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authorJames Le Cuirot <chewi@gentoo.org>2016-04-03 22:40:33 +0100
committerJames Le Cuirot <chewi@gentoo.org>2016-04-03 22:43:18 +0100
commitc07656a5f7189d994d99fcc1cb5e12c15521c03d (patch)
treeca6f0ca7396effa03408a9c233f946195698dc1e
parentdev-java/jamon: Remove vulnerable 1.01-r3 wrt bug #499330 (diff)
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sci-biology/readseq: Remove dead package, see bug #550148
-rw-r--r--sci-biology/readseq/Manifest2
-rw-r--r--sci-biology/readseq/files/20080420-no-bundling.patch14
-rw-r--r--sci-biology/readseq/metadata.xml12
-rw-r--r--sci-biology/readseq/readseq-20080420-r1.ebuild42
-rw-r--r--sci-biology/readseq/readseq-20100513.ebuild38
5 files changed, 0 insertions, 108 deletions
diff --git a/sci-biology/readseq/Manifest b/sci-biology/readseq/Manifest
deleted file mode 100644
index bcd1dfa237bf..000000000000
--- a/sci-biology/readseq/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST readseq-20100513.zip 628406 SHA256 878b689828bdf59a73c377c314fe504b9f18569ed5cd512acdb264cf90e72601 SHA512 6e2a2207e3a1f14e5cc4f7ffd2c74563b6deb088dda02727611359a17e1b157d9c661715d1f896d1573786cb88f61d3b952ab7a53e6dc30f2dcbcead58604b32 WHIRLPOOL 6f5b7ff075a081f521971689d014ad3ea6ffdc50db1b24766712d21fb86f83d7767f9afa76473f0be6f36560c8572c7051337cde8020cb9562dfef96a2bfdc8a
-DIST readseq-source-20080420.zip 627341 SHA256 d91ccadcbf5fde29525c639ece6ae132e0db863a7e63f96f69647e591617e8dd SHA512 cbc7afa46d2f0cfb30aa75ab88e4942a18ddf46a03a4cfb8d7e07bd23bce3fe015483899d371b947a0f1d6ec464b8c1238df7f7fc89753bb75dbb284f1e07b48 WHIRLPOOL fb180c53cb0555887d5278871498d66840d1d27da47ef6a947f0cd048bfb79762faf9493a645be6909bf41c5627131f3ced8d29b8241372d1e6034dc7524004d
diff --git a/sci-biology/readseq/files/20080420-no-bundling.patch b/sci-biology/readseq/files/20080420-no-bundling.patch
deleted file mode 100644
index f2e1708f8821..000000000000
--- a/sci-biology/readseq/files/20080420-no-bundling.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff --git a/build.xml b/build.xml
-index e3d723c..4b44d6f 100644
---- a/build.xml
-+++ b/build.xml
-@@ -229,9 +229,6 @@
-
- <!-- for now, unjar xml classes into build/classes and rejar in readseq.jar -->
-
-- <unjar overwrite="false" src="${orgxml.jar}" dest="${build.home}/classes" />
-- <unjar overwrite="false" src="${xml.jar}" dest="${build.home}/classes" />
--
- <!-- <copy todir="${build.home}/classes""> -->
- <!-- <src dir="${basedir}/META-INF"/> -->
- <!-- </copy> -->
diff --git a/sci-biology/readseq/metadata.xml b/sci-biology/readseq/metadata.xml
deleted file mode 100644
index 351fed01ff61..000000000000
--- a/sci-biology/readseq/metadata.xml
+++ /dev/null
@@ -1,12 +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>
- <longdescription>
- Reads and writes nucleic/protein sequences in various formats. Data
- files may have multiple sequences.
- </longdescription>
-</pkgmetadata>
diff --git a/sci-biology/readseq/readseq-20080420-r1.ebuild b/sci-biology/readseq/readseq-20080420-r1.ebuild
deleted file mode 100644
index c483fc242027..000000000000
--- a/sci-biology/readseq/readseq-20080420-r1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-MY_P="${PN}-source-${PV}"
-DESCRIPTION="Reads and writes nucleic/protein sequences in various formats"
-HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
-# Originally unversioned at
-# http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq-source.zip.
-# Renamed to the date of the modification and mirrored
-SRC_URI="https://dev.gentoo.org/~dberkholz/distfiles/${MY_P}.zip"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="!=sci-biology/meme-4.8.1
- >=virtual/jre-1.4"
-DEPEND=">=virtual/jdk-1.4
- app-arch/unzip"
-
-S=${WORKDIR}
-
-java_prepare() {
- rm "${S}"/lib/* || die
- epatch "${FILESDIR}"/${PV}-*
-}
-
-src_install() {
- java-pkg_dojar build/readseq.jar
- java-pkg_dolauncher
-}
-
-pkg_postinst() {
- elog "Documentation is available at"
- elog "http://iubio.bio.indiana.edu/soft/molbio/readseq/java/Readseq2-help.html"
-}
diff --git a/sci-biology/readseq/readseq-20100513.ebuild b/sci-biology/readseq/readseq-20100513.ebuild
deleted file mode 100644
index 3f18380ad040..000000000000
--- a/sci-biology/readseq/readseq-20100513.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Reads and writes nucleic/protein sequences in various formats"
-HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
-SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.zip"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="!=sci-biology/meme-4.8.1
- >=virtual/jre-1.4"
-DEPEND=">=virtual/jdk-1.4
- app-arch/unzip"
-
-S=${WORKDIR}
-
-java_prepare() {
- rm "${S}"/lib/* || die
- epatch "${FILESDIR}"/20080420-*
-}
-
-src_install() {
- java-pkg_dojar build/readseq.jar
- java-pkg_dolauncher
-}
-
-pkg_postinst() {
- elog "Documentation is available at"
- elog "http://iubio.bio.indiana.edu/soft/molbio/readseq/java/Readseq2-help.html"
-}