diff options
Diffstat (limited to 'sci-biology/bioruby')
| -rw-r--r-- | sci-biology/bioruby/Manifest | 8 | ||||
| -rw-r--r-- | sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild | 37 | ||||
| -rw-r--r-- | sci-biology/bioruby/bioruby-1.5.1.ebuild | 22 | ||||
| -rw-r--r-- | sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch | 29 | ||||
| -rw-r--r-- | sci-biology/bioruby/metadata.xml | 8 |
5 files changed, 104 insertions, 0 deletions
diff --git a/sci-biology/bioruby/Manifest b/sci-biology/bioruby/Manifest new file mode 100644 index 000000000000..0404ed685d63 --- /dev/null +++ b/sci-biology/bioruby/Manifest @@ -0,0 +1,8 @@ +AUX bioruby-1.4.3.0001-fix-tests.patch 1082 SHA256 a2347c4e0c731ab24d3054002837de16821b26956e0ffeac97c62b6591c7ca5a SHA512 0a46f8d049521d90993274b52d7bece39464999a4286ac2052a7c8cfb97fe31af7eeadfc8d42c2cbd71f80aca6ac6a778eeb1de7341368ef2ee726444b74752e WHIRLPOOL 05aad8aa4e2a60c5215b6a26ccd942b8fa687a5bce99a0918db6f3a859be961ba131c5a74c3badfede98019a70c793c0153de873aff1d984872383fc4fe3ddc7 +DIST bio-1.5.1.gem 1445376 SHA256 896c19af7e724e038baceae20c00688872b70c69ef966ef3adc42696d001b441 SHA512 822ac6c3d85847193fc1992087abc868e4d1a7cfca82da6ab1830af2927a2a582c3993bc681e129a6aac224ed1cb0b33056d8cc02d3e36d68c9d6a4153c321ca WHIRLPOOL fc8ca3cc508e5d1c95b986cb64eaf28641833498110530a625836117d4a55e9bc01e91da9cd9d71ec40de209e4adb683fff0337260d7b0d8fe30b0659bed94c6 +DIST bioruby-1.4.3.0001.tar.gz 1500656 SHA256 20d6548e1c5977464afd74019693dde9e45a030d48d974db08a7b85c4214fb35 SHA512 77ad96388e1e8b1dccab582a3bc309b99b36cac1803f79b42707fc4dbf439de31ed491ce5e1c2e59f695643756ae0df2e275bbcd9ad6827f251b52edd677d821 WHIRLPOOL ccb952d4cd3b8700acbf356a0965842b068aa2fb861dfab58e7442e5570ab79604a8be1fb86a9d80d6bc9a8f9dc886daf98cb84fe7298b4f334e0e6be198f9e7 +EBUILD bioruby-1.4.3.0001-r1.ebuild 720 SHA256 2defe33e7f52e6890931b9ef9643b763a9ad6f94d9cfd6f7610419a4fea060e7 SHA512 9a929ffe9e804ce835d0399fad4afa9dd8b0d9d2acfd234d2944168826e05d77e538c1163ad5add74b62433a10319b1b492d91ddd8786ba52dabbf7b27ea2b8f WHIRLPOOL ecfc151b2cf910cea88fea75b3574c02fe7def8b90c8244693a1a71adda0106e3e3d8ce42b0ea6f2d5432806a6ad87356e4d679b62f630385daf7b9e466d7db2 +EBUILD bioruby-1.5.1.ebuild 440 SHA256 273aff24621c87dadbf37ac00f31432f279487cdc9ab80f338909744065d6c0d SHA512 b6812050b69f792b268d9e06e0d72f19d4b7a01d4fcb8fd8aa335ac111359f4585de8f7a55793192c94a7291f2caf0e038668aa5a0a5171b762a3fc04f6d1e2d WHIRLPOOL 7f4e5e605429b7068e60ab49858056cbcce2fb63c816ecd60fb7bb5b0a4339d1abc30f2080910ae477bb80537ab269ebf428e40fa319207b7beb137fc6a3f6f4 +MISC ChangeLog 2846 SHA256 1d408014c718f1a4b2a324cd81468717dfbf8a87b69ef66ae6c99ddc7ec080e3 SHA512 4b7ca4cb97ca78cb79560e84d45252611c724f31b575c4e7fa9baea0d4c6839e920e35caee8c0daba2554bab58d8e5a6de315e3413e0026a457374a09d3e553e WHIRLPOOL ab646e4c28ea30be0d4ea0cbe69958055c5c0ab069541df6b50d7ecc10f7f9b5f04455d7271b269896ae68c9d4c93f0a0a3a8c6eeacfc23097d0019c01680793 +MISC ChangeLog-2015 3291 SHA256 a26c4357e8b5e77a8320cf18d5ddc8edd842e1343834dc205b1f9d6d3756f5f3 SHA512 189d5703b69ad3c25521c1a28f2aa75b373581f0202d3021d0d553d76b7437b2c81b357e244a3cb2d72072e03ae91f986a207cfd2b7b794d909af5b5e1615a12 WHIRLPOOL ed208d74756d193040c859611bb07ca238bf3e89d4c62e00df366523c96cf266871b516eceb689e383c96c9391c4bb5c673767241e67ff5c6f1462309a3547a4 +MISC metadata.xml 261 SHA256 15c95fe0beb2b86b616b7ac1be6f1118bd598d907b441a94d87721c0d6f36855 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a WHIRLPOOL c00a986f98ceb4fa20ffdb0c411de9841218f8af6f7499a20a34258db4cd74cead97ef2ee18ac8cac7eae7db3c95084cbf8aa3a36f95a1ed7efbb0e088eb50c8 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..de7ff26eeb4b --- /dev/null +++ b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +USE_RUBY="ruby21 ruby22" + +inherit ruby-fakegem + +DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" +LICENSE="Ruby" +HOMEPAGE="http://bioruby.org/" +SRC_URI="http://${PN}.org/archive/${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-1.5.1.ebuild b/sci-biology/bioruby/bioruby-1.5.1.ebuild new file mode 100644 index 000000000000..f5e558c7ff33 --- /dev/null +++ b/sci-biology/bioruby/bioruby-1.5.1.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +USE_RUBY="ruby21 ruby22 ruby23" + +RUBY_FAKEGEM_NAME="bio" + +RUBY_FAKEGEM_EXTRAINSTALL="etc" + +inherit ruby-fakegem + +DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" +LICENSE="Ruby" +HOMEPAGE="http://bioruby.org/" + +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~ppc ~x86" + +ruby_add_rdepend "dev-ruby/libxml" 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 + diff --git a/sci-biology/bioruby/metadata.xml b/sci-biology/bioruby/metadata.xml new file mode 100644 index 000000000000..8417d1580d40 --- /dev/null +++ b/sci-biology/bioruby/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> |