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author | 2015-08-05 14:02:44 +0000 | |
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committer | 2015-08-05 14:02:44 +0000 | |
commit | 1c2bf52b717fb8c1a8a9494e9f0feb386ea8596a (patch) | |
tree | 95120f23f9998cc15f9b5def4bbe6aa63f161c0e /sci-biology | |
parent | Fix oops commit with cvs directly (diff) | |
download | historical-1c2bf52b717fb8c1a8a9494e9f0feb386ea8596a.tar.gz historical-1c2bf52b717fb8c1a8a9494e9f0feb386ea8596a.tar.bz2 historical-1c2bf52b717fb8c1a8a9494e9f0feb386ea8596a.zip |
pkgmove from dev-java/ to sci-biology/
Signed-off-by: Patrice Clement <monsieurp@gentoo.org>
Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0x93491BB8
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/biojava/ChangeLog | 26 | ||||
-rw-r--r-- | sci-biology/biojava/Manifest | 20 | ||||
-rw-r--r-- | sci-biology/biojava/biojava-1.6.ebuild | 73 | ||||
-rw-r--r-- | sci-biology/biojava/biojava-1.7.ebuild | 73 | ||||
-rw-r--r-- | sci-biology/biojava/metadata.xml | 6 |
5 files changed, 198 insertions, 0 deletions
diff --git a/sci-biology/biojava/ChangeLog b/sci-biology/biojava/ChangeLog new file mode 100644 index 000000000000..8369f17f1275 --- /dev/null +++ b/sci-biology/biojava/ChangeLog @@ -0,0 +1,26 @@ +# ChangeLog for dev-java/biojava +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biojava/ChangeLog,v 1.1 2015/08/05 14:02:36 monsieurp Exp $ + + 24 May 2014; Pacho Ramos <pacho@gentoo.org> metadata.xml: + Cleanup due #199047 + + 20 Mar 2010; Petteri Räty <betelgeuse@gentoo.org> biojava-1.7.ebuild: + Keyword ~x86. + +*biojava-1.7 (10 Jul 2009) + + 10 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +biojava-1.7.ebuild: + Version bump + + 07 Feb 2009; weaver <weaver@gentoo.org> metadata.xml: + Assume ownership + +*biojava-1.6 (25 Jan 2009) + + 25 Jan 2009; weaver <weaver@gentoo.org> +metadata.xml, + +biojava-1.6.ebuild: + Import from Java overlay, thanks to serkan + + 22 Jan 2009; Alistair Bush <ali_bush@gentoo.org> ChangeLog: + Add ChangeLog for QA. diff --git a/sci-biology/biojava/Manifest b/sci-biology/biojava/Manifest new file mode 100644 index 000000000000..cb407dbae521 --- /dev/null +++ b/sci-biology/biojava/Manifest @@ -0,0 +1,20 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST biojava-1.6-all.jar 24571007 SHA256 2d10334fe6022d1b64219505ba4d2a32027ab7218d775878506d3e7c00f6ce7e SHA512 300bd6e02fe052c810c52cb2cc4255628bee704af187ad746b97e57941778dc3a1996b3917db021d74db8c716f94c90c94c5a5e2d4bc212c06259381045f3034 WHIRLPOOL e5a52aaa6e9a9d6780d5f55b6d164db07388e9c595296d4e4a11dc241aa0745fa726279d19a0c97d1966b0a14c06af2b9b588873ad522aeeff881534f0871f10 +DIST biojava-1.7-all.jar 28062592 SHA256 5c5e7fc66bc79a07494fb7d935164ec2aab50dc2effb7644f89bfa4fc907bb3f SHA512 867862b45f014bcd1afd37691e91b948ede05e96f84c7051953d32dad49908781235aad80301e22a15fa8b4145e80c78cf3935d6e581a2e60b56c9308f8adaa8 WHIRLPOOL 5669293ce362e82562454c5902d523e69f64d90e117e75b5de844e0ef5866d250507b86f78245ac82f19932ad9aa196ad17d96a3f703187a3ab2daf00893af9b +EBUILD biojava-1.6.ebuild 2004 SHA256 a6c787e1463ac3c9a6a15efd6d9d9f7827ca3688b6527feef910bb3dedf9b29d SHA512 2bbf7273f3149be82c604c485144ff6ebc9ce4fd222bf356ebefa38429a4f93e3b84947548967a23ce0591dca87da17062bb658b493b8062018a122cf5d0b3b0 WHIRLPOOL 1d05f7f4aa6762de077e79793dbd0e83c4bb80690d3741ccbed790d88ccb99ce3917876acda2783b356c9cbe8118ce80a4bc6d97dc4483857488fabe0dd3fbee +EBUILD biojava-1.7.ebuild 2026 SHA256 9d994995677a07e18323e72e6c19fb09b4068bd0c1370e28022a55faa9c3e4a2 SHA512 5ab157b9ba634d85033911defc65b48d857386027dd64b95528b0932370042d7238a183b8c5113f769ed3e7b3b6950b80201840e1489429659756d6395f1ac94 WHIRLPOOL 8156bc40fb8284899d8e4a23ade8b45601e7fcbc3246c721ddfeee13ec349489a866c4623ae8b6e9cb2e7dd8b060110a3cb8c0a4d4e63d16e86e6adfa62732ae +MISC ChangeLog 815 SHA256 3b4032bcb9b0d9f27bcd843196e5332d5301f404cea4334d392b11652beb8bee SHA512 b43456bff1ad36187d2666416956f069fbc89529a0603bd84532d49103849413278546fbdba8ce2a9a31a972116bdb88051122687fdcbccaf86a05620384d449 WHIRLPOOL 3ce15f2a8aef814454615644d53dc479d7f7663b1012a2bbc10b68b7322b6c8b35c1375d6e88ca9381eeea67c918c6b89b8ab4a88ab89c9db70c4f77387d83bf +MISC metadata.xml 184 SHA256 b1eba987253b6431655eb740d92c9317127741c254ccf58811333144072fed15 SHA512 810509270c115326274543d26ae73517c79690223fdc33cecd2ac55a5ad2a0bc5bf773f52f865bfd1e57caaf6e932f4622d6403b3248a4bb50a9d782c43cec3b WHIRLPOOL a2e20616a149551b2873be9eb84ce99ebad34323db12c2ced66731775e69d9ef7fbf952256019d6e573f420bb87b37dd8e147e29a479c0480fc349345caaf467 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2 + +iQEcBAEBCAAGBQJVwiWyAAoJEJGRpfGTSRu4q/8H/0zMH1sjgR6julyuVtUspN9U +rm0NMHWTdArnVNW6Bg1UJFlTNDEEji2u4UXOjhbD5TgPSQ6sO/JJP8nZFn26upfL +RrJdCUJqDzBkddqDQ6njONxoHegkrSu6VMOUc/DJHdjxx5En0jMbYh1NbsnkuVJ0 +Cxq5y0xq7lnhfseL9IJ4Iqd7c+jPpJw6BgqY/iG7cGDvxBNYKs85ZPHwNQsDICBt +GNWrF3UBBG9Tct0UVjuH38X/XZ++2Yc9W4XfikZQEp6JZvk/cX8jjRkTutHUHw19 +nADno5yMzHhTXZE64QblGUvEssddH0oz9EAILk+tJeWzf9YRW2z5pioPXAskMDE= +=jxO9 +-----END PGP SIGNATURE----- diff --git a/sci-biology/biojava/biojava-1.6.ebuild b/sci-biology/biojava/biojava-1.6.ebuild new file mode 100644 index 000000000000..1a1373eccde8 --- /dev/null +++ b/sci-biology/biojava/biojava-1.6.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biojava/biojava-1.6.ebuild,v 1.1 2015/08/05 14:02:36 monsieurp Exp $ + +# TODO: +# -Fix javadoc generation OutOfMemoryError +# -Add launchers for 2 apps in biojava-apps.jar +# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag) + +EAPI=2 + +#JAVA_PKG_IUSE="doc source test" +JAVA_PKG_IUSE="source test" + +inherit eutils java-pkg-2 java-ant-2 + +DESCRIPTION="A Java framework for processing biological data" +HOMEPAGE="http://biojava.org" +SRC_URI="http://www.biojava.org/download/bj16/all/${P}-all.jar" +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +COMMON_DEPEND="dev-java/jgrapht:0 + dev-java/commons-cli:1 + dev-java/commons-dbcp:0 + dev-java/commons-pool:0 + dev-java/bytecode:0" + +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPEND}" +DEPEND=">=virtual/jdk-1.5 + app-arch/unzip + ${COMMON_DEPEND} + test? + ( + dev-java/junit:4 + dev-java/ant-junit4 + )" + +S="${WORKDIR}/biojava-live_${PV}" + +JAVA_ANT_IGNORE_SYSTEM_CLASSES="true" + +src_prepare() { + einfo "Removing budled jars." + find . -name "*.jar" -print -delete + rm -r doc/* + java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar + java-pkg_jar-from commons-cli-1 + java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar + java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar + java-pkg_jar-from bytecode +} + +src_compile() { + #ANT_OPTS="${ANT_OPTS} -Xmx512m" + eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all) +} + +src_install() { + java-pkg_newjar ant-build/biojava.jar ${PN}.jar + java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar + java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar + #use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos} + use source && java-pkg_dosrc {src,apps,demos}/org +} + +src_test() { + java-pkg_jar-from junit-4 junit.jar junit-4.4.jar + ANT_TASKS="ant-junit4" eant runtests +} diff --git a/sci-biology/biojava/biojava-1.7.ebuild b/sci-biology/biojava/biojava-1.7.ebuild new file mode 100644 index 000000000000..759af51894d5 --- /dev/null +++ b/sci-biology/biojava/biojava-1.7.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biojava/biojava-1.7.ebuild,v 1.1 2015/08/05 14:02:36 monsieurp Exp $ + +# TODO: +# -Fix javadoc generation OutOfMemoryError +# -Add launchers for 2 apps in biojava-apps.jar +# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag) + +EAPI=2 + +#JAVA_PKG_IUSE="doc source test" +JAVA_PKG_IUSE="source test" + +inherit eutils java-pkg-2 java-ant-2 + +DESCRIPTION="A Java framework for processing biological data" +HOMEPAGE="http://biojava.org" +SRC_URI="http://www.biojava.org/download/bj17/all/${P}-all.jar" +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +COMMON_DEPEND="dev-java/jgrapht:0 + dev-java/commons-cli:1 + dev-java/commons-dbcp:0 + dev-java/commons-pool:0 + dev-java/commons-collections:0 + dev-java/bytecode:0" + +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPEND}" +DEPEND=">=virtual/jdk-1.5 + app-arch/unzip + ${COMMON_DEPEND} + test? + ( + dev-java/junit:4 + dev-java/ant-junit4 + )" + +S="${WORKDIR}/biojava-${PV}" + +JAVA_ANT_IGNORE_SYSTEM_CLASSES="true" + +src_prepare() { + einfo "Removing bundled jars..." + find . -name "*.jar" -print -delete + java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar + java-pkg_jar-from commons-cli-1 + java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar + java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar + java-pkg_jar-from bytecode +} + +src_compile() { + #ANT_OPTS="${ANT_OPTS} -Xmx512m" + eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all) +} + +src_install() { + java-pkg_newjar ant-build/biojava.jar ${PN}.jar + java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar + java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar + #use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos} + use source && java-pkg_dosrc {src,apps,demos}/org +} + +src_test() { + java-pkg_jar-from junit-4 junit.jar junit-4.4.jar + ANT_TASKS="ant-junit4" eant runtests +} diff --git a/sci-biology/biojava/metadata.xml b/sci-biology/biojava/metadata.xml new file mode 100644 index 000000000000..0a18364544e8 --- /dev/null +++ b/sci-biology/biojava/metadata.xml @@ -0,0 +1,6 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <herd>java</herd> +</pkgmetadata> |