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 1.8.6 or earlier

(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

(WONT_FIX) In some cases, temporary files and directories may not be removed because of the lack of FileUtils.remove_entry_secure.

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.

(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.

(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.

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.

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

Bio::UniProtKB

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

Bio::PDB

Bio::PDB should be updated to follow PDB format version 3.3.

Bio::Blast::Report

NCBI announces that that they are makeing a new version of BLAST XML data format. BioRuby should support it.

Bio::Blast::Default::Report

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

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.

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.