bio 1.4.3.0001 → 1.5.0

data/KNOWN_ISSUES.rdoc

@@ -30,10 +30,10 @@ Encoding::CompatibilityError or "ArgumentError: invalid byte sequence in
 (WONT_FIX) Ruby 1.9.0 is NOT supported because it isn't a stable release.
 Use Ruby 1.9.1 or later.
 
-==== Ruby 1.8.5 or earlier
+==== Ruby 1.8.6 or earlier
 
-(WONT_FIX) Problems observed only with Ruby 1.8.5 or earlier will not be
-fixed. Note that Ruby 1.8.5 or earlier is no longer supported, as described
+(WONT_FIX) Problems observed only with Ruby 1.8.6 or earlier will not be
+fixed. Note that Ruby 1.8.6 or earlier is no longer supported, as described
 in README.rdoc.
 
 ==== Ruby 1.8.2 or earlier
@@ -41,12 +41,6 @@ in README.rdoc.
 (WONT_FIX) In some cases, temporary files and directories may not be
 removed because of the lack of FileUtils.remove_entry_secure.
 
-=== Issues about SOAP/WSDL
-
-SOAP4R (SOAP and WSDL implementation) is no longer bundled with Ruby 1.9.
-In addition, because of the API changes in recent SOAP4R, some
-classes/modules using SOAP4R may not work.
-
 === Problem with REXML DoS vulnerability patch before 09-Nov-2008
 
 (WONT_FIX) If you have applied a patch taken from
@@ -146,53 +140,25 @@ 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
-the latest Ensembl. For a workaround, use an archive server. For example,
-"jul2008.archive.ensembl.org" seems to be the last server before the renewal.
-  human = Bio::Ensembl.new("Homo_sapiens", "jul2008.archive.ensembl.org")
-
-Alternatively, consider using Ruby Ensembl API.
-* http://github.com/jandot/ruby-ensembl-api
-
-=== Bio::DBGET and sample/dbget
+=== Bio::UniProtKB
 
-(WONT_FIX) Because the DBGET service have not been publically available for
-a long time, we give up support for Bio::DBGET and sample/dbget. Instead,
-using Bio::TogoWS or Bio::KEGG::API is recommended.
-
-=== Bio::NCBI::SOAP
-
-It seems that Bio::NCBI::SOAP (in lib/bio/io/ncbisoap.rb) does not work
-correctly, even running on Ruby 1.8.x. Instead, use Bio::NCBI::REST.
+Bio::UniProtKB should be updated to follow UniProtKB format changes described
+in http://www.uniprot.org/docs/sp_news.htm .
 
-=== Bio::KEGG::Taxonomy and sample/demo_kegg_taxonomy.rb
+=== Bio::PDB
 
-Bio::KEGG::Taxonomy fails to parse current KEGG taxonomy data file probably
-because of the growth of the data size.
+Bio::PDB should be updated to follow PDB format version 3.3.
 
-=== Bio::SPTR
+=== Bio::Blast::Report
 
-Bio::SPTR should be updated to follow UniProtKB format changes described
-in http://www.uniprot.org/docs/sp_news.htm .
+NCBI announces that that they are makeing a new version of BLAST XML data
+format. BioRuby should support it.
 
-=== http://bioruby.org/cgi-bin/biofetch.rb and Bio::Fetch.query
+=== Bio::Blast::Default::Report
 
-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.
+Bio::Blast::Default::Report currently supports legacy BLAST only.
+It may be better to support BLAST+ text output format, although NCBI
+do not recommend to do so because the format is unstable.
 
 == 4. Compatibility issues with other libraries/extensions
 
@@ -206,12 +172,6 @@ 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

@@ -2,7 +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>
+            Copyright (C) 2011-2015 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.
@@ -31,7 +31,7 @@ analysis can be executed within the BioRuby script, and the results
 can be fully parsed to extract the portion you need.  BioRuby supports
 major biological database formats and provides many ways for accessing
 them through flatfile indexing, SQL, web services etc.  Various web
-services including KEGG API can be easily utilized by BioRuby.
+services can be easily utilized by BioRuby.
 
 
 == FOR MORE INFORMATION
@@ -45,6 +45,7 @@ See RELEASE_NOTES.rdoc for news and important changes in this version.
 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-1.4.3.rdoc:: News and incompatible changes from 1.4.2 to 1.4.3.
 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.
@@ -55,11 +56,11 @@ doc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.
 
 doc/Tutorial.rd:: BioRuby Tutorial.
 doc/Tutorial.rd.html:: HTML version of Tutorial.rd.
-doc/KEGG_API.rd:: Documents about KEGG API, including usage of Bio::KEGG::API.
 
 ==== BioRuby development
 
 ChangeLog:: History of changes.
+doc/ChangeLog-1.4.3:: changes from 1.4.2 to 1.4.3.
 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.
@@ -68,7 +69,6 @@ README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including
 
 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
 
@@ -99,13 +99,13 @@ The stable release is freely available from the BioRuby website.
 {RubyGems (packaging system for Ruby)}[http://rubygems.org/] version of
 the BioRuby package is also available for easy installation.
 
-* http://rubyforge.org/projects/bioruby/
+* https://rubygems.org/gems/bio
 
 === git
 
 If you need the latest development version, this is provided at
 
-* http://github.com/bioruby/bioruby
+* https://github.com/bioruby/bioruby
 
 and can be obtained by the following procedure:
 
@@ -114,8 +114,9 @@ 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 1.9.3-p194 or later, or Ruby 1.8.7-p358 or later is recommended.
+* Ruby 1.8.7 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
+  * Ruby 2.1.6 or later, or Ruby 2.2.2 or later is recommended.
+  * This is the final version running on Ruby 1.8, tested with Ruby1.8.7-p374.
   * See KNOWN_ISSUES.rdoc for Ruby version specific problems.
 
 
@@ -123,22 +124,20 @@ and can be obtained by the following procedure:
 
 Some optional libraries can be utilized to extend BioRuby's functionality.
 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.
+or download and install from the following web sites.
 
 For faster parsing of the BLAST XML output format:
 
-* {RAA:xmlparser}[http://raa.ruby-lang.org/project/xmlparser/]
+* {xmlparser}[https://rubygems.org/gems/xmlparser]
   * For Ruby 1.8: {gem install xmlparser}[http://rubygems.org/gems/xmlparser]
-  * For Ruby 1.9: http://www.yoshidam.net/Ruby.html#xmlparser
+  * For Ruby 1.9 or later: 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:
 
 * {GitHub:ruby-bdb}[https://github.com/knu/ruby-bdb]
-  (which took over {RAA:bdb}[http://raa.ruby-lang.org/project/bdb/])
+  (which took over {bdb}[https://github.com/ruby-bdb/bdb])
   (No RubyGems available)
   * {Oracle Berkeley DB}[http://www.oracle.com/technetwork/database/berkeleydb/index.html] and C compiler will be required.
   
@@ -159,11 +158,6 @@ For parsing PhyloXML format files:
   * {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
 
@@ -174,7 +168,7 @@ If you are using RubyGems, just type
   % gem install bio
 
 Alternatively, manually download bio-X.X.X.gem from 
-http://rubyforge.org/projects/bioruby/ and install it by using gems command.
+http://bioruby.org/archive/ and install it by using gems command.
 
 RubyGems is bundled with Ruby 1.9.1 or later. For Ruby 1.8.7 or earlier,
 download and install RubyGems from http://rubygems.org/ .
@@ -303,9 +297,9 @@ BioRuby can be freely distributed under the same terms as Ruby.
 See the file COPYING (or COPYING.ja written in Japanese).
 
 As written in the file COPYING, see the file LEGAL for files distributed
-under different license. For example, setup.rb which comes from
-{RAA:setup}[http://raa.ruby-lang.org/project/setup/] developed by Minero Aoki
-(http://i.loveruby.net/en/projects/setup/) is licensed under LGPL 2.1.
+under different license. For example, setup.rb which comes from "setup"
+developed by Minero Aoki (http://i.loveruby.net/en/projects/setup/) is
+licensed under LGPL 2.1.
 
 
 == REFERENCE

data/RELEASE_NOTES.rdoc

@@ -1,222 +1,285 @@
-= BioRuby 1.4.3.0001 RELEASE NOTES
+= BioRuby 1.5.0 RELEASE NOTES
 
-Some bug fixes have been made to the BioRuby 1.4.3.0001 after the version
-1.4.3 is released.
+A lot of changes have been made to the BioRuby 1.5.0 after the version 1.4.3
+is released. This document describes important and/or incompatible changes
+since the BioRuby 1.4.3 release.
 
-== Bug fixes
+For known problems, see KNOWN_ISSUES.rdoc.
 
-=== Ruby 2.0 support
+== NEWS
 
-* "gem install bio" failed with Ruby 2.0 or later versions.
-* lib/bio/db/gff.rb: Set script encoding to US-ASCII.
+=== Full support of Ruby 2.0.0, 2.1, and 2.2
 
-=== Other bug fixes
+Ruby 2.0.0, 2.1, and 2.2 are now recommended Ruby versions for running
+BioRuby codes.
 
-* Bio::BLAST::Default::Report parse error when subject sequence contains
-  spaces. (https://redmine.open-bio.org/issues/3385)
+=== Support of Ruby 1.8 will be stopped
 
+This release is the final BioRuby version that can be run on Ruby 1.8.
 
-= BioRuby 1.4.3 RELEASE NOTES
+=== License is updated to the new Ruby's License
 
-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 1.4.2 release.
+BioRuby is distributed under the same license as Ruby's. In October 2011,
+Ruby's License was changed from a dual license with GPLv2 to a dual license
+with 2-clause BSDL.available. Since BioRuby 1.5.0, we have updated to the
+new version of Ruby's License. For details about the license, see COPYING
+or COPYING.ja and BSDL. In addition, please do not forget to see LEGAL for
+exception files that are subjected to different licenses.
 
-For known problems, see KNOWN_ISSUES.rdoc.
+=== Semantic Versioning will be introduced
+
+We will adopt the Semantic Versioning since the next release version, which
+will be BioRuby 1.5.1. This means that BioRuby 1.5.0 are NOT subject to the
+Semantic Versioning.
+
+
+== New features and improvements
+
+=== New method Bio::FastaFormat#first_name
 
-== New features
+Bio::FastaFormat#first_name method is added to get the first word in the
+definition line. This method was proposed by Ben J. Woodcroft.
 
-=== Bio::KEGG::KGML
+=== Accuracy of Bio::SiRNA
 
-* 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.
+Accuracy of siRNA designing algorithms in Bio::SiRNA is improved,
+contributed by meso_cacase.
 
-== Improvements
+=== Speed up of Bio::ClustalW::Report
 
-=== Portability running on JRuby and Rubinius
+Running speed of Bio::ClustalW::Report is optimized, contributed by
+Andrew Grimm.
 
-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.
+=== Many warning messages are squashed
 
-=== Testing on Travis CI
+Most warning messages when running ruby with "-w" option, e.g. "assigned
+but unused variable", "instance variable @xxx not initialized", are
+suppressed. Fixes are contributed by Kenichi Kamiya, Andrew Grimm, and
+BioRuby core members.
+
+=== Refactoring of codes
+
+Many existing codes are reviewed and refactored. Patches are contributed
+by Iain Barnett, Kenichi Kamiya, and BioRuby core members.
 
-BioRuby is now using Travis CI (http://travis-ci.org/), a hosted continuous
-integration service for the open source community.
 
 == Bug fixes
 
-=== Strange behavior related with "circular require" is fixed
-
-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
-
-* 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.
+=== Bugs due to remote server changes
 
-== Known issues
+==== Bio::PubMed
+
+Bio::PubMed#search, query, and pmfetch are re-implemented by using NCBI
+E-Utilities. They were broken because unofficial API was used.
+Paul Leader reported the bug and gave discussion.
+
+==== Bio::Hinv
+
+Bio::Hinv did not work because of the API server URL is changed.
+
+==== Bio::TogoWS::REST
+
+* Bio::TogoWS::REST#search with offset and limit did not work due to
+  TogoWS server spec change about URI escape.
+* Bio::TogoWS::REST#convert did not work because of the spec change of
+  TogoWS REST API.
+
+=== Bio::Fetch
+
+Bio::Fetch with default parameters did not work because BioRuby's default
+BioFetch server had been down. We have decided not to restore the service.
+For smooth migration of codes using BioRuby's BioFetch server, we provide
+"bio-old-biofetch-emulator" gem. See below "Imcompatible changes" for details.
+
+The bug was reported and discussed by Jose Irizarry, Robert A. Heiler, and
+others.
+
+=== BioSQL
+
+* Only do gsub on bio_ref.reference.authors if it exists.
+* Missing require when generating genbank output for BioSQL sequence.
+
+Contributed by Brynjar Smari Bjarnason.
+
+=== Bugs found in data format parsers
+
+* Bio::PDB#seqres SEQRES serNum digits were extended in PDB v3.2 (2008).
+  Thanks to a researcher who sent the patch.
+* Bio::Blast::Default::Report parse error when subject sequence contains
+  spaces. Edward Rice reported the bug.
+* Bio::UniProtKB#gene_name raised NoMethodError when gene_names method
+  returns nil. It should return nil. Candidate fix sent by Jose Irizarry.
+* Bio::PhyloXML::Parser.open_uri did not return block return value when
+  giving a block.
+
+=== Other bugs
+
+* lib/bio/shell/plugin/seq.rb: String#step and #skip (extended by bioruby
+  shell) did not yield the last part of the string due to a change from
+  Ruby 1.8 to 1.9.
+* Documentation and typo fixes. Contributed by many persons, including
+  Iain Barnett and ctSkennerton.
+
+
+== Renamed features
+
+=== Bio::SPTR, Bio::UniProt, Bio::SwissProt, and Bio::TrEMBL => Bio::UniProtKB
+
+The classes for parsing UniProtKB (former SwissProt and TrEMBL) data,
+Bio::SPTR, Bio::UniProt, Bio::SwissProt, and Bio::TrEMBL, are unified into
+the new class name Bio::UniProtKB, and old names are deprecated.
+
+For keeping backward compatibility, old class names Bio::SPTR, Bio::UniProt,
+Bio::SwissProt, and Bio::TrEMBL are still available, but warning message
+will be shown when using the old class names. These old class names will be
+deleted in the future.
+
+The file contatining Bio::UniProtKB class definition is also changed to
+lib/bio/db/embl/uniprotkb.rb. For keeping backward compatibility, old
+files sptr.rb, uniprot.rb, tremble.rb are still kept, but they will be
+removed in the future.
 
-The following issues are added or updated. See KNOWN_ISSUES.rdoc for other
-already known issues.
 
-=== JRuby
+== Deprecated features
 
-On JRuby, errors may be raised due to the following unfixed bugs in JRuby.
+=== Bio::RefSeq, Bio::DDBJ
 
-* {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::RefSeq and Bio::DDBJ are deprecated because they are only an alias of
+Bio::GenBank. Warning message will be shown when loading the classes and
+initializing new instances. Please use Bio::GenBank instead.
 
-With older version of JRuby, you may be bothered by the following bugs that
-have already been fixed in the head of JRuby.
+lib/bio/db/genbank/ddbj.rb and lib/bio/db/genbank/refseq.rb which contain
+Bio::DDBJ and Bio::RefSeq, respectively, are also deprecated. For keeping
+backward compatibility, old file are still kept, but they will be removed
+in the future.
 
-* {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
 
-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.
+== Removed features
 
-* {JRUBY-5678}[http://jira.codehaus.org/browse/JRUBY-5678] tmpdir cannot
-  be delete when jruby has sudo/root rights
+=== Bio::SOAPWSDL
 
-=== Rubinius
+Bio::SOAPWSDL (lib/bio/io/soapwsdl.rb) is removed because SOAP4R
+(SOAP/WSDL library in Ruby) is no longer bundled with Ruby since Ruby 1.9.
+For Ruby 1.9 or later, some gems of SOAP4R are available, but we think they
+are not well-maintained. Moreover, many SOAP servers have been retired
+(see below). So, we give up maintaining Bio::SOAPWSDL and all SOAP client
+classes in BioRuby.
 
-According to Travis-CI, unit tests have failed on 1.9 mode of Rubinius.
+=== Bio::EBI::SOAP
+
+Bio::EBI::SOAP (lib/bio/io/ebisoap.rb) is removed because Bio::SOAPWSDL
+is removed.
+
+=== Bio::KEGG::API
+
+Bio::KEGG::API is removed because KEGG API SOAP service was discontinued in
+December 31, 2012. See http://www.kegg.jp/kegg/rest/ for the announcement
+of service discontinuation.
+
+=== Bio::DBGET
+
+Bio::DBGET is removed because it only supports old original DBGET protocols
+that was discontinued in 2004. Note that the DBGET is still available via
+the web. See http://www.genome.jp/en/gn_dbget.html for details.
+
+=== Bio::Ensembl
+
+Bio::Ensembl is removed because it does not work after the renewal of Ensembl
+web site in 2008. Instead, bio-ensembl gem which supports recent ensembl API
+is available.
+
+=== Bio::DDBJ::XML, Bio::DDBJ::REST
+
+Bio::DDBJ::XML and Bio::DDBJ::REST are removed because DDBJ Web API (WABI)
+web services were suspended in 2012 and then they were completely renewed
+with incompatible APIs in 2013.
+
+=== Bio::HGC::HiGet
+
+Bio::HGC::HiGet (lib/bio/io/higet.rb) is removed because the HiGet web server
+http://higet.hgc.jp/ have been down since 2011, and we think that the server
+will not be restored again.
+
+=== Bio::NCBI::SOAP
+
+Bio::NCBI::SOAP is removed because it always raises error during the parsing
+of WSDL files provided by NCBI. In addition, NCBI announced that the SOAP
+web service for the E-utilities will be terminated on July 1, 2015. Instead,
+Bio::NCBI::REST, REST client for the NCBI E-utility web service, is available.
+
+=== Bio::KEGG::Taxonomy
+
+Bio::KEGG::Taxonomy is removed because it does not work correctly. It raises
+error, it falls into infinite loop, or it returns apparently broken data.
+Moreover, KEGG closed public FTP site and the file "taxonomy" could only be
+obtained by paid subscribers.
+
+=== Bio.method_missing
+
+Bio.method_missing, that aims to provide shortcuts of Bio::Shell methods
+with shorter name without typing "Shell", is removed because most of the
+methods raises error mainly due to bypassing of initialization procedure.
+In addition, we now think that the use of method_missing should generally
+be avoid unless it is really necessary.
+
+=== extconf.rb
+
+extconf.rb, an alternative way to install BioRuby to the system, is removed
+because of avoiding potential confusions. Nowadays, extconf.rb is usually
+only used for building native extensions, but no native extensions are
+included in this release. Use gem or setup.rb to install BioRuby.
+
+
+== Incompatible changes
+
+Also see the above "Renamed features", "Deprecated features", and
+"Removed features" sections.
+
+=== Bio::Fetch
+
+The BioRuby default BioFetch server http://bioruby.org/cgi-bin/biofetch.rb,
+that was the default server for Bio::Fetch before BioRuby 1.4, is deprecated.
+Due to the service stop, default server URL in Bio::Fetch is removed, and
+we decide not to give any server URL by default for Bio::Fetch.
+
+As an alternative, new class Bio::Fetch::EBI which uses the EBI Dbfetch
+server is added. When changing codes form Bio::Fetch to Bio::Fetch::EBI,
+be careful of the differences of database names, default and available
+data formats between the former BioRuby BioFetch server and the EBI Dbfetch
+server.
+
+Methods directly affected are:
+
+* Bio::Fetch.new (Bio::Fetch#initialize) does not have default server URL,
+  and URL of a server must always be explicitly given as the first argument.
+* Bio::Fetch.query is removed.
+
+For the purpose running old codes, it is recommended to install
+bio-old-biofetch-emulator gem. The bio-old-biofetch-emulator gem emulates
+old BioRuby's default BioFetch server by using other existing web services.
+See https://rubygems.org/gems/bio-old-biofetch-emulator for details.
+We think many codes can run with no changes by simply installing the gem and
+adding "-r bio-old-biofetch-emulator" into the command-line when executing
+ruby.
+
+
+== Known issues
+
+The following issues are added or updated. See KNOWN_ISSUES.rdoc for other
+already 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.
+=== Bio::PDB
 
-* {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
+Bio::PDB should be updated to follow PDB format version 3.3.
 
-=== DDBJ Web API related classes (Bio::DDBJ::*, Bio::BLAST::Remote::DDBJ)
+=== Bio::Blast::Report
 
-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.
+NCBI announces that that they are makeing a new version of BLAST XML data
+format. BioRuby should support it.
 
-=== SOAP4R with Ruby 1.9
+=== Bio::Blast::Default::Report
 
-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.
+Bio::Blast::Default::Report currently supports legacy BLAST only.
+It may be better to support BLAST+ text output format, although NCBI
+do not recommend to do so because the format is unstable.