bio 1.4.2 → 1.4.3

data/KNOWN_ISSUES.rdoc

@@ -1,5 +1,5 @@
 = KNOWN_ISSUES.rdoc - Known issues and bugs in BioRuby
-Copyright:: Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>
+Copyright:: Copyright (C) 2009-2012 Naohisa Goto <ng@bioruby.org>
 License::   The Ruby License
 
 = Known issues and bugs in BioRuby
@@ -15,7 +15,7 @@ they are not BioRuby's issues and/or it is very difficult to fix them.
 === Ruby 1.9.1 or later
 
 Some classes/modules/methods still may not work or may return incorrect
-results in Ruby 1.9.1, especially those not covered by the unit tests.
+results in Ruby 1.9.X, especially those not covered by the unit tests.
 
 ==== String encodings
 
@@ -66,6 +66,48 @@ deprecated in RubyGems 0.9.0 and removed in RubyGems 1.0.1.
   require 'rubygems'
   require_gem 'bio'
 
+=== JRuby
+
+On JRuby, errors may be raised due to the following unfixed bugs in JRuby.
+
+* {JRUBY-6195}[http://jira.codehaus.org/browse/JRUBY-6195] Process.spawn
+  (and related methods) ignore option hash
+* {JRUBY-6818}[http://jira.codehaus.org/browse/JRUBY-6818] Kernel.exec,
+  Process.spawn (and IO.popen etc.) raise error when program is an array
+  containing two strings
+
+(WONT_FIX) With older version of JRuby, you may be bothered by the following
+bugs that have already been fixed in the head of JRuby.
+
+* {JRUBY-6658}[http://jira.codehaus.org/browse/JRUBY-6658] Problem when
+  setting up an autoload entry, defining a class via require, then redefining
+  the autoload entry
+* {JRUBY-6666}[http://jira.codehaus.org/browse/JRUBY-6666] Open3.popen3
+  failing due to missing handling for [path, argv[0]] array
+* {JRUBY-6819}[http://jira.codehaus.org/browse/JRUBY-6819]
+  java.lang.ArrayIndexOutOfBoundsException in String#each_line
+
+(WONT_FIX) Due to JRUBY-5678 (resolved issue) and the difference of behavior
+between CRuby and JRuby written in the comments of the issue tracking page,
+when running BioRuby on JRuby with sudo or root rights, TMPDIR environment
+variable should be set to a directory that is not world-writable. Currently,
+the workaround is needed for running BioRuby tests with JRuby on Travis-CI.
+
+* {JRUBY-5678}[http://jira.codehaus.org/browse/JRUBY-5678] tmpdir cannot
+  be delete when jruby has sudo/root rights
+
+=== Rubinius
+
+According to Travis-CI, unit tests have failed on 1.9 mode of Rubinius.
+
+(WONT_FIX) With older version of Rubinius, you may be bothered by the
+following bugs that have already been fixed in the head of Rubinius.
+
+* {Rubinius Issue #1693}[https://github.com/rubinius/rubinius/issues/1693]
+  String#split gives incorrect output when splitting by /^/
+* {Rubinius Issue #1724}[https://github.com/rubinius/rubinius/issues/1724]
+  Creating Struct class with length attribute
+
 == 2. OS and/or architecture-dependent issues
 
 === Microsoft Windows
@@ -104,6 +146,14 @@ Windows 95/98/98SE/ME because of the limitation of COMMAND.COM.
 
 == 3. Known issues and bugs in BioRuby
 
+=== DDBJ Web API related classes (Bio::DDBJ::*, Bio::BLAST::Remote::DDBJ)
+
+The DDBJ Web API is stopping after their system replacement in March 2012.
+(See the announcement though it is written only in Japanese:
+http://www.ddbj.nig.ac.jp/replace/rp120601-j.html)
+Due to the stop of the DDBJ Web API, Bio::DDBJ::* and Bio::BLAST::Remote::DDBJ
+which are using the web API can not be used.
+
 === Bio::Ensembl
 
 Due to the renewal of Ensembl web site, Bio::Ensembl does not work for
@@ -135,6 +185,15 @@ because of the growth of the data size.
 Bio::SPTR should be updated to follow UniProtKB format changes described
 in http://www.uniprot.org/docs/sp_news.htm .
 
+=== http://bioruby.org/cgi-bin/biofetch.rb and Bio::Fetch.query
+
+BioRuby's default BioFetch server http://bioruby.org/cgi-bin/biofetch.rb is
+down for years. Please use other server, such as EBI Dbfetch
+(http://www.ebi.ac.uk/Tools/dbfetch/dbfetch).
+
+Due to the stop of the http://bioruby.org/cgi-bin/biofetch.rb service,
+Bio::Fetch.query always raises error.
+
 == 4. Compatibility issues with other libraries/extensions
 
 === ActiveRecord
@@ -147,6 +206,12 @@ know which version is suitable.
 BioRuby Shell on Web uses Ruby on Rails, but the author of the document does
 not know which version is suitable.
 
+==== SOAP4R with Ruby 1.9
+
+soap4r-ruby1.9 may raise "ununitialized constant XML::SaxParser" error with
+some combinations of XML parser libraries. It seems this is a bug of
+soap4r-ruby1.9.
+
 == 5. Historical descriptions
 
 === CVS

data/README.rdoc

@@ -2,6 +2,7 @@
 = README.rdoc - README for BioRuby
 Copyright:: Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>,
             Copyright (C) 2008      Jan Aerts <jandot@bioruby.org>
+            Copyright (C) 2011-2012 Naohisa Goto <ng@bioruby.org>
 License::   The Ruby License
 * The above statement is limited to this file. See below about BioRuby's
   copyright and license.
@@ -9,7 +10,7 @@ License::   The Ruby License
 
 = BioRuby
 
-Copyright (C) 2001-2011 Toshiaki Katayama <k@bioruby.org>
+Copyright (C) 2001-2012 Toshiaki Katayama <k@bioruby.org>
 
 BioRuby is an open source Ruby library for developing bioinformatics
 software.  Object oriented scripting language Ruby has many features
@@ -35,13 +36,16 @@ services including KEGG API can be easily utilized by BioRuby.
 
 == FOR MORE INFORMATION
 
+See RELEASE_NOTES.rdoc for news and important changes in this version.
+
 === Documents in this distribution
 
-==== General information
+==== Release notes, important changes and issues
 
 README.rdoc:: This file. General information and installation procedure.
 RELEASE_NOTES.rdoc:: News and important changes in this release.
 KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
+doc/RELEASE_NOTES-1.4.2.rdoc:: News and incompatible changes from 1.4.1 to 1.4.2.
 doc/RELEASE_NOTES-1.4.1.rdoc:: News and incompatible changes from 1.4.0 to 1.4.1.
 doc/RELEASE_NOTES-1.4.0.rdoc:: News and incompatible changes from 1.3.1 to 1.4.0.
 doc/Changes-1.3.rdoc:: News and incompatible changes from 1.2.1 to 1.3.0.
@@ -56,6 +60,7 @@ doc/KEGG_API.rd:: Documents about KEGG API, including usage of Bio::KEGG::API.
 ==== BioRuby development
 
 ChangeLog:: History of changes.
+doc/ChangeLog-before-1.4.2:: changes before 1.4.2.
 doc/ChangeLog-before-1.3.1:: changes before 1.3.1.
 README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
 
@@ -65,6 +70,9 @@ doc/Tutorial.rd.ja:: BioRuby Tutorial written in Japanese.
 doc/Tutorial.rd.ja.html:: HTML version of Tutorial.rd.ja.
 doc/KEGG_API.rd.ja:: Japanese translation of KEGG_API.rd.
 
+==== Sample codes
+
+In sample/, There are many sample codes and demo scripts.
 
 === WWW
 
@@ -107,38 +115,54 @@ and can be obtained by the following procedure:
 == REQUIREMENTS
 
 * Ruby 1.8.6 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
-  * Ruby 1.8.7-p352 or later is recommended.
-  * Not yet fully ready with Ruby 1.9, although many components can now work
-    in Ruby 1.9.1 and Ruby 1.9.2.
+  * Ruby 1.9.3-p194 or later, or Ruby 1.8.7-p358 or later is recommended.
+  * See KNOWN_ISSUES.rdoc for Ruby version specific problems.
 
 
 == OPTIONAL REQUIREMENTS
 
 Some optional libraries can be utilized to extend BioRuby's functionality.
-If your needs meets the following conditions, install them from the "Ruby
-Application Archive" at http://raa.ruby-lang.org/, RubyForge at
-http://rubyforge.org/, or the following web sites.
+If your needs meets the following conditions, install them by using RubyGems,
+or download and install from the "Ruby Application Archive" (RAA) at
+http://raa.ruby-lang.org/, RubyForge at http://rubyforge.org/, GitHub at
+http://github.com/, or the following web sites.
 
 For faster parsing of the BLAST XML output format:
 
 * {RAA:xmlparser}[http://raa.ruby-lang.org/project/xmlparser/]
+  * For Ruby 1.8: {gem install xmlparser}[http://rubygems.org/gems/xmlparser]
+  * For Ruby 1.9: http://www.yoshidam.net/Ruby.html#xmlparser
+  * In both cases, {The Expat XML Parser}[http://expat.sourceforge.net/]
+    and C compiler will be required.
 
 Creating faster flatfile index using Berkley DB:
 
-* {RAA:bdb}[http://raa.ruby-lang.org/project/bdb/]
-
+* {GitHub:ruby-bdb}[https://github.com/knu/ruby-bdb]
+  (which took over {RAA:bdb}[http://raa.ruby-lang.org/project/bdb/])
+  (No RubyGems available)
+  * {Oracle Berkeley DB}[http://www.oracle.com/technetwork/database/berkeleydb/index.html] and C compiler will be required.
+  
 Accessing BioSQL database created by other Open Bio* libraries:
 
-* {RubyForge:ActiveRecord}[http://rubyforge.org/projects/activerecord/]
-  and at least one driver (or adapter) from
-  {RubyForge:MySQL/Ruby}[http://rubyforge.org/projects/mysql-ruby/],
-  {RubyForge:postgres-pr}[http://rubyforge.org/projects/postgres-pr], or
-  {RubyForge:ActiveRecord Oracle enhanced adapter}[http://rubyforge.org/projects/oracle-enhanced/].
+* {gem install activerecord}[http://rubygems.org/gems/activerecord]
+  and at least one driver (or adapter):
+  * {gem install mysql}[http://rubygems.org/gems/mysql] or
+    {gem install mysql2}[http://rubygems.org/gems/mysql2]
+  * {gem install pg}[http://rubygems.org/gems/pg]
+  * {gem install sqlite-ruby}[http://rubygems.org/gems/sqlite-ruby] or
+    {gem install sqlite3}[http://rubygems.org/gems/sqlite3]
+  * {gem install activerecord-oracle_enhanced-adapter}[http://rubygems.org/gems/activerecord-oracle_enhanced-adapter]
 
 For parsing PhyloXML format files:
 
-* {RubyForge:libxml-ruby}[http://libxml.rubyforge.org/] (Ruby language
-  bindings for the {GNOME Libxml2 XML toolkit}[http://xmlsoft.org/])
+* {gem install libxml-ruby}[http://rubygems.org/gems/libxml-ruby]
+  * {GNOME Libxml2 XML toolkit}[http://xmlsoft.org/] and C compiler will be
+    required.
+
+(Only for Ruby 1.9.x) For using SOAP web services e.g. KEGG API:
+
+* {gem install soap4r-ruby1.9}[https://rubygems.org/gems/soap4r-ruby1.9]
+  * For Ruby 1.8.x, SOAP4R is bundled within the Ruby 1.8.x release.
 
 
 == INSTALL
@@ -147,7 +171,7 @@ For parsing PhyloXML format files:
 
 If you are using RubyGems, just type
 
-  % gems install bio
+  % gem install bio
 
 Alternatively, manually download bio-X.X.X.gem from 
 http://rubyforge.org/projects/bioruby/ and install it by using gems command.
@@ -180,17 +204,46 @@ The options "config", "setup", and "install" are still available.
   % su
   # ruby setup.rb install
 
-You can run tests by
-
-  % ruby setup.rb test
-
-and run
+You can run
 
   % ruby setup.rb --help
 
 for more details.
 
 
+=== Running self-test
+
+To check if bioruby works fine on a machine, self-test codes are bundled.
+Note that some tests may need internet connection.
+
+To run tests,
+
+ % ruby test/runner.rb
+
+If you are using Ruby 1.8.x and you want to use components installed by using
+RubyGems, explicit loading of RubyGems may be needed.
+
+ % ruby -rubygems test/runner.rb
+
+Alternatively, testrb, the test runner command of ruby, can be used.
+
+ % testrb test/
+
+With testrb, you can select tests to run, for example,
+
+ % testrb test/unit
+
+For those familiar with Rake,
+
+ % rake test
+
+also works.
+
+Before reporting test failure, please check KNOWN_ISSUES.rdoc about known
+platform-dependent issues.  We are happy if you write patches to solve the
+issues.
+
+
 == SETUP
 
 If you want to use the OBDA (Open Bio Database Access) to obtain database
@@ -255,6 +308,19 @@ under different license. For example, setup.rb which comes from
 (http://i.loveruby.net/en/projects/setup/) is licensed under LGPL 2.1.
 
 
+== REFERENCE
+
+If you use BioRuby in academic research, please consider citing the following
+publication.
+
+* BioRuby: Bioinformatics software for the Ruby programming language.
+  Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and 
+  Toshiaki Katayama.
+  Bioinformatics (2010) 26(20): 2617-2619.
+  * {doi: 10.1093/bioinformatics/btq475}[http://bioinformatics.oxfordjournals.org/content/26/20/2617]
+  * {PMID: 20739307}[http://www.ncbi.nlm.nih.gov/pubmed/20739307]
+
+
 == CONTACT
 
 Current staff of the BioRuby project can be reached by sending e-mail

data/README_DEV.rdoc

@@ -2,6 +2,7 @@
 
 Copyright::  Copyright (C) 2005, 2006 Toshiaki Katayama <k@bioruby.org>
 Copyright::  Copyright (C) 2006, 2008 Jan Aerts <jandot@bioruby.org>
+Copyright::  Copyright (C) 2011       Naohisa Goto <ng@bioruby.org>
 
 = HOW TO CONTRIBUTE TO THE BIORUBY PROJECT?
 
@@ -13,8 +14,9 @@ such as:
 * Add and correct documentation
 * Develop code for new features, etc.
 
-All of these are welcome!  However, this document describes the last option,
-how to contribute your code to the BioRuby distribution.
+All of these are welcome!  This document mainly focuses on the last option,
+how to contribute your code to the BioRuby distribution. This may also be
+helpful when you send large patches for existing codes.
 
 We would like to include your contribution as long as the scope of
 your module meets the field of bioinformatics.
@@ -25,6 +27,46 @@ Bioruby is now under git source control at http://github.com/bioruby/bioruby.
 There are two basic ways to contribute: with patches or pull requests. Both are
 explained on the bioruby wiki at http://bioruby.open-bio.org/wiki.
 
+=== Preparation before sending patches or pull requests
+
+Before sending patches or pull requests, rewriting history and reordering or
+selecting patches are recommended. See "Creating the perfect patch series"
+in the Git User's Manual.
+http://www.kernel.org/pub/software/scm/git/docs/user-manual.html#patch-series
+
+=== Sending your contribution
+
+==== With patches
+
+You can send patches with git-format-patch. For a smaller change, unified
+diff (diff -u) without using git can also be accepted.
+
+==== With pull requests
+
+We are happy if your commits can be pulled with fast-forward. For the purpose,
+using git-rebase before sending pull request is recommended. See "Keeping a
+patch series up to date using git rebase" in the Git User's Manual.
+http://www.kernel.org/pub/software/scm/git/docs/user-manual.html#using-git-rebase
+
+=== Notes for the treatment of contributions in the blessed repository
+
+==== Merging policy
+
+We do not always merge your commits as is.  We may edit, rewrite, reorder,
+select, and/or mix your commits before and/or after merging to the blessed
+repository.
+
+==== Git commit management policy
+
+We want to keep the commit history linear as far as possible, because it is
+easy to find problems and regressions in commits.  See "Why bisecting merge
+commits can be harder than bisecting linear history" in the Git User's Manual.
+http://www.kernel.org/pub/software/scm/git/docs/user-manual.html#bisect-merges
+
+Note that the above policy is only for the main 'blessed' repository, and it
+does not aim to restrict each user's fork.
+
+
 = LICENSE
 
 If you would like your module to be included in the BioRuby distribution,
@@ -50,6 +92,11 @@ You will need to follow the typical coding styles of the BioRuby modules:
 * Use 2 spaces for indentation.
 * Don't replace spaces to tabs.
 
+== Parenthesis in the method definition line should be written
+
+* Good: <tt>def example(str, ary)</tt>
+* Discouraged: <tt>def example str, ary</tt>
+
 == Comments
 
 Don't use <tt>=begin</tt> and <tt>=end</tt> blocks for comments.  If you need to
@@ -202,6 +249,24 @@ format of this information is as follows:
 
 Attribute accessors can be preceded by a short description.
 
+  # P-value (Float)
+  attr_reader :pvalue
+
+For writing rdoc documentation, putting two or more attributes in a line
+(such as <tt>attr_reader :evalue, :pvalue</tt>) is strongly discouraged.
+
+Methods looks like attributes can also be preceded by a short description.
+
+  # Scientific name (String)
+  def scientific_name
+    #...
+  end
+
+  # Scientific name (String)
+  def scientific_name=(str)
+    #...
+  end
+
 == Exception handling
 
 Don't use
@@ -211,6 +276,12 @@ Don't use
 in your code. Instead, try to avoid printing error messages. For fatal errors,
 use +raise+ with an appropriate message.
 
+Kernel#warn can only be used to notice incompatible changes to programmers.
+Typically it may be used for deprecated or obsolete usage of a method.
+For example,
+
+  warn "The Foo#bar method is obsoleted. Use Foo#baz instead."
+
 == Testing code should use 'test/unit'
 
 Unit tests should come with your modules by which you can assure what
@@ -283,3 +354,23 @@ a new module or making changes on existing modules.
 Finally, please maintain the code you've contributed. Please let us know (on 
 the bioruby list) before you commit, so that users can discuss on the change.
 
+= RUBY VERSION and IMPLEMENTATION
+
+We are mainly using Ruby MRI (Matz' Ruby Implementation, or Matz' Ruby
+Interpreter).  Please confirm that your code is running on current stable
+release versions of Ruby MRI.
+
+We are very happy if your code can run on both Ruby 1.8.x and 1.9.x.
+Note that Ruby 1.9.0 should be ignored because it was discontinued.
+Ruby 1.8.5 or earlier versions can also be ignored. See README.rdoc and
+RELEASE_NOTES.rdoc for recommended Ruby versions.
+
+It is welcome to support JRuby, Rubinius, etc, in addition to Ruby MRI.
+
+Of course, it is strongly encouraged to write code that is not affected by
+differences between Ruby versions and/or implementations, as far as possible.
+
+= OS and ARCHITECTURE
+
+We hope BioRuby can be run on both UNIX (and UNIX-like OS) and Microsoft
+Windows.

data/RELEASE_NOTES.rdoc

@@ -1,132 +1,204 @@
-= BioRuby 1.4.2 RELEASE NOTES
+= BioRuby 1.4.3 RELEASE NOTES
 
-A lot of changes have been made to the BioRuby 1.4.2 after the version 1.4.1
+A lot of changes have been made to the BioRuby 1.4.3 after the version 1.4.2
 is released. This document describes important and/or incompatible changes
-since the BioRuby 1.4.1 release.
+since the BioRuby 1.4.2 release.
 
 For known problems, see KNOWN_ISSUES.rdoc.
 
 == New features
 
-=== Speed-up of Bio::RestrictionEnzyme::Analysis.cut
+=== Bio::KEGG::KGML
 
-The running speed of Bio::RestrictionEnzyme::Analysis.cut is significantly
-increased. The new code is 50 to 80 fold faster than the previous code
-when cutting 1Mbp sequence running on Ruby 1.9.2p180. The code is written
-by Tomoaki NISHIYAMA and Naohisa Goto.
+* New class Bio::KEGG::KGML::Graphics for storing a graphics element.
+  In the instance of the class, "coords" attribute is now available.
+* New class Bio::KEGG::KGML::Substrate for storing a substrate element.
+* New class Bio::KEGG::KGML::Product for storing a product element.
+* New method Bio::KEGG::KGML::Reaction#id.
+* Improve RDoc documentation.
+* Unit tests are added.
+* There are incompatible changes. See Incompatible changes below.
 
-=== New classes Bio::DDBJ::REST, REST interface for DDBJ web service
+== Improvements
 
-For DDBJ Web API for Biology (WABI) web service, in additon to SOAP, REST
-(REpresentational State Transfer) interface is added as Bio::DDBJ::REST.
-Currently, only selected APIs are implemented.
+=== Portability running on JRuby and Rubinius
 
-=== Bio::Blast with remote DDBJ server uses REST instead of SOAP
+Many failures and errors running on JRuby and Rubinius are resolved.
+Some of them are due to BioRuby bugs, and some of them are due to JRuby or
+Rubinius bugs. Artem Tarasov reported bugs in BioRuby and submitted bug
+reports to Rubinius. Clayton Wheeler and Naohisa Goto fixed bugs in BioRuby
+and submitted bug reports to JRuby.
 
-Bio::Blast with remote DDBJ server uses REST instead of SOAP, because
-Soap4r (SOAP library for Ruby) does not work well with Ruby 1.9.
-We can now use remote DDBJ BLAST server with Ruby 1.9.
+=== Testing on Travis CI
 
-=== Tutorial is updated
-
-The Tutorial.rd is updated by Pjotr Prins and Michael O'Keefe.
-
-=== Many unit tests are added
-
-Added many unit tests for Bio::GenBank, Bio::GenPept, Bio::NBRF, Bio::PDB
-and so on. Most of them are developed by Kazuhiro Hayashi during the
-Google Summer of Code 2010.
-
-=== Other new features
-
-* New method Bio::Fastq#to_s for convenience. Note that the use of the method
-  may cause loss of performance. To get each input sequence entry as-is,
-  consider using Bio::FlatFile#entry_raw. To output fastq format data,
-  consider using Bio::Sequence#output(:fastq).
-* New methods Bio::NCBI::REST::EFetch.nucleotide and protein,
-  to get data from "nucleotide" and "protein" database respectively.
-  Because NCBI changed not to accept "gb" format for the database
-  "sequence", the two new methods are added for convenience.
-* In BioRuby Shell, efetch method uses the above new methods.
-* In GenomeNet remote BLAST execution, database "mine-aa" and "mine-nt"
-  with KEGG organism codes are now supported.
-* Support for Ruby 1.9.2 / 1.9.3 is improved.
+BioRuby is now using Travis CI (http://travis-ci.org/), a hosted continuous
+integration service for the open source community.
 
 == Bug fixes
 
-=== Bio::Blast
-
-* Failure of remote BLAST execution is fixed, due to the changes in GenomeNet
-  and DDBJ.
-* When executing remote BLAST with "genomenet" server, options "-b" and "-v"
-  are now correctly used to limit the number of hits to be reported.
-
-=== Bio::SPTR (Bio::UniProt)
+=== Strange behavior related with "circular require" is fixed
 
-* Due to the UniProtKB format changes, ID, DE, and WEB RESOURCE of CC lines
-  were not correctly parsed. See also below about incompatible change of
-  the fix.
+Fixed: In previous versions, some bioruby files may be required more than
+two times, and this sometimes causes strange behavior, depending on the
+order of files in the disk.  In particular, unit tests running on JRuby
+sometimes crashes with strange errors. In BioRuby 1.4.3, almost all require
+and autoload lines are revised and are changed to avoid circular require.
+This also fixes crash on JRuby due to JRuby's autoload bug.
 
 === Other bug fixes
 
-* Bio::Reference#pubmed_url is updated to follow recent NCBI changes.
-* Fixed: Bio::Newick#reparse failure.
-* Fixed: In Bio::MEDLINE#reference, doi field should be filled.
-* Fixed: Bio::Reference#endnote fails when url is not set.
-* Fixed: Bio::FastaFormat#query passes nil to the given factory object.
-* Fixed: In BioRuby Shell, efetch() with no additional arguments fails
-  because of the NCBI site changes.
-* Fixed: In BioRuby Shell, getent() fails when EMBOSS seqret is not found.
-* Fixed: In BioRuby Shell, demo() fails due to the above two issues.
+* Fixed: Genomenet remote BLAST does not work.
+* Fixed: Bio::KEGG::KGML ignores "coords" field.
+* Fixed: Bio::NucleicAcid.to_re("s") typo
+* To suppress rare failure of chi-square equiprobability tests for
+  Bio::Sequence::Common#randomize, test code changed to retry up to 10 times
+  if the chi-square test fails.  The assertion fails if the chi-square test
+  fails 10 consecutive times, and this strongly suggests bugs in codes or in
+  the random number generator.
+* Fixed: Bio::EMBL#os raises RuntimeError. The fix includes incompatible
+  change. See below "Incompatible changes".
+* Fixed: bin/bioruby: Failed to save object with error message "can't convert
+  Symbol into String" on Ruby 1.9.
+
+== Incompatible changes and removed features
+
+=== Bio::FlatFile use binmode (binary mode) when opening a file
+
+In Bio::FlatFile.open and Bio::FlatFile.auto, binmode (binary mode) is used
+by default when opening a file, unless text mode is explicitly specified
+with open mode string or with options. Due to the change, files using CR+LF
+line separator might not be read correctly.
+
+=== Broader FASTQ file recognition
+
+Because PacBio RS sequencer may produce kilobases long reads and read buffer
+size (default 31 lines) for file format detection may not be sufficient to
+find the second id line starting with "+", the regular expression for FASTQ
+is truncated only to check the first id line starting with "@".
+
+=== Bio::KEGG::KGML
+
+* Bio::KEGG::KGML::Reaction#substrates and Bio::KEGG::KGML::Reaction#products
+  are changed to return an array containing Bio::KEGG::KGML::Substrate and
+  Bio::KEGG::KGML::Product objects, respectively. The changes enables us to
+  get ID of substrates and products that were thrown away in the previous
+  versions.
+* Most attribute methods that were different from the KGML attribute names
+  are renamed to the names compatible with the KGML attribute names. Old
+  method names are changed to aliases of them and marked as deprecated.
+  The old names will be removed in the future.
+  * Bio::KEGG::KGML::Entry#id (old name: entry_id)
+  * Bio::KEGG::KGML::Entry#type (old name: category)
+  * Bio::KEGG::KGML::Entry#entry1 (old name: node1)
+  * Bio::KEGG::KGML::Entry#entry2 (old name: node2)
+  * Bio::KEGG::KGML::Entry#type (old name: rel)
+  * Bio::KEGG::KGML::Reaction#name (old name: entry_id)
+  * Bio::KEGG::KGML::Reaction#type (old name: direction)
+* Following attribute methods are deprecated because two or more graphics
+  elements may exist in an entry element. They will be removed in the future.
+  Instead, please use instance methods of Bio::KEGG::KGML::Graphics, which
+  can be obtained from Bio::KEGG::KGML::Entry#graphics attribute.
+  * Bio::KEGG::KGML::Entry#label
+  * Bio::KEGG::KGML::Entry#shape
+  * Bio::KEGG::KGML::Entry#x
+  * Bio::KEGG::KGML::Entry#y
+  * Bio::KEGG::KGML::Entry#width
+  * Bio::KEGG::KGML::Entry#height
+  * Bio::KEGG::KGML::Entry#fgcolor
+  * Bio::KEGG::KGML::Entry#bgcolor
+
+=== Bio::EMBL#os
+
+Bio::EMBL#os, returns parser result of the EMBL OS line, no longer splits
+the content with comma, and it no longer raises error even if the OS line
+is not in the "Genus species (name)" format. The changes may affect the
+parsing of old EMBL files which contain two or more species names in an
+OS line.
+
+Note that Bio::EMBL#os returns an Array containing several Hash objects,
+and the argument is always ignored. The return value type and the meaning
+of the argument might be changed in the future.
+
+=== Tests
+
+* Tests using network connections are moved under test/network/.
+  To invoke these tests, run "rake test-network".
+* BIORUBY_TEST_LIB environment variable
+  * The directory name specified with BIORUBY_TEST_LIB is always added on the
+    top of $LOAD_PATH even if it is already included in the middle of
+    $LOAD_PATH.
+  * When BIORUBY_TEST_LIB is empty, it no longer add an empty string to
+    $LOAD_PATH.
+  * BIORUBY_TEST_LIB is ignored when BIORUBY_TEST_GEM is set.
+* BIORUBY_TEST_GEM environment variable
+  * New environment variable BIORUBY_TEST_GEM for testing installed
+    bio-X.X.X gem. Version number can be specified.
+    See the following examples with/without the version number:
+    * % env BIORUBY_TEST_GEM=1.4.2.5000 ruby test/runner.rb
+    * % env BIORUBY_TEST_GEM="" ruby test/runner.rb
+
+=== Other removed features
+
+* rdoc.zsh is removed because it have not been used for a long time.
 
-== Incompatible changes
+== Known issues
 
-=== Bio::Sequence#output(:fastq)
+The following issues are added or updated. See KNOWN_ISSUES.rdoc for other
+already known issues.
 
-In Fastq output formatter, default width value is changed from 70 to nil.
-The nil means "without wrapping". The new default behavior without wrapping
-is generally good with many recent applications that read fastq.
+=== JRuby
 
-=== Bio::SPTR CC line topic "WEB RESOURCE"
+On JRuby, errors may be raised due to the following unfixed bugs in JRuby.
 
-In the return value of Bio::SPTR#cc('WEB RESOURCE'), "NAME" and "NOTE"
-are now renamed to "Name" and "Note", respectively. The change is due to
-the UniProt format change since UniProtKB release 12.2 of 11-Sep-2007.
-(See http://www.uniprot.org/docs/sp_news.htm#rel12.2 for details.)
-Note that "Name" and "Note" are used even when parsing older format.
-The change would also affect Marshal.dump (and YAML.dump) data.
+* {JRUBY-6195}[http://jira.codehaus.org/browse/JRUBY-6195] Process.spawn
+  (and related methods) ignore option hash
+* {JRUBY-6818}[http://jira.codehaus.org/browse/JRUBY-6818] Kernel.exec,
+  Process.spawn (and IO.popen etc.) raise error when program is an array
+  containing two strings
 
-=== Bio::Blast with the remote GenomeNet server
+With older version of JRuby, you may be bothered by the following bugs that
+have already been fixed in the head of JRuby.
 
-When executing remote BLAST with "genomenet" server, options "-b" and "-v"
-are now correctly used to limit the number of hits to be reported.
-In 1.4.1 and before, "-B" and "-V" were mistakenly used for the purpose.
+* {JRUBY-6658}[http://jira.codehaus.org/browse/JRUBY-6658] Problem when
+  setting up an autoload entry, defining a class via require, then redefining
+  the autoload entry
+* {JRUBY-6666}[http://jira.codehaus.org/browse/JRUBY-6666] Open3.popen3
+  failing due to missing handling for [path, argv[0]] array
+* {JRUBY-6819}[http://jira.codehaus.org/browse/JRUBY-6819]
+  java.lang.ArrayIndexOutOfBoundsException in String#each_line
 
-=== Bio::Blast with the remote DDBJ server
+Due to JRUBY-5678 (resolved issue) and the difference of behavior between
+CRuby and JRuby written in the comments of the issue tracking page,
+when running BioRuby on JRuby with sudo or root rights, TMPDIR environment
+variable should be set to a directory that is not world-writable. Currently,
+the workaround is needed for running BioRuby tests with JRuby on Travis-CI.
 
-Bio::Blast with remote DDBJ server uses REST instead of SOAP.
+* {JRUBY-5678}[http://jira.codehaus.org/browse/JRUBY-5678] tmpdir cannot
+  be delete when jruby has sudo/root rights
 
-=== Bio::RestrictionEnzyme internal data structure change
+=== Rubinius
 
-Due to the speedup, internal data structure of the following classes
-are changed: Bio::RestrictionEnzyme::Range::SequenceRange,
-Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts,
-Bio::RestrictionEnzyme::Range::SequenceRange::Fragment.
-This indicates that Marshal.dump (and YAML.dump) data generated by older
-versions cannot be loaded by the new version, and vice versa, although
-public APIs of the classes keep compatibility.
+According to Travis-CI, unit tests have failed on 1.9 mode of Rubinius.
 
-== Known issues
+With older version of Rubinius, you may be bothered by the following bugs that
+have already been fixed in the head of Rubinius.
 
-The following issues are added or updated. See KNOWN_ISSUES.rdoc for other
-already known issues.
+* {Rubinius Issue #1693}[https://github.com/rubinius/rubinius/issues/1693]
+  String#split gives incorrect output when splitting by /^/
+* {Rubinius Issue #1724}[https://github.com/rubinius/rubinius/issues/1724]
+  Creating Struct class with length attribute
+
+=== DDBJ Web API related classes (Bio::DDBJ::*, Bio::BLAST::Remote::DDBJ)
 
-* Bio::SPTR should be updated to follow UniProtKB format changes.
-* Problems observed only with Ruby 1.8.5 or earlier will not be fixed.
-* Descriptions about very old RubyGems 0.8.11 or earlier and about CVS
-  repository are moved from README.rdoc.
+DDBJ Web API is stopping after their system replacement in March 2012.
+(See the announcement though it is written only in Japanese:
+http://www.ddbj.nig.ac.jp/replace/rp120601-j.html)
+Due to the stop of the DDBJ Web API, Bio::DDBJ::* and Bio::BLAST::Remote::DDBJ
+which are using the web API can not be used.
 
-== Other important news
+=== SOAP4R with Ruby 1.9
 
-* Required ruby version is now Ruby 1.8.6 or later (except 1.9.0).
+soap4r-ruby1.9 may raise "ununitialized constant XML::SaxParser" error with
+some combinations of XML parser libraries. It seems this is a bug of
+soap4r-ruby1.9.