2021-02-11 11:27:21 +00:00
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Thu Feb 4 03:08:07 UTC 2021 - Tina Müller <timueller+perl@suse.de>
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- updated to 1.7.8
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see /usr/share/doc/packages/perl-BioPerl/Changes
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1.7.8 2021-02-02 23:02:18-06:00 America/Chicago
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* Bio::SeqIO::interpro has been moved to a separate repository to
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deal with issues with XML::DOM::XPath bitrot [#347]
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* Pull requests:
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* Adjust Swiss-Prot FT A..B lines [#348] from @smoe
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* Update %FTQUAL_NO_QUOTE: List of qualifiers without quote [#339] from
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@hdevillers
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2019-12-09 08:31:41 +00:00
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Sun Dec 8 03:12:41 UTC 2019 - <timueller+perl@suse.de>
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- updated to 1.7.7
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see /usr/share/doc/packages/perl-BioPerl/Changes
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1.7.7 2019-12-07 13:41:36-06:00 America/Chicago
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* The program bp_chaos_plot has been removed.
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* GD is now no longer a dependency, suggestion or requirement.
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* #321 - GenBank format fix for un-quoted features, text wrapping
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* Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(),
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and a 'private' _sleep() function that mirror those from
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Bio::DB::WebDBSeqI, primarily for compliance with potential website
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restrictions for the number and frequency of queries (e.g. NCBI eUtils).
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* Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
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in last release.
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2019-09-19 15:08:24 +00:00
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-------------------------------------------------------------------
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Wed Sep 18 09:48:31 UTC 2019 - <timueller+perl@suse.de>
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- Add build dependency Gd
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- Remove deps.patch (not used anymore)
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-------------------------------------------------------------------
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Wed Sep 18 09:35:33 UTC 2019 - <timueller+perl@suse.de>
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- updated to 1.7.6
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see /usr/share/doc/packages/perl-BioPerl/Changes
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1.7.6 2019-08-28 12:37:01+01:00 Europe/London
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* The program bp_classify_hits_kingdom has been removed and is
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now part of the examples documentation instead.
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* GD is now listed as a suggestion instead of a requirement. The
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bp_chaos_plot program will now work with the GD module.
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* New method Bio::Tree::Statistics::transfer_bootstrap_expectation
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to compute Transfer Bootstrap Expectation (TBE) for internal
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nodes based on the methods outlined in Lemoine et al, Nature,
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2018.
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* New method Bio::SeqIO::fasta::next_seq_fast to retrieve next
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sequence in the stream faster but not perfect.
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2019-04-03 11:33:39 +00:00
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-------------------------------------------------------------------
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Wed Apr 3 06:45:03 UTC 2019 - Stephan Kulow <coolo@suse.com>
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- updated to 1.7.5
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see /usr/share/doc/packages/perl-BioPerl/Changes
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2018-09-27 16:23:25 +00:00
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-------------------------------------------------------------------
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Thu Sep 27 16:11:06 UTC 2018 - Christian Wittmer <chris@computersalat.de>
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- fix for boo#1089992
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* nothing provides /usr/local/bin/perl
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- fix license
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- fix wrong end of line encoding (dos)
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2018-02-19 14:41:26 +00:00
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-------------------------------------------------------------------
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Wed Feb 7 16:10:23 UTC 2018 - coolo@suse.com
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- updated to 1.007002
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see /usr/share/doc/packages/perl-BioPerl/Changes
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2012-07-26 14:27:51 +00:00
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-------------------------------------------------------------------
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Thu Jul 26 13:25:33 UTC 2012 - chris@computersalat.de
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- update to 1.6.901
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- [Notes]
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* Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
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modules using Ace will also be deprecated [lds, cjfields]
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* Minor bug fix release
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* Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
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* Address Build.PL issues when DBI is not present [hartzell]
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* Skip gbxml.t and Interpro tests when modules not installed [cjfields]
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* Remove deprecated code for perl 5.14.0 compat [cjfields]
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* Due to schema changes and lack of support for older versions, support
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for NeXML 0.9 is only (very) partially implemented.
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See: https://redmine.open-bio.org/issues/3207
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- [Bug fixes]
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* [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
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docs [genehack, cjfields]
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* $VERSION for CPAN/cpanm-based installs was broken; force setting of
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module version from dist_version (probably not the best way to do this,
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but it seems to work) [rbuels, cjfields]
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- update to 1.6.900 April 14, 2011
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- [Notes]
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* This will probably be the last release to add significant features to
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core modules; subsequent releases will be for bug fixes alone.
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We are planning on a restructuring of core for summer 2011, potentially
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as part of the Google Summer of Code. This may become BioPerl 2.0.
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* Version bump represents 'just prior to v 1.7'. We may have point
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releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
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This code essentially is what is on the github master branch.
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- [New features]
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* Core code updated for perl 5.12.x [cjfields, Charle Tilford]
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* Bio::Tree refactor
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- major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
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- removal of Scalar::Util::weaken code, which was causing odd headaches
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with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
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* Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
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many others]
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* Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
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[Warren Kretzschmar]
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* Bio::SeqIO::gbxml
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- bug 2515 - new contribution [Ryan Golhar, jhannah]
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* Bio::Assembly::IO
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- support for reading Maq, Sam and Bowtie files [maj]
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- support for reading 454 GS Assembler (Newbler) ACE files [fangly]
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- bug 2483: support for writing ACE files [Joshua Udall, fangly]
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- bug 2599: support DBLINK annotation in GenBank files [cjfields]
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- bug 2726: reading/writing granularity: whole scaffold or one contig
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at a time [Joshua Udall, fangly]
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* Bio::OntologyIO
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- Added parsing of xrefs to OBO files, which are stored as secondary
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dbxrefs of the cvterm [Naama Menda]
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- General Interpro-related code refactors [dukeleto, rbuels, cjfields]
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* PAML code updated to work with PAML 4.4d [DaveMessina]
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- [Bug fixes]
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* [3198] - sort tabular BLAST hits by score [DaveMessina]
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* a lot of BUG fixes, please see Changes file for more info
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- remove obsolete Build patch
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- remove Authors from description
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- add deps patch and send upstream
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2010-12-01 13:38:14 +00:00
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-------------------------------------------------------------------
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Wed Dec 1 13:30:46 UTC 2010 - coolo@novell.com
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- switch to perl_requires macro
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2010-08-21 20:16:05 +00:00
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-------------------------------------------------------------------
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Mon Aug 16 15:02:25 UTC 2010 - chris@computersalat.de
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- enabled some more optional tests
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o Algorithm::Munkres, Convert::Binary::C, GraphViz,
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PostScript::TextBlock, Spreadsheet::ParseExcel
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-------------------------------------------------------------------
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Wed Aug 4 16:11:26 UTC 2010 - chris@computersalat.de
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- add Build patch
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o do not try to connect CPAN ;)
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- added recommended pkgs
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o + BuildRequires (recommended) --with test
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-------------------------------------------------------------------
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Mon Aug 2 21:13:45 UTC 2010 - chris@computersalat.de
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- initial package 1.6.1
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* created by cpanspec 1.78
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