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KNOWN_ISSUES.rdoc describes known issues and bugs in current BioRuby
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= KNOWN_ISSUES.rdoc - Known issues and bugs in BioRuby | ||
Copyright:: Copyright (C) 2009 Naohisa Goto <ng@bioruby.org> | ||
License:: The Ruby License | ||
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= Known issues and bugs in BioRuby | ||
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Below are known issues and bugs in BioRuby. They will be fixed in the future, | ||
except items with (WONT_FIX) tags. | ||
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== 1. Ruby version specific issues | ||
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=== Ruby 1.9.1 or later | ||
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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. | ||
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==== String encodings | ||
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Currently, BioRuby do not care string encodings. In some cases, | ||
Encoding::CompatibilityError may be raised. | ||
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=== Ruby 1.9.0 | ||
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(WONT_FIX) Ruby 1.9.0 is NOT supported because it isn't a stable release. | ||
Use Ruby 1.9.1 or later. | ||
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=== Ruby 1.8.2 or earlier | ||
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(WONT_FIX) In some cases, temporary files and directories may not be | ||
removed because of the lack of FileUtils.remove_entry_secure. | ||
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(WONT_FIX) We will soon end support for Ruby 1.8.2. Note that Ruby | ||
1.8.1 or earlier is no longer supported, as described in README.rdoc. | ||
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=== Issues about SOAP/WSDL | ||
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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. | ||
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== 2. OS and/or architecture-dependent issues | ||
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=== Microsoft Windows | ||
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Following 4 tests failed because of the processing of file contents in the | ||
text mode. | ||
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* 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 | ||
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(WONT_FIX) Some methods that call external programs may not work in | ||
Windows 95/98/98SE/ME because of the limitation of COMMAND.COM. | ||
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== 3. Known issues and bugs in BioRuby | ||
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=== Bio::Ensembl | ||
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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") | ||
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Alternatively, consider using Ruby Ensembl API. | ||
* http://github.com/jandot/ruby-ensembl-api | ||
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