From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id D564F139694 for ; Mon, 3 Apr 2017 15:45:43 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id D4DCCE0CA3; Mon, 3 Apr 2017 15:45:42 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id A2823E0CA3 for ; Mon, 3 Apr 2017 15:45:41 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 7DF0333D3CE for ; Mon, 3 Apr 2017 15:45:40 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 28AD872DA for ; Mon, 3 Apr 2017 15:45:39 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" 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) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 49688704-d26e-4857-9ffc-b36979a4eb07 X-Archives-Hash: ff3bde2ce2fdbe452079be609dbbc0d6 commit: c2d81203011805abd24ae7adb6c8afc14ea02949 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Mon Apr 3 15:45:26 2017 +0000 Commit: Martin Mokrejs fold natur cuni 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" +}