pkgmove from dev-java/ to sci-biology/

5 files changed, 0 insertions, 194 deletions

diff --git a/dev-java/biojava/ChangeLog b/dev-java/biojava/ChangeLog
deleted file mode 100644
index 4a68603f502b..000000000000
--- a/dev-java/biojava/ChangeLog
+++ /dev/null
@@ -1,26 +0,0 @@
-# ChangeLog for dev-java/biojava
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-java/biojava/ChangeLog,v 1.5 2014/05/24 07:34:23 pacho 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/dev-java/biojava/Manifest b/dev-java/biojava/Manifest
deleted file mode 100644
index f4cdecc86c1e..000000000000
--- a/dev-java/biojava/Manifest
+++ /dev/null
@@ -1,16 +0,0 @@
------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 1998 SHA256 1718343a257764cd22a481821024e0cc86dfe18c1d6e592b5e3d0f266d94f140 SHA512 2b8fcb45e20a1668ec353ccc08ed0b9beeee57e3b5ec2b459fe284128dda512907bb4c69ac274a9718b5718f11147191ca0a58a29570f11e4998886d05b511a7 WHIRLPOOL 2061420fbda7aa97fcaa18e7b8b9cea9f734c5e6dbd44baaa1a743e2fbcac1f5b1793220de8ffdea6dc1cbb3b77b66c13f4eeb2e0c4b8cbd9cc5b47425fce2f0
-EBUILD biojava-1.7.ebuild 2024 SHA256 58f64d2b7082b8b3d3d7419cc2f9ec33e50a1f1bc5d79abe692f4de6cb421a0c SHA512 e9fefae4767ce89b9c65e554a2982973b51b3d9166226e94878c052a2f5ba16b9ca42f2ed3dcfe77656c0e68ae71d253739284428bf5fd258fc11cc214d24fe4 WHIRLPOOL 50f925c78c99d5d60c114ad24caed1fe67c474d754c1ad83dc702a146a1062ec44b1e20bbbf021cc715c94a5c6d2c885b39100287e08b5791617b2171d9b3cc7
-MISC ChangeLog 808 SHA256 56fc98dae29c0a36012d5d94a68d6004bf2185834623500393873f6ba6870420 SHA512 a7c12ad4e5adef6cb359a9e44986a9a63848d1b9ad2459e8a4c59c719f6b93133c6e53224bba6a8af1a63ee5aa10a336b87c68bce29b7d94e85e33baa6691441 WHIRLPOOL 592251c660d755fef362b33d9bd921d0532750d92f0793d302f7e8386a12023f57d67c168a469093c90306c13e064bd08462f678e1797cfe309cc4acee53f100
-MISC metadata.xml 159 SHA256 1c070a909e96d9d193f84ad9304d196febbe33b60a724cc4b0d20634bb82255b SHA512 269cf19c37f2d136b926f546ec83ffdbc1374b2b6e26f8a31f21854143380386c31bfc7b2a0b9c47fb1f7c02607ddbdd43e517cb5c3270515e465c4dd7788843 WHIRLPOOL afb402fec04cddb3184b69eb8a8d36b404edd2870fd06c8f5e99be39c341ea6fa7542e0b680fac05529522ed33838e8279381d7a6de9dbc58fe55841229d8a51
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.22 (GNU/Linux)
-
-iEYEAREIAAYFAlOAS4AACgkQCaWpQKGI+9Tk1QCfUz8hL9mhvsTqlBQTPnYFG5xP
-ZMkAnjWvl+s5byhmJDN3/lLU4qsPvDyf
-=cEUm
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diff --git a/dev-java/biojava/biojava-1.6.ebuild b/dev-java/biojava/biojava-1.6.ebuild
deleted file mode 100644
index 0db0b2efb96f..000000000000
--- a/dev-java/biojava/biojava-1.6.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-java/biojava/biojava-1.6.ebuild,v 1.1 2009/01/25 19:33:17 weaver 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/dev-java/biojava/biojava-1.7.ebuild b/dev-java/biojava/biojava-1.7.ebuild
deleted file mode 100644
index d2e67430ec9f..000000000000
--- a/dev-java/biojava/biojava-1.7.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-java/biojava/biojava-1.7.ebuild,v 1.2 2010/03/20 13:39:10 betelgeuse 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/dev-java/biojava/metadata.xml b/dev-java/biojava/metadata.xml
deleted file mode 100644
index 604e0a4238bb..000000000000
--- a/dev-java/biojava/metadata.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>java</herd>
-</pkgmetadata>
-