Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/libs/rubymods
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv25773
Modified Files:
bioruby-rb.info bioruby-rb.patch
Log Message:
use upstream patch to fix encoding test failure
Index: bioruby-rb.info
===================================================================
RCS file:
/cvsroot/fink/dists/10.7/stable/main/finkinfo/libs/rubymods/bioruby-rb.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- bioruby-rb.info 21 Aug 2013 15:17:15 -0000 1.1
+++ bioruby-rb.info 23 Aug 2013 15:48:33 -0000 1.2
@@ -1,7 +1,7 @@
Info2: <<
Package: bioruby-rb%type_pkg[ruby]
Version: 1.4.3.0001
-Revision: 1
+Revision: 2
Type: ruby (1.9 2.0)
Description: Open source bioinformatics library for Ruby
License: GPL
@@ -29,7 +29,7 @@
Source-MD5: 309c17622f827501bc7f10d8b1c284a7
Source-Checksum: SHA1(aa9941d0b11da4b28b4054c25c624d7a70624c2e)
PatchFile: %{ni}.patch
-PatchFile-MD5: da9700d0c38f509f8f6665e750fac3a3
+PatchFile-MD5: 278c9bbfe58673ea9f470d3f50177e12
PatchScript: <<
%{default_script}
### make samples have the correct shebang
@@ -61,7 +61,7 @@
### prepare for u-a
for file in %i/bin/*; do
- mv $file $file-rb20
+ mv $file $file-rb%type_pkg[ruby]
done
<<
PostInstScript: <<
@@ -94,7 +94,7 @@
<<
DescPort: <<
Fix "invalid byte sequence in US-ASCII" error in
Bio::TestPhyloXML_class_methods
-http://wiki.lifesciencedb.jp/mw/index.php/BioRuby
Reported: https://github.com/bioruby/bioruby/issues/84
+Fixed: edda65b8fb32c2eee6b0652074981c31aa68b0eb
<<
<<
Index: bioruby-rb.patch
===================================================================
RCS file:
/cvsroot/fink/dists/10.7/stable/main/finkinfo/libs/rubymods/bioruby-rb.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- bioruby-rb.patch 21 Aug 2013 15:17:15 -0000 1.1
+++ bioruby-rb.patch 23 Aug 2013 15:48:33 -0000 1.2
@@ -1,10 +1,29 @@
+From edda65b8fb32c2eee6b0652074981c31aa68b0eb Mon Sep 17 00:00:00 2001
+From: Naohisa Goto <n...@bioruby.org>
+Date: Fri, 23 Aug 2013 23:51:59 +0900
+Subject: [PATCH] Test bug fix: Read test file with binary mode to avoid
+ encoding error
+
+ * Test bug fix: Read test file with binary mode to avoid string encoding
+ error. Thanks to nieder (github.com/nieder) who reports the bug.
+ (https://github.com/bioruby/bioruby/issues/84)
+---
+ test/unit/bio/db/test_phyloxml.rb | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/test/unit/bio/db/test_phyloxml.rb
b/test/unit/bio/db/test_phyloxml.rb
+index 0744c64..c24278d 100644
--- a/test/unit/bio/db/test_phyloxml.rb
+++ b/test/unit/bio/db/test_phyloxml.rb
-@@ -100,6 +100,7 @@ end #end module TestPhyloXMLData
+@@ -100,7 +100,7 @@ def test_open_with_block
end
def test_new
-+ Encoding.default_external="UTF-8"
- str = File.read(TestPhyloXMLData.example_xml)
+- str = File.read(TestPhyloXMLData.example_xml)
++ str = File.open(TestPhyloXMLData.example_xml, "rb") { |f| f.read }
assert_instance_of(Bio::PhyloXML::Parser,
phyloxml = Bio::PhyloXML::Parser.new(str))
+ common_test_next_tree(phyloxml)
+--
+1.8.1.6
+
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