[gentoo-commits] proj/sci:master commit in: sci-biology/igv/

[Martin Mokrejs]

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"
+}