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From: "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
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Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
Message-ID: <1491234326.c2d81203011805abd24ae7adb6c8afc14ea02949.mmokrejs@gentoo>
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/igv/
X-VCS-Repository: proj/sci
X-VCS-Files: sci-biology/igv/igv-2.3.92.ebuild
X-VCS-Directories: sci-biology/igv/
X-VCS-Committer: mmokrejs
X-VCS-Committer-Name: Martin Mokrejs
X-VCS-Revision: c2d81203011805abd24ae7adb6c8afc14ea02949
X-VCS-Branch: master
Date: Mon, 3 Apr 2017 15:45:39 +0000 (UTC)
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commit: c2d81203011805abd24ae7adb6c8afc14ea02949
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 3 15:45:26 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 3 15:45:26 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c2d81203
sci-biology/igv: version bump, cannot compile FlowSignalDistributionPanel.java:222
It seem this is related to Gentoo ebuild unbundling some of the bundled libs.
I can compile vanilla sources using ant without this issue.
[javac] Compiling 889 source files to /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/tmp
[javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/org/broad/igv/tools/sort/BAMSorter.java:33: warning: NotImplementedException is internal proprietary API and may be removed in a future release
[javac] import sun.reflect.generics.reflectiveObjects.NotImplementedException;
[javac] ^
[javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable
[javac] dataset.addValue(data[j], seriename, cat);
[javac] ^
[javac] class file for org.jfree.util.PublicCloneable not found
[javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/com/iontorrent/views/FlowSignalDistributionPanel.java:266: error: cannot access Drawable
[javac] CategoryPlot plot = freechart.getCategoryPlot();
[javac] ^
[javac] class file for org.jfree.ui.Drawable not found
[javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/org/broad/igv/tools/sort/BAMSorter.java:102: warning: NotImplementedException is internal proprietary API and may be removed in a future release
[javac] throw new NotImplementedException();
Package-Manager: Portage-2.3.5, Repoman-2.3.1
sci-biology/igv/igv-2.3.92.ebuild | 87 +++++++++++++++++++++++++++++++++++++++
1 file changed, 87 insertions(+)
diff --git a/sci-biology/igv/igv-2.3.92.ebuild b/sci-biology/igv/igv-2.3.92.ebuild
new file mode 100644
index 000000000..72b0dcff1
--- /dev/null
+++ b/sci-biology/igv/igv-2.3.92.ebuild
@@ -0,0 +1,87 @@
+# 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-17:*
+ >=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"
+}