bio 1.4.3 → 1.4.3.0001

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data/ChangeLog CHANGED
@@ -1,3 +1,74 @@
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+ commit 960497899e75c0fe36ef662ec4a0159559c836b1
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Sat May 25 03:41:51 2013 +0900
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+
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+ regenerate bioruby.gemspec with rake regemspec
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+
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+ bioruby.gemspec | 4 +---
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+ 1 file changed, 1 insertion(+), 3 deletions(-)
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+
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+ commit e8fa160e158970259d915abc6113cb425537b8d6
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Sat May 25 03:38:17 2013 +0900
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+
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+ Bio::BIORUBY_EXTRA_VERSION set to ".0001" (Release version with patches)
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+
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+ lib/bio/version.rb | 2 +-
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
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+ commit 9d84d408479aa261b239e3f371f60262782bfb76
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Sat May 25 03:37:55 2013 +0900
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+
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+ Added release notes for 1.4.3.0001 release
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+
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+ RELEASE_NOTES.rdoc | 18 ++++++++++++++++++
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+ 1 file changed, 18 insertions(+)
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+
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+ commit 1d3530cd1424f2cc0123057424b5c892f45dc93b
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Sat May 25 02:46:32 2013 +0900
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+
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+ Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files
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+
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+ * Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files.
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+ Because ChangeLog is not rdoc format, rdoc bundled with Ruby 2.0
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+ raises error during parsing.
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+
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+ bioruby.gemspec.erb | 4 ++--
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+ 1 file changed, 2 insertions(+), 2 deletions(-)
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+ commit be72602cb42e6d09d465b9636257335dccb278a4
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Jan 10 01:27:03 2013 +0900
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+
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+ Ruby 2.0 support: Set script encoding to US-ASCII for gff.rb.
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+ lib/bio/db/gff.rb | 1 +
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+ 1 file changed, 1 insertion(+)
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+ commit 091f6951d23c5ed2418981b2cf94733b1ee7a8b1
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Mon Oct 1 21:11:14 2012 +0900
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+
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+ Bug fix: parse error when subject sequence contains spaces
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+
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+ * Bug fix: parse error when subject sequence contains spaces.
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+ Thanks to Edward Rice who reports the bug. (Bug #3385)
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+ (https://redmine.open-bio.org/issues/3385)
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+
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+ lib/bio/appl/blast/format0.rb | 38 +++++++++++++++++++-------------------
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+ 1 file changed, 19 insertions(+), 19 deletions(-)
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+ commit ad0d7a1712d8b02358763233d38e67a0fff54917
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Wed Aug 22 00:18:14 2012 +0900
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+
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+ BioRuby 1.4.3 is re-released
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+
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+ ChangeLog | 9 +++++++++
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+ 1 file changed, 9 insertions(+)
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+
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  commit 51ab2dec144c99a14ca9009c7b589b500f1cad5f
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  Author: Naohisa Goto <ng@bioruby.org>
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  Date: Wed Aug 22 00:12:47 2012 +0900
@@ -5,7 +76,7 @@ Date: Wed Aug 22 00:12:47 2012 +0900
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  Preparation to re-release BioRuby 1.4.3
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  ChangeLog | 22 ++++++++++++++++++++++
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- 1 files changed, 22 insertions(+), 0 deletions(-)
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+ 1 file changed, 22 insertions(+)
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  commit 5ff159d12252393ff04afe52b59a315d15c63d18
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -18,7 +89,7 @@ Date: Wed Aug 22 00:00:40 2012 +0900
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  RELEASE_NOTES.rdoc | 2 ++
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  lib/bio/shell/core.rb | 1 +
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+ 2 files changed, 3 insertions(+)
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  commit 74c6ce09413e7ddde1431d74e10cc9c4cdbb95ba
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -27,7 +98,7 @@ Date: Tue Aug 21 22:35:18 2012 +0900
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  BioRuby 1.4.3 is released.
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  ChangeLog | 21 +++++++++++++++++++++
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+ 1 file changed, 21 insertions(+)
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  commit 61af85b6cfc7bb1f3668ed68232113eb0751e7ea
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  Author: Naohisa Goto <ng@bioruby.org>
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  KNOWN_ISSUES.rdoc | 9 +++++++++
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  RELEASE_NOTES.rdoc | 9 +++++++++
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+ 2 files changed, 18 insertions(+)
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  commit 2fdd7a3b3555a33dead31181c9526af22f24916f
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -77,7 +148,7 @@ Date: Mon Aug 20 19:44:39 2012 +0900
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  update recommended Ruby versions and the year in copyright lines
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  README.rdoc | 7 +++----
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- 1 files changed, 3 insertions(+), 4 deletions(-)
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+ 1 file changed, 3 insertions(+), 4 deletions(-)
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  commit b156227749e5ada74330e837c9ce48a16e6a6a2f
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -112,8 +183,8 @@ Date: Mon Aug 20 19:04:50 2012 +0900
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  Note that _call_command_popen_jruby19 will be removed in the future
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  after the bugs are fixed.
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- lib/bio/command.rb | 98 ++++++++++++++++++++++++++++++++++++++++++++++-----
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- 1 files changed, 88 insertions(+), 10 deletions(-)
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+ lib/bio/command.rb | 98 ++++++++++++++++++++++++++++++++++++++++++++++------
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+ 1 file changed, 88 insertions(+), 10 deletions(-)
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  commit 05f51fa2e871e71c2b20559eb05e456768a4f7d6
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  Author: Naohisa Goto <ng@bioruby.org>
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  available services.
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  etc/bioinformatics/seqdatabase.ini | 27 +++++++++++++++++++++++++++
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- 1 files changed, 27 insertions(+), 0 deletions(-)
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+ 1 file changed, 27 insertions(+)
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  create mode 100644 etc/bioinformatics/seqdatabase.ini
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  commit a4264cc3667b98289c09efc7ccba9c8e86f6d89c
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  known issue about http://bioruby.org/cgi-bin/biofetch.rb server down
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  KNOWN_ISSUES.rdoc | 9 +++++++++
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+ 1 file changed, 9 insertions(+)
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  commit 4a8193f7b91ff703c8f3dc6e6a6ae0c981a404e6
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -180,7 +251,7 @@ Date: Wed Aug 8 09:41:20 2012 +1000
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  fill in missing piece of documentation in FastaFormat
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  lib/bio/db/fasta.rb | 2 +-
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- 1 files changed, 1 insertions(+), 1 deletions(-)
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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  commit 83bf09d4d81803c8d06e0d45ca25e7c09016161c
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  Author: Naohisa Goto <ng@bioruby.org>
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  RELEASE_NOTE.rdoc modified to reflect recent changes
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- RELEASE_NOTES.rdoc | 107 ++++++++++++++++++++++++++++++++++++++++++++-------
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- 1 files changed, 92 insertions(+), 15 deletions(-)
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+ RELEASE_NOTES.rdoc | 107 ++++++++++++++++++++++++++++++++++++++++++++--------
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+ 1 file changed, 92 insertions(+), 15 deletions(-)
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  commit c3afb1eb98cf8777ee021624c3d2eab92b3543f2
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  Author: Naohisa Goto <ng@bioruby.org>
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  Descriptions about JRuby, Rubinius, DDBJ Web API, SOAP4R etc.
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  KNOWN_ISSUES.rdoc | 45 +++++++++++++++++++++++++++++++++++++++++++--
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- 1 files changed, 43 insertions(+), 2 deletions(-)
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+ 1 file changed, 43 insertions(+), 2 deletions(-)
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  commit 01da7401a011aa519c43a021f89f6e7f769b4649
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -207,7 +278,7 @@ Date: Tue Aug 7 23:55:09 2012 +0900
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  regenerate bioruby.gemspec with rake regemspec
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  bioruby.gemspec | 3 +--
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- 1 files changed, 1 insertions(+), 2 deletions(-)
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+ 1 file changed, 1 insertion(+), 2 deletions(-)
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  commit 9f70c27d9b75408fddae8384a2a09715b959dcb5
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -216,7 +287,7 @@ Date: Tue Aug 7 23:51:56 2012 +0900
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  improve documentation; version changed to 1.4.3-pre1
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  lib/bio/version.rb | 13 +++++++++++--
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- 1 files changed, 11 insertions(+), 2 deletions(-)
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+ 1 file changed, 11 insertions(+), 2 deletions(-)
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  commit c11f12c8aa56b8509cd082f3478e96374210e5d7
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -225,7 +296,7 @@ Date: Tue Aug 7 23:31:41 2012 +0900
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  Remove autorequire which have been deprecated
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  bioruby.gemspec.erb | 1 -
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- 1 files changed, 0 insertions(+), 1 deletions(-)
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+ 1 file changed, 1 deletion(-)
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  commit 7792b092033d2c819f2bcad0e206f27608481db5
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  Author: Ben J Woodcroft <donttrustben@gmail.com>
@@ -250,7 +321,7 @@ Date: Fri Aug 3 22:36:12 2012 +0900
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  FileUtils#remove_entry_secure.
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  .travis.yml | 52 ++++++++++++++++++----------------------------------
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- 1 files changed, 18 insertions(+), 34 deletions(-)
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  commit 553fd102c533c42675f93895557e3e00d36fd3e7
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  Author: Naohisa Goto <ng@bioruby.org>
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  Improve tests for BLAST "-m 8" tabular format parser
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  test/unit/bio/appl/blast/test_report.rb | 119 +++++++++++++++++++++++++++++++
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+ 1 file changed, 119 insertions(+)
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  commit 3e1c062dbc168bd558ca8408a6da115aa570f3a7
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -268,7 +339,7 @@ Date: Fri Aug 3 22:05:07 2012 +0900
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  Improve test and suppress warning: assigned but unused variable
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  test/unit/bio/io/flatfile/test_buffer.rb | 1 +
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  commit 7e29ce1f050e9e5b23299372d8ddfae781447dc3
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@@ -277,7 +348,7 @@ Date: Fri Aug 3 22:02:21 2012 +0900
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  Improve test and suppress warning: assigned but unused variable
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  test/unit/bio/db/test_newick.rb | 2 ++
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  commit 1053b62069df74f336934e4ed0f3f217e4ad3312
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  Author: Naohisa Goto <ng@bioruby.org>
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  Thanks to Andrew Grimm: https://github.com/bioruby/bioruby/pull/64
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  lib/bio/db/gff.rb | 8 ++++----
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- 1 files changed, 4 insertions(+), 4 deletions(-)
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  commit e55794f65b3fb45c99e61d45220fe42f718426a3
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  Author: Naohisa Goto <ng@bioruby.org>
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  * warning: even though it seems like symbol literal
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  commit 174a38ea8c4ecea70724bf6ec8e72b2e4259853b
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  Author: Naohisa Goto <ng@bioruby.org>
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  Modified to follow changes of GenomeNet BLAST site
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  lib/bio/appl/blast/genomenet.rb | 6 +++---
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  commit 93e24935840dcdec76984313719700134d69daf2
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  suppress warnings: instance variable @comment not initialized
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  commit 0ad3818fedb707a26e849877bde1f8dab006b848
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  suppress warnings: URI.escape/URI.unescape is obsolete
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  Author: Naohisa Goto <ng@bioruby.org>
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  (https://github.com/bioruby/bioruby/pull/49)
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  Next bioruby release version will be 1.4.3.
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  fix typo
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  Bug fix: Genomenet remote blast: catch up changes of the server
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  regenerate bioruby.gemspec with rake regemspec
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  * Next BioRuby release version will be 1.4.3.
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  of substrates and products that were thrown away in the previous
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  rdoc documentation for Bio::KEGG::KGML
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  autoload should not be used for libraries outside bio
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  commit c81dce87f53d3ea7c7d2335e077fa609f2737779
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -579,7 +650,7 @@ Date: Thu Jul 5 23:03:40 2012 +0900
579
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  .travis.yml: include ruby 1.9.2 test
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  .travis.yml | 2 ++
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- 1 files changed, 2 insertions(+), 0 deletions(-)
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+ 1 file changed, 2 insertions(+)
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  commit 34709d114089c722b5da796028ffb91021761fdd
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -588,7 +659,7 @@ Date: Thu Jul 5 23:00:37 2012 +0900
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  Remove old comment lines
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  lib/bio/sequence/format.rb | 6 ------
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- 1 files changed, 0 insertions(+), 6 deletions(-)
662
+ 1 file changed, 6 deletions(-)
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  commit e0d5ed61e0101e2e72ad024dccd58c8c90def2b9
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -607,8 +678,8 @@ Date: Thu Jul 5 22:42:17 2012 +0900
607
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  raised in the finalizer callback of Bio::Command::Tmpdir. This
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  commit fixes the problem.
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- lib/bio/command.rb | 56 +++++++++++++++++++++++++++------------------------
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- 1 files changed, 30 insertions(+), 26 deletions(-)
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+ lib/bio/command.rb | 56 ++++++++++++++++++++++++++++------------------------
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+ 1 file changed, 30 insertions(+), 26 deletions(-)
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  commit cca98d1378ce66d6db84cc9c1beadd39ed0e0fee
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -647,29 +718,29 @@ Date: Thu Jul 5 21:04:28 2012 +0900
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  because its method definitions are divided into two files:
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  analysis.rb, analysis_basic.rb.
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650
- lib/bio/util/restriction_enzyme/analysis.rb | 13 ++++++++-----
651
- lib/bio/util/restriction_enzyme/analysis_basic.rb | 7 ++++---
652
- lib/bio/util/restriction_enzyme/cut_symbol.rb | 5 +++--
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- lib/bio/util/restriction_enzyme/dense_int_array.rb | 3 +++
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- lib/bio/util/restriction_enzyme/double_stranded.rb | 7 +++----
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- .../double_stranded/aligned_strands.rb | 7 +++----
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- .../double_stranded/cut_location_pair.rb | 7 +++----
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- .../cut_location_pair_in_enzyme_notation.rb | 7 +++----
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- .../double_stranded/cut_locations.rb | 7 +++----
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- .../cut_locations_in_enzyme_notation.rb | 7 +++----
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- lib/bio/util/restriction_enzyme/range/cut_range.rb | 7 +++----
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- .../util/restriction_enzyme/range/cut_ranges.rb | 7 +++----
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- .../range/horizontal_cut_range.rb | 7 +++----
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- .../restriction_enzyme/range/sequence_range.rb | 7 +++----
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- .../range/sequence_range/calculated_cuts.rb | 7 +++----
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- .../range/sequence_range/fragment.rb | 7 +++----
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- .../range/sequence_range/fragments.rb | 7 +++----
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- .../restriction_enzyme/range/vertical_cut_range.rb | 7 +++----
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- lib/bio/util/restriction_enzyme/single_strand.rb | 6 +++---
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- .../cut_locations_in_enzyme_notation.rb | 7 +++----
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- .../restriction_enzyme/single_strand_complement.rb | 7 +++----
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- .../util/restriction_enzyme/sorted_num_array.rb | 3 +++
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- .../util/restriction_enzyme/string_formatting.rb | 7 +++----
721
+ lib/bio/util/restriction_enzyme/analysis.rb | 13 ++++++++-----
722
+ lib/bio/util/restriction_enzyme/analysis_basic.rb | 7 ++++---
723
+ lib/bio/util/restriction_enzyme/cut_symbol.rb | 5 +++--
724
+ lib/bio/util/restriction_enzyme/dense_int_array.rb | 3 +++
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+ lib/bio/util/restriction_enzyme/double_stranded.rb | 7 +++----
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+ .../restriction_enzyme/double_stranded/aligned_strands.rb | 7 +++----
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+ .../double_stranded/cut_location_pair.rb | 7 +++----
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+ .../cut_location_pair_in_enzyme_notation.rb | 7 +++----
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+ .../restriction_enzyme/double_stranded/cut_locations.rb | 7 +++----
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+ .../double_stranded/cut_locations_in_enzyme_notation.rb | 7 +++----
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+ lib/bio/util/restriction_enzyme/range/cut_range.rb | 7 +++----
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+ lib/bio/util/restriction_enzyme/range/cut_ranges.rb | 7 +++----
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+ .../util/restriction_enzyme/range/horizontal_cut_range.rb | 7 +++----
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+ lib/bio/util/restriction_enzyme/range/sequence_range.rb | 7 +++----
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+ .../range/sequence_range/calculated_cuts.rb | 7 +++----
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+ .../restriction_enzyme/range/sequence_range/fragment.rb | 7 +++----
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+ .../restriction_enzyme/range/sequence_range/fragments.rb | 7 +++----
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+ .../util/restriction_enzyme/range/vertical_cut_range.rb | 7 +++----
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+ lib/bio/util/restriction_enzyme/single_strand.rb | 6 +++---
740
+ .../single_strand/cut_locations_in_enzyme_notation.rb | 7 +++----
741
+ .../util/restriction_enzyme/single_strand_complement.rb | 7 +++----
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+ lib/bio/util/restriction_enzyme/sorted_num_array.rb | 3 +++
743
+ lib/bio/util/restriction_enzyme/string_formatting.rb | 7 +++----
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  23 files changed, 75 insertions(+), 81 deletions(-)
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  commit 7df4843288ffde6d7132a5651fe978301f8ebd2b
@@ -679,7 +750,7 @@ Date: Thu Jul 5 20:18:08 2012 +0900
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  workaround to avoid JRuby autoload bug
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  lib/bio/util/restriction_enzyme.rb | 4 +---
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- 1 files changed, 1 insertions(+), 3 deletions(-)
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+ 1 file changed, 1 insertion(+), 3 deletions(-)
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  commit 97d95f2b400006d4229a7ce69d7d8a5cdce42764
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -688,7 +759,7 @@ Date: Wed Jul 4 22:00:27 2012 +0900
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  changed require to autoload for the workaround of JRuby autoload bug
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  lib/bio/feature.rb | 5 ++---
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- 1 files changed, 2 insertions(+), 3 deletions(-)
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+ 1 file changed, 2 insertions(+), 3 deletions(-)
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  commit 530b82a45731c2a71a110826341be425de1271e0
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -697,7 +768,7 @@ Date: Wed Jul 4 22:00:06 2012 +0900
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  workaround to avoid JRuby autoload bug
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  lib/bio/sequence/common.rb | 4 +---
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- 1 files changed, 1 insertions(+), 3 deletions(-)
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+ 1 file changed, 1 insertion(+), 3 deletions(-)
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702
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  commit 8614f31b36fb93d6e49d109268d646ff3032cd1a
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -709,7 +780,7 @@ Date: Wed Jul 4 21:28:52 2012 +0900
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  * Changed to require bio/db.rb because it is always loaded.
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  lib/bio/db/kegg/genes.rb | 6 +++---
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- 1 files changed, 3 insertions(+), 3 deletions(-)
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+ 1 file changed, 3 insertions(+), 3 deletions(-)
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  commit ea500006ed56857139c858bdfeb98773e5ca541e
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -718,7 +789,7 @@ Date: Thu Jun 28 21:36:35 2012 +0900
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  Rakefile: use own mktmpdir
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  Rakefile | 59 +++++++++++++++++++++++++++++++++++++++++++----------------
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- 1 files changed, 43 insertions(+), 16 deletions(-)
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+ 1 file changed, 43 insertions(+), 16 deletions(-)
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  commit 452fadcab61083dcb9d01ee05d300eae5cb23fee
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -727,7 +798,7 @@ Date: Thu Jun 28 20:37:59 2012 +0900
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  .travis.yml: remove "rake regemspec" from after_install
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  .travis.yml | 2 --
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- 1 files changed, 0 insertions(+), 2 deletions(-)
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+ 1 file changed, 2 deletions(-)
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732
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  commit 3fad822af3d7e558a58b71fd8ec2a7061b49f9f2
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -736,7 +807,7 @@ Date: Thu Jun 28 20:36:59 2012 +0900
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  regenerate bioruby.gemspec with rake regemspec
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738
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  bioruby.gemspec | 2 ++
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- 1 files changed, 2 insertions(+), 0 deletions(-)
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+ 1 file changed, 2 insertions(+)
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741
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  commit ea6e96fc654c797664b118a6326a84e4f9b1a8a3
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -745,7 +816,7 @@ Date: Thu Jun 28 20:35:49 2012 +0900
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  print message when doing Dir.chdir
746
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747
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  Rakefile | 17 +++++++++++------
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- 1 files changed, 11 insertions(+), 6 deletions(-)
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+ 1 file changed, 11 insertions(+), 6 deletions(-)
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750
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  commit c2fcd5e8cc71da38dc3c6d1f8c8d0233e47398b3
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -754,7 +825,7 @@ Date: Thu Jun 28 20:28:41 2012 +0900
754
825
  In tar-install, removed dependency to regemspec
755
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  Rakefile | 2 +-
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- 1 files changed, 1 insertions(+), 1 deletions(-)
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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  commit 67a7e83d516aab5d60f8263525b359be8b0ffc0b
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -766,7 +837,7 @@ Date: Thu Jun 28 20:23:24 2012 +0900
766
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  that may be related with http://jira.codehaus.org/browse/JRUBY-5678
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768
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  Rakefile | 61 ++++++++++++++++++++++++++++++++++++++++++++++---------------
769
- 1 files changed, 46 insertions(+), 15 deletions(-)
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+ 1 file changed, 46 insertions(+), 15 deletions(-)
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771
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  commit cff098034a338bbe9579d6c7b4380c7132a38ef5
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -778,7 +849,7 @@ Date: Thu Jun 28 19:23:57 2012 +0900
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  because they are useless with Bundler
779
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780
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  Rakefile | 13 -------------
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- 1 files changed, 0 insertions(+), 13 deletions(-)
852
+ 1 file changed, 13 deletions(-)
782
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783
854
  commit d5c054265af4f80318cbfa5a5bbdee6125219de2
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -788,7 +859,7 @@ Date: Thu Jun 28 18:10:05 2012 +0900
788
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789
860
  .travis.yml | 1 +
790
861
  gemfiles/prepare-gemspec.rb | 25 +++++++++++++++++++++++++
791
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862
+ 2 files changed, 26 insertions(+)
792
863
  create mode 100644 gemfiles/prepare-gemspec.rb
793
864
 
794
865
  commit 05b6172123f42a1d8d46668d8a3d5f698c371704
@@ -815,7 +886,7 @@ Date: Thu Jun 28 17:06:28 2012 +0900
815
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  descriptions are modified for danger operations
816
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817
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  Rakefile | 4 ++--
818
- 1 files changed, 2 insertions(+), 2 deletions(-)
889
+ 1 file changed, 2 insertions(+), 2 deletions(-)
819
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820
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  commit a209688952c922d9ba45c227874990bccd3da7c0
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -824,7 +895,7 @@ Date: Mon Jun 25 23:25:51 2012 +0900
824
895
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826
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  bioruby.gemspec | 5 +++++
827
- 1 files changed, 5 insertions(+), 0 deletions(-)
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+ 1 file changed, 5 insertions(+)
828
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829
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  commit 8f6459497be0e9ca7dc3eb2eb9606e42d97ad60c
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -850,7 +921,7 @@ Date: Mon Jun 25 21:01:06 2012 +0900
850
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  * Default task is changed from "test" to "see-env".
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923
  Rakefile | 110 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
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+ 1 file changed, 107 insertions(+), 3 deletions(-)
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855
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  commit 3b400042cd361e1ab6d0fb0d8c8cce14a6c2ae10
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@@ -863,7 +934,7 @@ Date: Mon Jun 25 20:58:13 2012 +0900
863
934
  included in the middle of $LOAD_PATH.
864
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865
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866
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868
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  commit 848304b6f90310f8fa15c80ba06655ae5cae5053
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -881,8 +952,8 @@ Date: Mon Jun 25 20:42:07 2012 +0900
881
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  ignored.
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884
- test/bioruby_test_helper.rb | 49 ++++++++++++++++++++++++++++++++----------
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955
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  commit 9453a6773c24f866698370195fd8e767443a38b9
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  Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
@@ -899,7 +970,7 @@ Date: Fri Jun 1 18:06:40 2012 +0900
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900
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904
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905
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@@ -915,8 +986,8 @@ Date: Fri Jun 8 15:36:29 2012 +0900
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916
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917
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918
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921
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  commit 20dde52f7da784d4d9ac551957700cd96e842ef6
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -955,7 +1026,7 @@ Date: Thu May 10 23:13:56 2012 -0400
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  test_tree.rb: to use %f instead of %g to prevent odd behavior.
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957
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  test/unit/bio/test_tree.rb | 22 +++++++++++-----------
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  commit 5e80e4394bf2a5e4ee472fe84ab76239b293e1b5
961
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@@ -964,7 +1035,7 @@ Date: Thu May 10 23:04:55 2012 -0400
964
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  Fixed spurious JRuby failures in test_tree.rb due to floating point differences.
965
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966
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967
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1038
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  commit 459d4da894e9a9b9db0d793e3711dc45bae2089b
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@@ -976,7 +1047,7 @@ Date: Thu May 10 16:23:13 2012 +0400
976
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  not guaranteed.
977
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  test/unit/bio/db/test_soft.rb | 2 +-
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  commit 7e730691d6ec597a610dc0d4665db3598fcfde59
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -990,7 +1061,7 @@ Date: Thu May 10 00:06:19 2012 +0900
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  lib/bio/db/fastq/format_fastq.rb | 1 -
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1064
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -1002,7 +1073,7 @@ Date: Wed May 9 15:54:20 2012 +0900
1002
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  and libexpat1-dev are already installed.
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@@ -1025,11 +1096,11 @@ Date: Tue May 1 18:11:09 2012 +0900
1025
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1026
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1027
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  .travis.yml | 73 ++++++++++++++++++++++++++++++++++++++
1028
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1033
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1034
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@@ -1054,7 +1125,7 @@ Date: Sat Feb 25 15:26:27 2012 -0600
1054
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1055
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1056
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1057
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1128
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1059
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1060
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@@ -1067,7 +1138,7 @@ Date: Thu Jan 12 22:24:37 2012 +0900
1067
1138
  ( https://github.com/bioruby/bioruby/issues/44 )
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1069
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  commit f33abf9bbd90c3c1e320f06447fdb54ffd094c5d
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@@ -1075,7 +1146,7 @@ Date: Fri Nov 25 11:20:08 2011 +0000
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1076
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1079
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1080
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@@ -1086,7 +1157,7 @@ Date: Thu Nov 24 13:32:37 2011 +0900
1086
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  Bug fix: rake aborted without git
1087
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1088
1159
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1089
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1160
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1091
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  commit c2139739988ef731d61bf1a8cdba2dc5c48393bd
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -1095,7 +1166,7 @@ Date: Thu Nov 24 13:07:10 2011 +0900
1095
1166
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1096
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1097
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1098
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1169
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  Author: Naohisa Goto <ng@bioruby.org>
@@ -1104,7 +1175,7 @@ Date: Thu Nov 24 13:05:07 2011 +0900
1104
1175
  Added workaround for changes of a module name and file names to require.
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1176
 
1106
1177
  Rakefile | 21 +++++++++++++++++++--
1107
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1178
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  commit 39f847cf8d453476275361078b831da43d400816
1110
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@@ -1113,7 +1184,7 @@ Date: Thu Nov 24 12:08:47 2011 +0900
1113
1184
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1114
1185
 
1115
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  Rakefile | 6 ++++--
1116
- 1 files changed, 4 insertions(+), 2 deletions(-)
1187
+ 1 file changed, 4 insertions(+), 2 deletions(-)
1117
1188
 
1118
1189
  commit 688779e71a27e861fb01e07f816384561b8cfe45
1119
1190
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1125,7 +1196,7 @@ Date: Thu Nov 24 11:49:30 2011 +0900
1125
1196
  to run tests in test/network.
1126
1197
 
1127
1198
  Rakefile | 10 ++++++++++
1128
- 1 files changed, 10 insertions(+), 0 deletions(-)
1199
+ 1 file changed, 10 insertions(+)
1129
1200
 
1130
1201
  commit 53719535defcb0fefb3cf8bebe3fad6716bf7de2
1131
1202
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1134,7 +1205,7 @@ Date: Thu Nov 24 11:28:38 2011 +0900
1134
1205
  test/runner.rb: Run tests only in test/unit and test/functional.
1135
1206
 
1136
1207
  test/runner.rb | 22 ++++++++++++++++------
1137
- 1 files changed, 16 insertions(+), 6 deletions(-)
1208
+ 1 file changed, 16 insertions(+), 6 deletions(-)
1138
1209
 
1139
1210
  commit fb9ee403db6b447aee73ebb7f12ff5a5b73d6c52
1140
1211
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1199,7 +1270,7 @@ Date: Wed Nov 23 15:03:08 2011 +0900
1199
1270
 
1200
1271
  test/unit/bio/appl/blast/test_rpsblast.rb | 1 +
1201
1272
  test/unit/bio/io/flatfile/test_buffer.rb | 1 +
1202
- 2 files changed, 2 insertions(+), 0 deletions(-)
1273
+ 2 files changed, 2 insertions(+)
1203
1274
 
1204
1275
  commit 07ce32da009baa2c4e81f6d96f45e3dac49da183
1205
1276
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1226,7 +1297,7 @@ Date: Wed Nov 23 14:17:25 2011 +0900
1226
1297
  RELEASE_NOTES.rdoc | 7 ++
1227
1298
  lib/bio/io/flatfile/buffer.rb | 84 ++++++++++++++++++
1228
1299
  test/unit/bio/io/flatfile/test_buffer.rb | 139 ++++++++++++++++++++++++++++++
1229
- 3 files changed, 230 insertions(+), 0 deletions(-)
1300
+ 3 files changed, 230 insertions(+)
1230
1301
 
1231
1302
  commit 48bd150a6180d59879872bd85dd95c7ddf1a19c0
1232
1303
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1235,7 +1306,7 @@ Date: Tue Nov 22 17:32:23 2011 +0900
1235
1306
  Test bug fix: fixed incomplete Windows platform detection.
1236
1307
 
1237
1308
  test/unit/bio/test_command.rb | 13 +++++++++----
1238
- 1 files changed, 9 insertions(+), 4 deletions(-)
1309
+ 1 file changed, 9 insertions(+), 4 deletions(-)
1239
1310
 
1240
1311
  commit d499bcee7956b1a0a4c04aeb106e50a0839167b0
1241
1312
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1263,7 +1334,7 @@ Date: Tue Nov 22 14:21:34 2011 +0900
1263
1334
  and removing the temporary files raise erro on Windows.
1264
1335
 
1265
1336
  test/unit/bio/db/test_phyloxml_writer.rb | 24 +++++++++++++++---------
1266
- 1 files changed, 15 insertions(+), 9 deletions(-)
1337
+ 1 file changed, 15 insertions(+), 9 deletions(-)
1267
1338
 
1268
1339
  commit a9022c61b98746e98a83f1cfd902e0e6b11c7bbb
1269
1340
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1280,7 +1351,7 @@ Date: Tue Nov 22 13:55:15 2011 +0900
1280
1351
  * Added tests about the above changes.
1281
1352
 
1282
1353
  lib/bio/db/phyloxml/phyloxml_parser.rb | 57 +++++++++++++++++++++++++++++---
1283
- test/unit/bio/db/test_phyloxml.rb | 56 ++++++++++++++++++++++++++++++-
1354
+ test/unit/bio/db/test_phyloxml.rb | 56 +++++++++++++++++++++++++++++--
1284
1355
  2 files changed, 106 insertions(+), 7 deletions(-)
1285
1356
 
1286
1357
  commit 893cbe6ca993eca08427074059c2ba03621ea889
@@ -1290,7 +1361,7 @@ Date: Sat Nov 5 00:49:10 2011 +0900
1290
1361
  Ruby 1.9 should be fully supported, and optional requirements are revised.
1291
1362
 
1292
1363
  README.rdoc | 48 +++++++++++++++++++++++++++++++++---------------
1293
- 1 files changed, 33 insertions(+), 15 deletions(-)
1364
+ 1 file changed, 33 insertions(+), 15 deletions(-)
1294
1365
 
1295
1366
  commit 38b1715c2d6bad39560e0846781ca903b1c16eda
1296
1367
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1299,7 +1370,7 @@ Date: Fri Nov 4 22:12:38 2011 +0900
1299
1370
  Added REFERENCE.
1300
1371
 
1301
1372
  README.rdoc | 12 ++++++++++++
1302
- 1 files changed, 12 insertions(+), 0 deletions(-)
1373
+ 1 file changed, 12 insertions(+)
1303
1374
 
1304
1375
  commit 9a766cd17236bbe1e28d6972001dd5e3ed596123
1305
1376
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1308,7 +1379,7 @@ Date: Fri Nov 4 21:39:20 2011 +0900
1308
1379
  Removed "setup.rb test" and added about running tests.
1309
1380
 
1310
1381
  README.rdoc | 39 ++++++++++++++++++++++++++++++++++-----
1311
- 1 files changed, 34 insertions(+), 5 deletions(-)
1382
+ 1 file changed, 34 insertions(+), 5 deletions(-)
1312
1383
 
1313
1384
  commit 39737179b06366e1d5acf2e5ac930e41b3a4ee38
1314
1385
  Author: Pjotr Prins <pjotr.public01@thebird.nl>
@@ -1341,8 +1412,8 @@ Date: Tue Sep 13 23:05:39 2011 +0900
1341
1412
  * Added some coding styles.
1342
1413
  * Added descriptions about Ruby versions and OS.
1343
1414
 
1344
- README_DEV.rdoc | 95 +++++++++++++++++++++++++++++++++++++++++++++++++++++-
1345
- 1 files changed, 93 insertions(+), 2 deletions(-)
1415
+ README_DEV.rdoc | 95 +++++++++++++++++++++++++++++++++++++++++++++++++++++--
1416
+ 1 file changed, 93 insertions(+), 2 deletions(-)
1346
1417
 
1347
1418
  commit 3c952c4a782501b21f36ece5bcab672dab12fc6d
1348
1419
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1351,7 +1422,7 @@ Date: Tue Sep 13 13:21:20 2011 +0900
1351
1422
  README.rdoc: for release notes and changelog, about sample files.
1352
1423
 
1353
1424
  README.rdoc | 10 +++++++++-
1354
- 1 files changed, 9 insertions(+), 1 deletions(-)
1425
+ 1 file changed, 9 insertions(+), 1 deletion(-)
1355
1426
 
1356
1427
  commit fba9a6c0f1f79dd567ca54ba085b6258ac8efb31
1357
1428
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1360,7 +1431,7 @@ Date: Tue Sep 13 13:20:05 2011 +0900
1360
1431
  RELEASE_NOTES.rdoc: mentioned about removal of rdoc.zsh.
1361
1432
 
1362
1433
  RELEASE_NOTES.rdoc | 6 +++++-
1363
- 1 files changed, 5 insertions(+), 1 deletions(-)
1434
+ 1 file changed, 5 insertions(+), 1 deletion(-)
1364
1435
 
1365
1436
  commit 685b6bb7b98083e1b50e73baf4e7fa71bc9a39fa
1366
1437
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1386,7 +1457,7 @@ Date: Mon Sep 12 20:54:06 2011 +0900
1386
1457
  See "rake -T" for more information.
1387
1458
 
1388
1459
  rdoc.zsh | 8 --------
1389
- 1 files changed, 0 insertions(+), 8 deletions(-)
1460
+ 1 file changed, 8 deletions(-)
1390
1461
  delete mode 100644 rdoc.zsh
1391
1462
 
1392
1463
  commit 272d9106cec43b0f219edd92a6f7bd3f9875a761
@@ -1400,7 +1471,7 @@ Date: Mon Sep 12 20:35:47 2011 +0900
1400
1471
  For the changes before 1.3.1, see doc/ChangeLog-before-1.3.1.
1401
1472
 
1402
1473
  ChangeLog | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1403
- 1 files changed, 64 insertions(+), 0 deletions(-)
1474
+ 1 file changed, 64 insertions(+)
1404
1475
  create mode 100644 ChangeLog
1405
1476
 
1406
1477
  commit 941493378f9884978c81d5f63ee4ed5c175d4bea
@@ -1414,7 +1485,7 @@ Date: Mon Sep 12 20:28:28 2011 +0900
1414
1485
  in Rakefile.
1415
1486
 
1416
1487
  Rakefile | 9 +++++++++
1417
- 1 files changed, 9 insertions(+), 0 deletions(-)
1488
+ 1 file changed, 9 insertions(+)
1418
1489
 
1419
1490
  commit 1c89e6546223c3c05ea79b8ade4b493580851efa
1420
1491
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1435,7 +1506,7 @@ Date: Mon Sep 12 20:22:49 2011 +0900
1435
1506
  ChangeLog updated: add log about 1.4.2 release
1436
1507
 
1437
1508
  ChangeLog | 9 +++++++++
1438
- 1 files changed, 9 insertions(+), 0 deletions(-)
1509
+ 1 file changed, 9 insertions(+)
1439
1510
 
1440
1511
  commit 1c02ab0488e4097a2cf5c16180c3179c78e3d572
1441
1512
  Author: Naohisa Goto <ng@bioruby.org>
@@ -1444,7 +1515,7 @@ Date: Mon Sep 12 19:40:54 2011 +0900
1444
1515
  New RELEASE_NOTES.rdoc for next release version.
1445
1516
 
1446
1517
  RELEASE_NOTES.rdoc | 47 +++++++++++++++++++++++++++++++++++++++++++++++
1447
- 1 files changed, 47 insertions(+), 0 deletions(-)
1518
+ 1 file changed, 47 insertions(+)
1448
1519
  create mode 100644 RELEASE_NOTES.rdoc
1449
1520
 
1450
1521
  commit 4e63e69e98c0c440ec476ef3407fcc8fd2411056
@@ -1466,4 +1537,4 @@ Date: Fri Sep 2 12:02:41 2011 +0900
1466
1537
  Bio::BIORUBY_EXTRA_VERSION set to ".5000" (unstable version).
1467
1538
 
1468
1539
  lib/bio/version.rb | 2 +-
1469
- 1 files changed, 1 insertions(+), 1 deletions(-)
1540
+ 1 file changed, 1 insertion(+), 1 deletion(-)
@@ -1,3 +1,21 @@
1
+ = BioRuby 1.4.3.0001 RELEASE NOTES
2
+
3
+ Some bug fixes have been made to the BioRuby 1.4.3.0001 after the version
4
+ 1.4.3 is released.
5
+
6
+ == Bug fixes
7
+
8
+ === Ruby 2.0 support
9
+
10
+ * "gem install bio" failed with Ruby 2.0 or later versions.
11
+ * lib/bio/db/gff.rb: Set script encoding to US-ASCII.
12
+
13
+ === Other bug fixes
14
+
15
+ * Bio::BLAST::Default::Report parse error when subject sequence contains
16
+ spaces. (https://redmine.open-bio.org/issues/3385)
17
+
18
+
1
19
  = BioRuby 1.4.3 RELEASE NOTES
2
20
 
3
21
  A lot of changes have been made to the BioRuby 1.4.3 after the version 1.4.2
@@ -3,7 +3,7 @@
3
3
  #
4
4
  Gem::Specification.new do |s|
5
5
  s.name = 'bio'
6
- s.version = "1.4.3"
6
+ s.version = "1.4.3.0001"
7
7
 
8
8
  s.author = "BioRuby project"
9
9
  s.email = "staff@bioruby.org"
@@ -653,9 +653,7 @@ Gem::Specification.new do |s|
653
653
 
654
654
  s.has_rdoc = true
655
655
  s.extra_rdoc_files = [
656
- "ChangeLog",
657
656
  "KNOWN_ISSUES.rdoc",
658
- "LEGAL",
659
657
  "README.rdoc",
660
658
  "README_DEV.rdoc",
661
659
  "RELEASE_NOTES.rdoc",
@@ -88,8 +88,8 @@ Gem::Specification.new do |s|
88
88
  def rdoc_files.add_file(name)
89
89
  self.push(name) unless self.include?(name)
90
90
  end
91
- rdoc_files.add_file "ChangeLog"
92
- rdoc_files.add_file "LEGAL"
91
+ #rdoc_files.add_file "ChangeLog"
92
+ #rdoc_files.add_file "LEGAL"
93
93
  rdoc_files.sort.collect { |x| x.dump }.join(",\n ")
94
94
  ###### Above is executed in ERB environment ######
95
95
  %>
@@ -1124,31 +1124,31 @@ module Bio
1124
1124
  while sc.rest?
1125
1125
  #p pos_st, len_seq
1126
1126
  #p nextline.to_s
1127
- if r = sc.skip(/(Query|Sbjct)\: *(\d+) */) then
1127
+ if r = sc.skip(/Query\: *(\d+) */) then
1128
1128
  pos_st = r
1129
- qs = sc[1]
1130
- pos1 = sc[2]
1129
+ pos1 = sc[1]
1131
1130
  len_seq = sc.skip(/[^ ]*/)
1132
1131
  seq = sc[0]
1133
1132
  sc.skip(/ *(\d+) *\n/)
1134
1133
  pos2 = sc[1]
1135
- if qs == 'Query' then
1136
- raise ScanError unless nextline == :q
1137
- qpos1 = pos1.to_i unless qpos1
1138
- qpos2 = pos2.to_i
1139
- qseq << seq
1140
- nextline = :m
1141
- elsif qs == 'Sbjct' then
1142
- if nextline == :m then
1143
- mseq << (' ' * len_seq)
1144
- end
1145
- spos1 = pos1.to_i unless spos1
1146
- spos2 = pos2.to_i
1147
- sseq << seq
1148
- nextline = :q
1149
- else
1150
- raise ScanError
1134
+ raise ScanError unless nextline == :q
1135
+ qpos1 = pos1.to_i unless qpos1
1136
+ qpos2 = pos2.to_i
1137
+ qseq << seq
1138
+ nextline = :m
1139
+ elsif r = sc.scan(/Sbjct\: *(\d+) *.+ +(\d+) *\n/) then
1140
+ pos1 = sc[1]
1141
+ pos2 = sc[2]
1142
+ raise ScanError unless pos_st
1143
+ raise ScanError unless len_seq
1144
+ seq = r[pos_st, len_seq]
1145
+ if nextline == :m then
1146
+ mseq << (' ' * len_seq)
1151
1147
  end
1148
+ spos1 = pos1.to_i unless spos1
1149
+ spos2 = pos2.to_i
1150
+ sseq << seq
1151
+ nextline = :q
1152
1152
  elsif r = sc.scan(/ {6}.+/) then
1153
1153
  raise ScanError unless nextline == :m
1154
1154
  mseq << r[pos_st, len_seq]
@@ -1,3 +1,4 @@
1
+ # coding: US-ASCII
1
2
  #
2
3
  # = bio/db/gff.rb - GFF format class
3
4
  #
@@ -23,7 +23,7 @@ module Bio
23
23
  # "-preN" (N=0..99) :: Pre-release test version.
24
24
  # "-rcN" (N=0..99) :: Release candidate version.
25
25
  #
26
- BIORUBY_EXTRA_VERSION = nil
26
+ BIORUBY_EXTRA_VERSION = ".0001"
27
27
 
28
28
  # Version identifier, including extra version string (String)
29
29
  # Unlike BIORUBY_VERSION, it is not comparable.
metadata CHANGED
@@ -3,7 +3,7 @@ name: !binary |-
3
3
  Ymlv
4
4
  version: !ruby/object:Gem::Version
5
5
  version: !binary |-
6
- MS40LjM=
6
+ MS40LjMuMDAwMQ==
7
7
  prerelease:
8
8
  platform: ruby
9
9
  authors:
@@ -13,7 +13,7 @@ autorequire:
13
13
  bindir: !binary |-
14
14
  Ymlu
15
15
  cert_chain: []
16
- date: 2012-08-21 00:00:00.000000000 Z
16
+ date: 2013-05-24 00:00:00.000000000 Z
17
17
  dependencies: []
18
18
  description: !binary |-
19
19
  QmlvUnVieSBpcyBhIGxpYnJhcnkgZm9yIGJpb2luZm9ybWF0aWNzIChiaW9s
@@ -33,12 +33,8 @@ executables:
33
33
  YnJfcG1mZXRjaC5yYg==
34
34
  extensions: []
35
35
  extra_rdoc_files:
36
- - !binary |-
37
- Q2hhbmdlTG9n
38
36
  - !binary |-
39
37
  S05PV05fSVNTVUVTLnJkb2M=
40
- - !binary |-
41
- TEVHQUw=
42
38
  - !binary |-
43
39
  UkVBRE1FLnJkb2M=
44
40
  - !binary |-