gentoo resync : 15.09.2019

5 files changed, 0 insertions, 130 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 58e636e73b74..4cd06f52c8e2 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/goby/Manifest b/sci-biology/goby/Manifest
deleted file mode 100644
index c4fd6f5d84c4..000000000000
--- a/sci-biology/goby/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-DIST goby_1.9.7.3-deps.zip 19959489 BLAKE2B 75280cdbb24c29b8ed5ca88ca03d40578b90944078f02cfddd99b14951d0411254e6dc5c863b6b770b2c74eafc0409776715d0c8396ba1a5cc98ecf3cebe0f2c SHA512 a077e18d6bb7603522108de2b3c50d1b7a281c9e1a8d5d78c85b660285d743baf7b52ceaea44903a5a27adfa80ea5823d5aaa47a3f2ec426e7ddb17fd67a477d
-DIST goby_1.9.7.3-src.zip 15642000 BLAKE2B 4df4788104639a80810314793b935ef0c6931c09d4e87a65a9ffb33e9e22bbe4106d2f323c8726db1b08cbc56a5ddf1ac09f3a21060e0ba8e0a3f7418cba1168 SHA512 f213908e745e6c6d86895412f3ad14a8e0f2f3fbaba9205bffd7415982fc53181ca0b03b543063d0cbcd87f881d1b58eedb38a5090fa7ac20bdc513e54f83dd5
-DIST goby_1.9.8.1-deps.zip 20820943 BLAKE2B ad4173f42cdf66e9849e0e76fda37a22c9591c57004873f42320bf408a0cb5c0217b23deb3114e3dacdc1ea53e5f2717c8a640dc68b34db4c47f299d6e9dffac SHA512 16cf79e2dab8cfc62f9d012b88b0d81e712e67cf2f70582969624a019863f21ee20a4ce0517d5b74782d8d200318451e3f889fb967c6935e896d526d2a6fc02e
-DIST goby_1.9.8.1-src.zip 15748880 BLAKE2B 06fda375ff926137c6abc18b8b388e3d49731600f98fe1c23e6607a0ff0ef4c818acec356e86eacb6b20d2e9600e0ee7a9b5770e524c1b30266cc4a3c9b5bbee SHA512 68e772f1a60d1c78d2b08ee203f462e6ac19a46124d25ac1bd7c69065d8122ce6dbfbd3cc6aa287b13b11d5442e9b41609463a8391ffe037249655a212284ff0
-EBUILD goby-1.9.7.3-r1.ebuild 1531 BLAKE2B b76fd81aee6c1f67b6f749c8e153f52c985e564f1e81bd68c27a2d90c6e39617a1b8f91ac1ab66fcdfb523ccf13653ba68db09da90f872d077b958977f9aab4e SHA512 b8a99a082b6453db69ce740912d823e2f5b0009ded8082fa66955882e1b88fc86c92b374a17d0d8d9870624119ba2509f8cefb3e5165b87a22cd540e9c40c768
-EBUILD goby-1.9.8.1-r1.ebuild 1531 BLAKE2B b76fd81aee6c1f67b6f749c8e153f52c985e564f1e81bd68c27a2d90c6e39617a1b8f91ac1ab66fcdfb523ccf13653ba68db09da90f872d077b958977f9aab4e SHA512 b8a99a082b6453db69ce740912d823e2f5b0009ded8082fa66955882e1b88fc86c92b374a17d0d8d9870624119ba2509f8cefb3e5165b87a22cd540e9c40c768
-MISC metadata.xml 330 BLAKE2B ddd0725ad965e39412cd06f12b75923da7cb52da5d584d6b10751ed17d5148e7555668e8c112bdab833e4d467ab41e936128a09ee1c832f06fe0b5ddd4ffb679 SHA512 7d7909e5632e5d2c18241237d5e06501e50d2d1fe07a618e8a028fbdd17bc2a420e23bead1529c6cfe76a82fdb04fd636b911230b57722ad9bd16e796baeb87e
diff --git a/sci-biology/goby/goby-1.9.7.3-r1.ebuild b/sci-biology/goby/goby-1.9.7.3-r1.ebuild
deleted file mode 100644
index 9cab1b56d54e..000000000000
--- a/sci-biology/goby/goby-1.9.7.3-r1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
-EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf-java,fastutil,log4j,jsap,commons-configuration,commons-math-2"
-EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
-
-JAVA_ANT_REWRITE_CLASSPATH="true"
-
-#inherit java-pkg-2 java-ant-2 subversion
-inherit java-pkg-2 java-ant-2
-
-MY_P="${PN}_${PV}"
-
-DESCRIPTION="A DNA sequencing data management framework"
-HOMEPAGE="http://campagnelab.org/software/goby/"
-SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
-	http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-IUSE="+cpp"
-KEYWORDS="~amd64 ~x86"
-
-COMMON_DEPS="dev-java/commons-logging
-	dev-java/commons-lang:2.1
-	dev-java/commons-io:1
-	dev-java/protobuf-java:0
-	dev-java/fastutil:0
-	dev-java/log4j
-	dev-java/jsap
-	dev-java/commons-configuration
-	dev-java/commons-math:2"
-DEPEND=">=virtual/jdk-1.6
-	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
-	${COMMON_DEPS}
-	cpp? ( ~sci-biology/goby-cpp-${PV} )"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	sed -i '/sge/ d' build.xml || die
-	java-pkg-2_src_prepare
-}
-
-src_install() {
-	java-pkg_dojar goby*.jar
-	java-pkg_dolauncher goby --jar goby.jar
-
-	insinto /usr/share/${PN}
-	doins -r python
-	dodoc CHANGES.txt
-}
diff --git a/sci-biology/goby/goby-1.9.8.1-r1.ebuild b/sci-biology/goby/goby-1.9.8.1-r1.ebuild
deleted file mode 100644
index 9cab1b56d54e..000000000000
--- a/sci-biology/goby/goby-1.9.8.1-r1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
-EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf-java,fastutil,log4j,jsap,commons-configuration,commons-math-2"
-EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
-
-JAVA_ANT_REWRITE_CLASSPATH="true"
-
-#inherit java-pkg-2 java-ant-2 subversion
-inherit java-pkg-2 java-ant-2
-
-MY_P="${PN}_${PV}"
-
-DESCRIPTION="A DNA sequencing data management framework"
-HOMEPAGE="http://campagnelab.org/software/goby/"
-SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
-	http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-IUSE="+cpp"
-KEYWORDS="~amd64 ~x86"
-
-COMMON_DEPS="dev-java/commons-logging
-	dev-java/commons-lang:2.1
-	dev-java/commons-io:1
-	dev-java/protobuf-java:0
-	dev-java/fastutil:0
-	dev-java/log4j
-	dev-java/jsap
-	dev-java/commons-configuration
-	dev-java/commons-math:2"
-DEPEND=">=virtual/jdk-1.6
-	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
-	${COMMON_DEPS}
-	cpp? ( ~sci-biology/goby-cpp-${PV} )"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	sed -i '/sge/ d' build.xml || die
-	java-pkg-2_src_prepare
-}
-
-src_install() {
-	java-pkg_dojar goby*.jar
-	java-pkg_dolauncher goby --jar goby.jar
-
-	insinto /usr/share/${PN}
-	doins -r python
-	dodoc CHANGES.txt
-}
diff --git a/sci-biology/goby/metadata.xml b/sci-biology/goby/metadata.xml
deleted file mode 100644
index a1e19f7893ca..000000000000
--- a/sci-biology/goby/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?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>
-  <use>
-    <flag name="cpp">Compile C/C++ API</flag>
-  </use>
-</pkgmetadata>