From f647982e1c3cfa2fa9b465e2d123f8228729b46d Mon Sep 17 00:00:00 2001 From: "Francisco J. Ossandon" Date: Thu, 1 May 2014 14:25:06 -0400 Subject: [PATCH] Added some changes and bugfixes --- Changes | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/Changes b/Changes index a9dac71ed..c9d6a372e 100644 --- a/Changes +++ b/Changes @@ -20,8 +20,12 @@ CPAN releases are branched from 'master'. 1.6.924 [Significant changes] + * Bug/feature issue tracking has moved to GitHub Issues: https://github.com/bioperl/bioperl-live/issues + * DB_File has been demoted from "required" to "recommended", + which should make easier for Windows users to install BioPerl + if they don't need that module. [New features] @@ -59,6 +63,15 @@ CPAN releases are branched from 'master'. [Bug fixes] + * Abstract: Fixed ActivePerl incapability of removing temporary files + because of problems closing tied filehandles [fjossandon] + * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing + because ActivePerl were producing a ".index.pag" and ".index.dir" + files instead of a single ".index" file (like Strawberry Perl). + Now those temporary files are correctly considered and deleted. [fjossandon] + * Test files: Added missing module requirements (DB_File and Data::Stag) + to several tests files that were failing because those modules were + not present. Now those test files are correctly skipped instead. [fjossandon] * Blast: Added support to changes in bl2seq from BLAST+ output, which now uses "Subject=" instead of ">" to start hit lines [yschensandiego] * Phylip: Return undef in "next_aln" at file end to avoid @@ -349,7 +362,7 @@ CPAN releases are branched from 'master'. * [3034] - AlignIO::clustal output [Bernd, DaveMessina] * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields] * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields] - * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields] + * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields] * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with PAML 4.4d [DaveMessina] * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon, @@ -369,7 +382,7 @@ CPAN releases are branched from 'master'. * [2944] - Bio::Tools::GFF score [cjfields] * [2942] - correct MapTiling output [maj] * [2939] - PDB residue insertion codes [John May, maj] - * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj] + * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj] * [2928] - GuessSeqFormat raw [maj] * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields] * [2922] - open() directive issue [cjfields] @@ -378,7 +391,7 @@ CPAN releases are branched from 'master'. * [2899] - SeqFeature::Store host issues [lstein, dbolser] * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser, cjfields] - * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields] + * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields] * [2876] - CDD search with RemoteBlast [Malcolm Cook] * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina] * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields] @@ -535,7 +548,7 @@ CPAN releases are branched from 'master'. * Bio::SeqIO::raw - add option for 'single' and 'multiple' * Bio::SeqIO::scf - - bug 2881 - fix scf round-tripping [Adam Søgren] + - bug 2881 - fix scf round-tripping [Adam Søgren] * Bio::SeqUtils - bug 2766, 2810 - copy over tags from features, doc fixes [David Jackson] -- 2.11.4.GIT