commit: 364176df552e6c6491272f59d111a8ddc9c7a4eb Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Sat Mar 20 10:30:26 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Sat Mar 20 10:30:26 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=364176df
sci-biology/igv: remove masked package Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 7 -- .../igv/files/2.3.52-remove-oracle.jdbc.patch | 21 ------ sci-biology/igv/igv-2.3.47.ebuild | 82 -------------------- sci-biology/igv/igv-2.3.81.ebuild | 87 ---------------------- sci-biology/igv/igv-2.3.88.ebuild | 87 ---------------------- sci-biology/igv/igv-2.3.92.ebuild | 87 ---------------------- sci-biology/igv/metadata.xml | 11 --- 7 files changed, 382 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 0b7ff0512..ec0ed5550 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,13 +30,6 @@ #--- END OF EXAMPLES --- -# Andrew Ammerlaan <[email protected]> (06 March 2021) -# Newer versions use gradle build system which is currently not -# support by portage, old versions do not build, ebuilds don't -# have any keywords -# Masked for removal in 14 days, if you need this please complain -sci-biology/igv - # Andrew Ammerlaan <[email protected]> (06 March 2021) # Does not fetch, last update in 2009 # Masked for removal in 14 days, if you need this please complain diff --git a/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch b/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch deleted file mode 100644 index 7d2274833..000000000 --- a/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff --git a/src/org/broad/igv/lists/GeneListEditDialog.java b/src/org/broad/igv/lists/GeneListEditDialog.java -index f1aff7d..87d2dd1 100644 ---- a/src/org/broad/igv/lists/GeneListEditDialog.java -+++ b/src/org/broad/igv/lists/GeneListEditDialog.java -@@ -22,15 +22,12 @@ - - package org.broad.igv.lists; - --import oracle.jdbc.proxy.annotation.Pre; --import org.broad.igv.Globals; - import org.broad.igv.PreferenceManager; - import org.broad.igv.ui.util.MessageUtils; - - import java.awt.*; - import java.awt.event.*; - import java.io.*; --import java.net.URLEncoder; - import java.util.ArrayList; - import java.util.Arrays; - import javax.swing.*; - diff --git a/sci-biology/igv/igv-2.3.47.ebuild b/sci-biology/igv/igv-2.3.47.ebuild deleted file mode 100644 index 751ad3943..000000000 --- a/sci-biology/igv/igv-2.3.47.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit java-pkg-2 java-ant-2 - -[ "$PV" == "9999" ] && inherit git-r3 - -if [ "$PV" == "9999" ]; then - #ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"; - #ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"; - EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"; - KEYWORDS="" -else - SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip" - KEYWORDS="" - # binaries - # http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip - # http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip -fi - -DESCRIPTION="Integrative Genomics Viewer" -HOMEPAGE="http://www.broadinstitute.org/igv/"; - -LICENSE="LGPL-2.1" -SLOT="0" -IUSE="" -KEYWORDS="~amd64" - -COMMON_DEPS=" - dev-java/absolutelayout - dev-java/jama:0 - dev-java/commons-logging:0 - >=dev-java/commons-io-2.1:1 - dev-java/commons-math:2 - dev-java/commons-jexl:2 - dev-java/jcommon:1.0 - dev-java/jfreechart:1.0 - dev-java/jlfgr:0 - dev-java/log4j:0 - dev-java/gson:2.2.2 - dev-java/guava:20 - dev-java/swing-layout:1 - dev-java/jgrapht:0 - dev-java/junit:4" - -DEPEND=">=virtual/jdk-1.7 - app-arch/unzip - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.7 - ${COMMON_DEPS}" - -S="${WORKDIR}/IGV-${PV}" - -EANT_BUILD_TARGET="all" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_NEEDS_TOOLS="true" -EANT_EXTRA_ARGS="-Dnotests=true" - -EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1," -EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4" - -java_prepare() { - mv lib oldlib || die - mkdir lib || die - - mv -v oldlib/{htsjdk-1.124.jar,bcprov-debug-jdk15on-147.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die - mv -v oldlib/batik* lib || die - - rm -rvf oldlib/* || die - - epatch "${FILESDIR}"/"${PV}"-remove-oracle.jdbc.patch -} - -src_install() { - java-pkg_newjar igv.jar - - for i in lib/*.jar; do java-pkg_dojar $i; done - - java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main -} diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.81.ebuild deleted file mode 100644 index 5fabefeb3..000000000 --- a/sci-biology/igv/igv-2.3.81.ebuild +++ /dev/null @@ -1,87 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit java-pkg-2 java-ant-2 - -[ "$PV" == "9999" ] && inherit git-r3 - -if [ "$PV" == "9999" ]; then - #ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"; - #ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"; - EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"; - KEYWORDS="" -else - SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip" - KEYWORDS="" - # binaries - # http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip - # http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip -fi - -DESCRIPTION="Integrative Genomics Viewer" -HOMEPAGE="http://www.broadinstitute.org/igv/"; - -LICENSE="LGPL-2.1" -SLOT="0" -IUSE="" -KEYWORDS="" # igv-2.3.81/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable - -# actually more exactly the COMMON_DEPS should contain: -# >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696 -COMMON_DEPS=" - dev-java/absolutelayout:0 - dev-java/jama:0 - dev-java/commons-compress - dev-java/commons-logging:0 - >=dev-java/commons-io-2.1:1 - dev-java/commons-math:2 - dev-java/commons-jexl:2 - dev-java/jcommon:* - dev-java/jfreechart:1.0 - dev-java/jlfgr:0 - dev-java/log4j:0 - dev-java/gson:2.2.2 - dev-java/guava:20 - dev-java/swing-layout:1 - dev-java/jgrapht:0 - dev-java/junit:4" - -DEPEND=">=virtual/jdk-1.7 - app-arch/unzip - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.7 - ${COMMON_DEPS}" - -S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you fetched wrong file with the precompiled jar - -EANT_BUILD_TARGET="all" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_NEEDS_TOOLS="true" -EANT_EXTRA_ARGS="-Dnotests=true" - -EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1," -EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4" - -java_prepare() { - mv lib oldlib || die - mkdir lib || die - - mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar,mysql-connector-java-3.1.14-bin.jar} lib || die - mv -v oldlib/batik* lib || die - - rm -rvf oldlib/* || die -} - -src_install() { - java-pkg_newjar igv.jar - - for i in lib/*.jar; do java-pkg_dojar $i; done - - java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main -} - -pkg_postinst(){ - einfo "You may want to install sci-biology/blat for easy sequence searches inside igv" -} diff --git a/sci-biology/igv/igv-2.3.88.ebuild b/sci-biology/igv/igv-2.3.88.ebuild deleted file mode 100644 index 8011ea888..000000000 --- a/sci-biology/igv/igv-2.3.88.ebuild +++ /dev/null @@ -1,87 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit java-pkg-2 java-ant-2 - -[ "$PV" == "9999" ] && inherit git-r3 - -if [ "$PV" == "9999" ]; then - #ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"; - #ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"; - EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"; - KEYWORDS="" -else - SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip" - KEYWORDS="" - # binaries - # http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip - # http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip -fi - -DESCRIPTION="Integrative Genomics Viewer" -HOMEPAGE="http://www.broadinstitute.org/igv/"; - -LICENSE="LGPL-2.1" -SLOT="0" -IUSE="" -KEYWORDS="" # see upstream issue #332 - -# actually more exactly the COMMON_DEPS should contain: -# >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696 -COMMON_DEPS=" - dev-java/absolutelayout:0 - dev-java/jama:0 - dev-java/commons-compress - dev-java/commons-logging:0 - >=dev-java/commons-io-2.1:1 - dev-java/commons-math:2 - dev-java/commons-jexl:2 - dev-java/jcommon:* - dev-java/jfreechart:1.0 - dev-java/jlfgr:0 - dev-java/log4j:0 - dev-java/gson:2.2.2 - dev-java/guava:20 - dev-java/swing-layout:1 - dev-java/jgrapht:0 - dev-java/junit:4" - -DEPEND=">=virtual/jdk-1.7 - app-arch/unzip - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.7 - ${COMMON_DEPS}" - -S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you fetched wrong file with the precompiled jar - -EANT_BUILD_TARGET="all" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_NEEDS_TOOLS="true" -EANT_EXTRA_ARGS="-Dnotests=true" - -EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1," -EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4" - -java_prepare() { - mv lib oldlib || die - mkdir lib || die - - mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar,mysql-connector-java-3.1.14-bin.jar} lib || die - mv -v oldlib/batik* lib || die - - rm -rvf oldlib/* || die -} - -src_install() { - java-pkg_newjar igv.jar - - for i in lib/*.jar; do java-pkg_dojar $i; done - - java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main -} - -pkg_postinst(){ - einfo "You may want to install sci-biology/blat for easy sequence searches inside igv" -} diff --git a/sci-biology/igv/igv-2.3.92.ebuild b/sci-biology/igv/igv-2.3.92.ebuild deleted file mode 100644 index 8011ea888..000000000 --- a/sci-biology/igv/igv-2.3.92.ebuild +++ /dev/null @@ -1,87 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit java-pkg-2 java-ant-2 - -[ "$PV" == "9999" ] && inherit git-r3 - -if [ "$PV" == "9999" ]; then - #ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"; - #ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"; - EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"; - KEYWORDS="" -else - SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip" - KEYWORDS="" - # binaries - # http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip - # http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip -fi - -DESCRIPTION="Integrative Genomics Viewer" -HOMEPAGE="http://www.broadinstitute.org/igv/"; - -LICENSE="LGPL-2.1" -SLOT="0" -IUSE="" -KEYWORDS="" # see upstream issue #332 - -# actually more exactly the COMMON_DEPS should contain: -# >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696 -COMMON_DEPS=" - dev-java/absolutelayout:0 - dev-java/jama:0 - dev-java/commons-compress - dev-java/commons-logging:0 - >=dev-java/commons-io-2.1:1 - dev-java/commons-math:2 - dev-java/commons-jexl:2 - dev-java/jcommon:* - dev-java/jfreechart:1.0 - dev-java/jlfgr:0 - dev-java/log4j:0 - dev-java/gson:2.2.2 - dev-java/guava:20 - dev-java/swing-layout:1 - dev-java/jgrapht:0 - dev-java/junit:4" - -DEPEND=">=virtual/jdk-1.7 - app-arch/unzip - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.7 - ${COMMON_DEPS}" - -S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you fetched wrong file with the precompiled jar - -EANT_BUILD_TARGET="all" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_NEEDS_TOOLS="true" -EANT_EXTRA_ARGS="-Dnotests=true" - -EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1," -EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4" - -java_prepare() { - mv lib oldlib || die - mkdir lib || die - - mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar,mysql-connector-java-3.1.14-bin.jar} lib || die - mv -v oldlib/batik* lib || die - - rm -rvf oldlib/* || die -} - -src_install() { - java-pkg_newjar igv.jar - - for i in lib/*.jar; do java-pkg_dojar $i; done - - java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main -} - -pkg_postinst(){ - einfo "You may want to install sci-biology/blat for easy sequence searches inside igv" -} diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml deleted file mode 100644 index 8b6e6434a..000000000 --- a/sci-biology/igv/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>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">broadinstitute/IGV</remote-id> - </upstream> -</pkgmetadata>
