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KNOWN_ISSUES.rdoc - Known issues and bugs in BioRuby

Copyright

Copyright (C) 2009-2012 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Known issues and bugs in BioRuby

Below are known issues and bugs in BioRuby. Patches to fix them are welcome. We hope they will be fixed in the future.

Items marked with (WONT_FIX) tags would not be fixed within BioRuby because they are not BioRuby's issues and/or it is very difficult to fix them.

1. Ruby version specific issues

Ruby 1.9.1 or later

Some classes/modules/methods still may not work or may return incorrect results in Ruby 1.9.X, especially those not covered by the unit tests.

String encodings

Currently, BioRuby do not care string encodings. In some cases, Encoding::CompatibilityError or “ArgumentError: invalid byte sequence in (encoding name)” may be raised.

End-of-life Ruby versions

Ruby 1.9.0

(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

(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 in README.rdoc.

Ruby 1.8.2 or earlier

(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 www.ruby-lang.org/en/news/2008/08/23/dos-vulnerability-in-rexml/ before 09 Nov 2008 12:40 +0900, because of the bug in the patch, parsing of Blast XML results with REXML parser may fail. The bug is already fixed and new patch is available on the above URL. Note that some Linux distributions would have incorporated the patch in their manners, and may have the same problem.

RubyGems 0.8.11 or earlier

(WONT_FIX) With very old version of RubyGems, use 'require_gem' which was deprecated in RubyGems 0.9.0 and removed in RubyGems 1.0.1.

#!/usr/bin/env ruby
require 'rubygems'
require_gem 'bio'

JRuby

On JRuby, errors may be raised due to the following unfixed bugs in JRuby.

  • JRUBY-6195 Process.spawn (and related methods) ignore option hash

  • 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 Problem when setting up an autoload entry, defining a class via require, then redefining the autoload entry

  • JRUBY-6666 Open3.popen3 failing due to missing handling for [path, argv[0]] array

  • 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 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.

2. OS and/or architecture-dependent issues

Microsoft Windows

Text mode issues

Following 4 tests failed on mswin32 (and maybe on mingw32 and bccwin32) because of the conversion of line feed codes in the text mode.

  • test_ended_pos and test_start_pos in test/unit/bio/io/test_flatfile.rb

  • test_pos in test/unit/bio/io/flatfile/test_buffer.rb

  • test_entry_pos in test/unit/bio/appl/blast/test_rpsblast.rb

This indicates that br_bioflat.rb and Bio::FlatFileIndex may create incorrect indexes on mswin32, mingw32, and bccwin32. In addition, Bio::FlatFile may return incorrect data.

String escaping of command-line arguments

After BioRuby 1.4.1, in Ruby 1.9.X running on Windows, escaping of command-line arguments are processed by the Ruby interpreter. Before BioRuby 1.4.0, the escaping is executed in Bio::Command#escape_shell_windows, and the behavior is different from the Ruby interpreter's one.

Curreltly, due to the change, test/functional/bio/test_command.rb may fail on Windows with Ruby 1.9.X.

Windows 95/98/98SE/ME

(WONT_FIX) Some methods that call external programs may not work in Windows 95/98/98SE/ME because of the limitation of COMMAND.COM.

OpenVMS, BeOS, OS/2, djgpp, Windows CE

(WONT_FIX) BioRuby may not work on these platforms.

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: 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::SPTR

Bio::SPTR should be updated to follow UniProtKB format changes described in www.uniprot.org/docs/sp_news.htm .

bioruby.org/cgi-bin/biofetch.rb and Bio::Fetch.query

BioRuby's default BioFetch server bioruby.org/cgi-bin/biofetch.rb is down for years. Please use other server, such as EBI Dbfetch (www.ebi.ac.uk/Tools/dbfetch/dbfetch).

Due to the stop of the bioruby.org/cgi-bin/biofetch.rb service, Bio::Fetch.query always raises error.

4. Compatibility issues with other libraries/extensions

ActiveRecord

BioSQL support uses ActiveRecord, but the author of the document does not know which version is suitable.

Ruby on Rails

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

For historical purposes: the anonymous CVS was provided at

and could be obtained by the following procedure.

% cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby login
CVS password: cvs (login with a password 'cvs' for the first time)
% cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby co bioruby

These may be closed without any prior notice.

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