NMU: Add missing dependency on libxml and ruby20 support. Fix tests see bug #489712

Package-Manager: portage-2.2.7/cvs/Linux x86_64

5 files changed, 83 insertions, 15 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/Manifest b/sci-biology/bioruby/Manifest
index 477147273c2c..776f14b63e54 100644
--- a/sci-biology/bioruby/Manifest
+++ b/sci-biology/bioruby/Manifest
@@ -1,17 +1,9 @@
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 DIST bioruby-1.3.1.tar.gz 944866 SHA256 07f3816215cd5e7d2825fa335184447626f804afd2932a09116ccf8521fd720c
 DIST bioruby-1.4.3.0001.tar.gz 1500656 SHA256 20d6548e1c5977464afd74019693dde9e45a030d48d974db08a7b85c4214fb35 SHA512 77ad96388e1e8b1dccab582a3bc309b99b36cac1803f79b42707fc4dbf439de31ed491ce5e1c2e59f695643756ae0df2e275bbcd9ad6827f251b52edd677d821 WHIRLPOOL ccb952d4cd3b8700acbf356a0965842b068aa2fb861dfab58e7442e5570ab79604a8be1fb86a9d80d6bc9a8f9dc886daf98cb84fe7298b4f334e0e6be198f9e7
 EBUILD bioruby-1.3.1.ebuild 650 SHA256 2dfc454e80994798081cd11ab86dd0eaae93aafdbe0b21aba44166ed5a8c094e SHA512 214e113ad0146d027682a04b1cfeef35a6bbd3b504e4250ce38a9efe447469400cfaf2406d9affb473ba302b4b70450f9c2777da285852a1d26b6092e8e4f0bd WHIRLPOOL 1fd7bcae7194c5c3f2af75ae0950e15096144f35084848abb458ec1ffa364f21ef40e9325cbd712da62ee1963e8f7eff59cc47cd98927c6bdc939fb548188f9a
+EBUILD bioruby-1.4.3.0001-r1.ebuild 859 SHA256 5c1c3b960705fd0de0ba95894472590e2cc57d737f848cf56749fa40c667feca SHA512 7a211581d857c1c754dff4356b01723cc6774c4fdcdfb8f52e754340094a0217bb72e8c04acddf46d8bf7d74d17753abb1e9c966d480688786e0a00825d0f602 WHIRLPOOL ca99eb85e5da33a93e5d583698e28e2386b86d49e726792b1f7bd5a4970d702cec320c559b5aab5ce0ea9d13489975596122d9592fae3982bc26725c5be0e428
 EBUILD bioruby-1.4.3.0001.ebuild 767 SHA256 999ecfd25ec34bbba32e3392cd2b879043b4f3882d00da6d1d02f4c1bfe1ad0d SHA512 b7b26d11e813df569c4b10c42caef0abe024d96c230702d7fefaa3100acbeb115cda21e529d0d84da9e86d202eebae0bc19b920dfe07de35304e21c47801e000 WHIRLPOOL 10f2dd928222a395cdbe4872e9dd614e806ee9c33c40ee4e0bfb327a0cf75853137b24394dd31539700409f7034daddd603c456eee1d01a1f9896b0418f2f87c
-EBUILD bioruby-9999.ebuild 842 SHA256 c0c813a4cf843d866d54c5829f49747187f445746616437b5c17570f49f3e30b SHA512 d69d16aa923dbc3746927518ccc3ef0dcf03d93ea458a44e62fad57706c8e56034e0ba86040365f17432744dc9b4195d9c8f678c2890fb137b9a24b339951adc WHIRLPOOL 87034d724ce12e629eee97082e5e9600c35cdb04099bb3eb4cf27e17dfb207b1ce423956e624ff1f0699ad24cd1e94b60634287bcb89f813b0f8f86d7413f7c1
-MISC ChangeLog 2558 SHA256 393494765e4eeb0b1523cff27f7eabf95d8d46c94018b758c1653d3d0229889a SHA512 4948c6d6d1cd81a9149428813dfce16bbf048ce260117ee8037359c31ff210d7f97eb5ec9816dcfc0518629effc4f6b4f2d8500febe9c3e65168f678a9812450 WHIRLPOOL 2eb8f0a2d78d14d13491129b1d2e8a47c359f9e091b0f2abc7b107a17089847b07e2b545b2d384443403a845328c5d2fad503fab9245124e9c6c79b3036a64ef
+EBUILD bioruby-9999.ebuild 885 SHA256 b9f4cec6a143da1ae0e1f9fe6134da5b7e63ba6bc6cc7adad20809ae2c4693c5 SHA512 0de5cf09500498334c33b5d369b2358f860090a0a0d0280f54893647021820c1aefced6991d19ecb6f9dd6a2cac69d47db50501cabbec6ca8b4d9d599a462fa1 WHIRLPOOL 01566eda8843fa20510e49ee3aa45feae38952fc771c4c18b73096c2b7471008167eff709b08dd819ede85f27db6148fb4fcd5bf124f28c62134fe86c1b16759
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 MISC metadata.xml 165 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 SHA512 f197731b98b313b41180dc4b553dab070b28f1badcb259973d528640166feaf8b6c48f56158431d1a4daac9b2873da05c2bd4e4ec269db310581d398a494d166 WHIRLPOOL 83774f905f256ee3dc965af16b472d0ac546314f46d02414b1da590eae1059f8076e63d67f763f9a3afb60a12072fd18c49937b039acbc8ac599ae45c0a04139
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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
+