From 06b10262be0bf797a3b133e4697e9b0955408944 Mon Sep 17 00:00:00 2001
From: Naohisa Goto <ng@bioruby.org>
Date: Mon, 26 Jan 2009 19:55:52 +0900
Subject: [PATCH] KNOWN_ISSUES.rdoc describes known issues and bugs in current
 BioRuby

---
 KNOWN_ISSUES.rdoc   | 66 +++++++++++++++++++++++++++++++++++++++++++++
 bioruby.gemspec     |  3 +++
 bioruby.gemspec.erb |  3 ++-
 3 files changed, 71 insertions(+), 1 deletion(-)
 create mode 100644 KNOWN_ISSUES.rdoc

diff --git a/KNOWN_ISSUES.rdoc b/KNOWN_ISSUES.rdoc
new file mode 100644
index 000000000..c3b33d25b
--- /dev/null
+++ b/KNOWN_ISSUES.rdoc
@@ -0,0 +1,66 @@
+= KNOWN_ISSUES.rdoc - Known issues and bugs in BioRuby
+Copyright:: Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>
+License::   The Ruby License
+
+= Known issues and bugs in BioRuby
+
+Below are known issues and bugs in BioRuby. They will be fixed in the future,
+except items with (WONT_FIX) tags.
+
+== 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 1.9.1, especially those not covered by the unit tests.
+
+==== String encodings
+
+Currently, BioRuby do not care string encodings. In some cases,
+Encoding::CompatibilityError may be raised.
+
+=== 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 1.8.2 or earlier
+
+(WONT_FIX) In some cases, temporary files and directories may not be
+removed because of the lack of FileUtils.remove_entry_secure.
+
+(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.
+
+=== 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.
+
+== 2. OS and/or architecture-dependent issues
+
+=== Microsoft Windows
+
+Following 4 tests failed because of the processing of file contents 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
+
+(WONT_FIX) Some methods that call external programs may not work in
+Windows 95/98/98SE/ME because of the limitation of COMMAND.COM.
+
+== 3. Known issues and bugs in BioRuby
+
+=== 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
+
diff --git a/bioruby.gemspec b/bioruby.gemspec
index bf61a172e..3094b81eb 100644
--- a/bioruby.gemspec
+++ b/bioruby.gemspec
@@ -15,6 +15,7 @@ Gem::Specification.new do |s|
   s.platform = Gem::Platform::RUBY
   s.files = [
     "ChangeLog",
+    "KNOWN_ISSUES.rdoc",
     "README.rdoc",
     "README_DEV.rdoc",
     "Rakefile",
@@ -229,6 +230,7 @@ Gem::Specification.new do |s|
     "lib/bio/shell/plugin/flatfile.rb",
     "lib/bio/shell/plugin/keggapi.rb",
     "lib/bio/shell/plugin/midi.rb",
+    "lib/bio/shell/plugin/ncbirest.rb",
     "lib/bio/shell/plugin/obda.rb",
     "lib/bio/shell/plugin/psort.rb",
     "lib/bio/shell/plugin/seq.rb",
@@ -441,6 +443,7 @@ Gem::Specification.new do |s|
 
   s.has_rdoc = true
   s.extra_rdoc_files = [ 
+    "KNOWN_ISSUES.rdoc",
     "README.rdoc",
     "README_DEV.rdoc",
     "doc/Changes-1.3.rdoc",
diff --git a/bioruby.gemspec.erb b/bioruby.gemspec.erb
index 464d36b51..43eafede5 100644
--- a/bioruby.gemspec.erb
+++ b/bioruby.gemspec.erb
@@ -18,7 +18,8 @@ Gem::Specification.new do |s|
     # When git-ls-files isn't available, creates a list from current files.
     unless $?.success? or files.size <= 0 then
       files =
-        [ "README.rdoc", "README_DEV.rdoc", "ChangeLog",
+        [ "README.rdoc", "README_DEV.rdoc", 
+          "ChangeLog", "KNOWN_ISSUES.rdoc",
           "Rakefile", "bioruby.gemspec.erb",
           "bioruby.gemspec", "setup.rb",
           "extconf.rb", "rdoc.zsh"