diff options
-rw-r--r-- | sci-biology/bioruby/ChangeLog | 9 | ||||
-rw-r--r-- | sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild | 38 | ||||
-rw-r--r-- | sci-biology/bioruby/bioruby-9999.ebuild | 6 | ||||
-rw-r--r-- | sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch | 29 |
4 files changed, 79 insertions, 3 deletions
diff --git a/sci-biology/bioruby/ChangeLog b/sci-biology/bioruby/ChangeLog index 432845c9118f..9642a5bcb3bb 100644 --- a/sci-biology/bioruby/ChangeLog +++ b/sci-biology/bioruby/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/bioruby # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioruby/ChangeLog,v 1.17 2013/10/24 14:31:54 chainsaw Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioruby/ChangeLog,v 1.18 2013/11/25 01:13:15 mrueg Exp $ + +*bioruby-1.4.3.0001-r1 (25 Nov 2013) + + 25 Nov 2013; Manuel Rüger <mrueg@gentoo.org> +bioruby-1.4.3.0001-r1.ebuild, + +files/bioruby-1.4.3.0001-fix-tests.patch, bioruby-9999.ebuild: + NMU: Add missing dependency on libxml and ruby20 support. Fix tests see bug + #489712 24 Oct 2013; Tony Vroon <chainsaw@gentoo.org> bioruby-1.4.3.0001.ebuild: Marked stable on AMD64 based on arch testing by Elijah "Armageddon" El diff --git a/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild new file mode 100644 index 000000000000..ec5740e9004b --- /dev/null +++ b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild,v 1.1 2013/11/25 01:13:15 mrueg Exp $ + +EAPI=5 + +USE_RUBY="ruby18 ruby19 ruby20" + +inherit ruby-fakegem + +DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" +LICENSE="Ruby" +HOMEPAGE="http://www.bioruby.org/" +SRC_URI="http://www.${PN}.org/archive/${P}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~ppc ~x86" + +ruby_add_rdepend "dev-ruby/libxml" + +PATCHES=( "${FILESDIR}"/${P}-fix-tests.patch ) + +each_ruby_configure() { + ${RUBY} setup.rb config || die +} + +each_ruby_compile() { + ${RUBY} setup.rb setup || die +} + +each_ruby_install() { + ${RUBY} setup.rb install --prefix="${D}" || die +} + +each_ruby_test() { + ${RUBY} -rubygems test/runner.rb || die +} diff --git a/sci-biology/bioruby/bioruby-9999.ebuild b/sci-biology/bioruby/bioruby-9999.ebuild index 3e2293783c7d..82342ab74b25 100644 --- a/sci-biology/bioruby/bioruby-9999.ebuild +++ b/sci-biology/bioruby/bioruby-9999.ebuild @@ -1,10 +1,10 @@ # Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioruby/bioruby-9999.ebuild,v 1.4 2013/09/14 12:55:24 mrueg Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioruby/bioruby-9999.ebuild,v 1.5 2013/11/25 01:13:15 mrueg Exp $ EAPI=5 -USE_RUBY="ruby18 ruby19" +USE_RUBY="ruby18 ruby19 ruby20" EGIT_REPO_URI="git://github.com/bioruby/bioruby.git https://github.com/bioruby/bioruby.git" @@ -18,6 +18,8 @@ SLOT="0" IUSE="" KEYWORDS="" +ruby_add_rdepend "dev-ruby/libxml" + all_ruby_unpack() { git-2_src_unpack } diff --git a/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch b/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch new file mode 100644 index 000000000000..71c4ca27104a --- /dev/null +++ b/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch @@ -0,0 +1,29 @@ +From edda65b8fb32c2eee6b0652074981c31aa68b0eb Mon Sep 17 00:00:00 2001 +From: Naohisa Goto <ng@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 +@@ -100,7 +100,7 @@ def test_open_with_block + end + + def test_new +- 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) +-- +1.8.4 + |