmer-2.3.1.tar.gz) = 1023122 bytes @ 1.2 log @Make hmmer honor $MKDIR for cross-platform install. Addresses pr#26650 from Georg Schwarz. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $ d5 1 a5 1 SHA1 (patch-aa) = b9b340a6ad48017100196ed78c7deb7374e39ea5 @ 1.1 log @Initial revision @ text @d1 1 a1 1 $NetBSD$ d5 1 a5 1 SHA1 (patch-aa) = c5aa41137bb339a584948b6dc88317c98b4ff6fd @ 1.1.1.1 log @Initial import of hmmer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. HMMER takes multiple sequence alignement as input and builds statistical model called "Hidden Markov Model" which can be used as a query into a sequence database to find and/or align additional homologues of the sequence family. @ text @@