[med-svn] [Git][med-team/igv][master] 4 commits: Refreshing dependencies
Pierre Gruet
gitlab at salsa.debian.org
Fri Nov 13 21:04:37 GMT 2020
Pierre Gruet pushed to branch master at Debian Med / igv
Commits:
bad060b2 by Pierre Gruet at 2020-11-13T20:42:08+01:00
Refreshing dependencies
- - - - -
ed4227e5 by Pierre Gruet at 2020-11-13T20:42:33+01:00
Rewriting d/copyright
- - - - -
5190edea by Pierre Gruet at 2020-11-13T20:43:10+01:00
Rewriting the classpath and deleting it from d/bin/igv
- - - - -
32116509 by Pierre Gruet at 2020-11-13T22:04:20+01:00
Upload to unstable
- - - - -
5 changed files:
- debian/bin/igv
- debian/changelog
- debian/control
- debian/copyright
- debian/igv.manifest
Changes:
=====================================
debian/bin/igv
=====================================
@@ -1,5 +1,5 @@
#!/bin/sh
set -eu
-exec java -cp /usr/share/java/ant.jar:/usr/share/java/jaxb-api.jar:/usr/share/java/igv.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/htsjdk.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-css.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-gui-util.jar:/usr/share/java/batik-gvt.jar:/usr/share/java/batik-parser.jar:/usr/share/java/batik-svg-dom.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-transcoder.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/java/commons-io.jar:/usr/share/java/commons-logging.jar:/usr/share/java/commons-math.jar:/usr/share/java/commons-net.jar:/usr/share/java/concurrent.jar:/usr/share/java/gson.jar:/usr/share/java/guava.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/jama.jar:/usr/share/java/jargs.jar:/usr/share/java/jcommon.jar:/usr/share/java/jfreechart.jar:/usr/share/java/jhdf5.jar:/usr/share/java/net.sourceforge.jlibdeps.jar:/usr/share/java/junit4.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/sam.jar:/usr/share/java/swing-layout.jar:/usr/share/java/xml-apis.jar:/usr/share/java/xml-apis-ext.jar:/usr/share/java/AbsoluteLayout.jar:/usr/share/java/bcprov.jar:/usr/share/java/jgrapht0.8.jar:/usr/share/java/jide-oss.jar:/usr/share/java/commons-io.jar:/usr/share/java/cofoja.jar:/usr/share/java/gson.jar org.broad.igv.ui.Main "$@"
+java -cp /usr/share/java/igv.jar org.broad.igv.ui.Main "$@"
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+igv (2.6.3+dfsg-3) unstable; urgency=medium
+
+ * Revising the list of dependencies and updating d/igv.manifest accordingly
+ * Refreshing d/copyright
+ * Lightening d/bin/igv as igv.jar has a sufficient classpath
+
+ -- Pierre Gruet <pgtdebian at free.fr> Fri, 13 Nov 2020 20:21:39 +0100
+
igv (2.6.3+dfsg-2) unstable; urgency=medium
* Correcting the module name of junit in build.gradle
=====================================
debian/control
=====================================
@@ -9,22 +9,14 @@ Priority: optional
Build-Depends: default-jdk,
debhelper-compat (= 13),
gradle-debian-helper,
- junit4,
+ junit4 <!nocheck>,
libbatik-java,
- libcofoja-java,
libcommons-logging-java,
libcommons-io-java,
libcommons-math-java,
- libcommons-net-java,
- libhttpclient-java,
- libhttpcore-java,
libjaxb-api-java,
libjcommon-java,
libjfreechart-java,
- libjhdf5-java,
- libjlibeps-java,
- libjama-java,
- libjargs-java,
libjaxp1.3-java,
liblog4j2-java,
liblog4j1.2-java,
@@ -33,7 +25,6 @@ Build-Depends: default-jdk,
libswing-layout-java,
libxml-commons-external-java,
libguava-java,
- libbcprov-java,
libjgrapht0.8-java,
libgoogle-gson-java,
javahelper,
@@ -41,6 +32,7 @@ Build-Depends: default-jdk,
libfest-assert-java,
libfest-util-java,
libfest-reflect-java,
+ libnb-absolutelayout-java,
ant
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/igv
@@ -53,11 +45,9 @@ Architecture: all
Depends: ${misc:Depends},
${java:Depends},
default-jre,
- libjhdf5-java,
libbatik-java,
libhtsjdk-java,
- liblog4j2-java,
- libpicard-java
+ liblog4j2-java
Recommends: libmariadb-java
Description: Integrative Genomics Viewer
The Integrative Genomics Viewer (IGV) is a high-performance viewer that
=====================================
debian/copyright
=====================================
@@ -27,19 +27,83 @@ Disclaimer: This package is not part of the Debian operating system.
Files: *
Copyright: 2007-2018 Broad Institute
-License: MIT
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- THE SOFTWARE.
+License: Expat
Files: lib/goby-io-igv*.jar
Copyright: 2012-2014 Campagne Laboratory, Weill Cornell Medical College
License: LGPL-3
- See `/usr/share/common-licenses/LGPL-3'.
+
+Files: src/main/java/biz/*
+Copyright: 2003-2010 Christian dHeureuse, Inventec Informatik AG, Zurich, Switzerland
+License: Expat
+
+Files: src/main/java/com/*
+Copyright: 2010-2012 penSec.IT UG
+ 2005 Ewan Mellor
+ 2002 Vidar Holen
+ 2002 Michal Ceresna
+ 2001-2012 Steve Purcell
+License: BSD-3-clause
+
+Files: src/main/java/org/apache/*
+Copyright: 1999 The Apache Software Foundation
+License: Apache-1.1
+
+Files: src/main/java/org/broad/igv/event/GenomeChangeEvent.java
+ src/main/java/org/broad/igv/event/IGVEventBus.java
+ src/main/java/org/broad/igv/event/IGVEventObserver.java
+ src/main/java/org/broad/igv/event/ReferenceFrameEvent.java
+ src/main/java/org/broad/igv/feature/basepair/*
+ src/main/java/org/broad/igv/feature/bionano/*
+ src/main/java/org/broad/igv/feature/genome/SequenceInterval.java
+ src/main/java/org/broad/igv/maf/MAFtoSAM.java
+ src/main/java/org/broad/igv/sam/InsertionManager.java
+ src/main/java/org/broad/igv/sam/InsertionSelectionEvent.java
+ src/main/java/org/broad/igv/sam/ReadStats.java
+ src/main/java/org/broad/igv/sam/cram/*
+ src/main/java/org/broad/igv/tools/RepeatMaskSplitter.java
+ src/main/java/org/broad/igv/tools/PairedUtils.java
+ src/main/java/org/broad/igv/tools/sort/BAMSorter.java
+ src/main/java/org/broad/igv/tools/sort/Sorter.java
+ src/main/java/org/broad/igv/tools/sort/SorterFactory.java
+ src/main/java/org/broad/igv/track/Range.java
+ src/main/java/org/broad/igv/track/ScalableTrack.java
+ src/main/java/org/broad/igv/ui/util/ByteSubArray.java
+ src/main/java/org/broad/igv/util/IntervalTree.java
+ src/main/java/org/broad/igv/util/TutorialUtils.java
+ src/test/java/org/broad/igv/sam/cram/CRAMReaderTest.java
+Copyright: 2015-2016 University of California San Diego
+License: Expat
+
+Files: src/main/java/org/broad/igv/feature/SpliceJunctionFeature.java
+ src/main/java/org/broad/igv/sam/SpliceJunctionHelper.java
+ src/main/java/org/broad/igv/sam/SpliceJunctionTrack.java
+Copyright: 2007-2015 Fred Hutchinson Cancer Research Center and Broad Institute
+License: Expat
+
+Files: src/main/java/org/broad/igv/goby/*
+ src/test/java/org/broad/igv/goby/*
+Copyright: 2007-2015 Institute for Computational Biomedicine
+License: Expat
+
+Files: src/main/java/org/broad/igv/renderer/SpliceJunctionRenderer.java
+Copyright: 2013 F. Hoffmann-La Roche Ltd and Tessella Inc.
+ 2007-2015 Fred Hutchinson Cancer Research Center and Broad Institute
+License: Expat
+
+Files: src/main/java/org/broad/igv/track/PackedFeaturesSpliceJunctions.java
+ src/main/java/org/broad/igv/ui/panel/RegionNavigatorDialog.java
+ src/main/java/org/broad/igv/util/ObservableForObject.java
+Copyright: 2007-2015 Fred Hutchinson Cancer Research Center and Broad Institute
+License: Expat
+
+Files: src/main/java8/apple/dts/samplecode/osxadapter/OSXAdapter.java
+Copyright: 2003-2007 Apple, Inc.
+License: AML
+
+Files: web/*
+Copyright: 2007, Memorial Sloan-Kettering Cancer Center.
+License: LGPL-2.1
Files: src/main/resources-jlfgr-1_0/*
Copyright: 2000 by Sun Microsystems, Inc.
@@ -86,10 +150,149 @@ License: other
Files: debian/*
Copyright: 2010-2011 Shaun Jackman <sjackman at debian.org>
- 2011 Charles Plessy <plessy at debian.org>
+ 2011 Charles Plessy <plessy at debian.org>
2013-2018 Olivier Sallou <osallou at debian.org>,
Andreas Tille <tille at debian.org>
+ 2020 Pierre Gruet <pgtdebian at free.fr>
License: ISC
Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
+
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+License: LGPL-3
+ On Debian systems the full text of the LGPL-3 can be found in
+ /usr/share/common-licenses/LGPL-3
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer. Redistributions in binary
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+ the following disclaimer in the documentation and/or other materials provided
+ with the distribution. Neither the name of the copyright holder nor the names
+ of its contributors may be used to endorse or promote products derived from
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+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
+
+License: Apache-1.1
+ The Apache Software License, Version 1.1
+ .
+ Copyright (c) 2000 The Apache Software Foundation. All rights
+ reserved.
+ .
+ Redistribution and use in source and binary forms, with or without
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+ Apache Software Foundation (http://www.apache.org/)."
+ Alternately, this acknowledgment may appear in the software itself,
+ if and wherever such third-party acknowledgments normally appear.
+ .
+ 4. The names "Apache" and "Apache Software Foundation" must
+ not be used to endorse or promote products derived from this
+ software without prior written permission. For written
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+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+License: LGPL-2.1
+ On Debian systems the full text of the LGPL-3 can be found in
+ /usr/share/common-licenses/LGPL-2.1
+
+License: AML
+ IMPORTANT: This Apple software is supplied to you by Apple Computer,
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=====================================
debian/igv.manifest
=====================================
@@ -1,2 +1,2 @@
usr/share/java/igv.jar:
- Class-Path: /usr/share/java/log4j-api.jar /usr/share/java/log4j-core.jar /usr/share/java/htsjdk.jar /usr/share/java/batik-awt-util.jar /usr/share/java/batik-css.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-gui-util.jar /usr/share/java/batik-gvt.jar /usr/share/java/batik-parser.jar /usr/share/java/batik-svg-dom.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-transcoder.jar /usr/share/java/batik-util.jar /usr/share/java/batik-xml.jar /usr/share/java/commons-io.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/commons-net.jar /usr/share/java/concurrent.jar /usr/share/java/gson.jar /usr/share/java/guava.jar /usr/share/java/httpclient.jar /usr/share/java/httpcore.jar /usr/share/java/jama.jar /usr/share/java/jargs.jar /usr/share/java/jcommon.jar /usr/share/java/jfreechart.jar /usr/share/java/jhdf5.jar /usr/share/java/net.sourceforge.jlibdeps.jar /usr/share/java/junit4.jar /usr/share/java/log4j-1.2.jar /usr/share/java/sam.jar /usr/share/java/swing-layout.jar /usr/share/java/xml-apis.jar /usr/share/java/xml-apis-ext.jar /usr/share/java/AbsoluteLayout.jar /usr/share/java/bcprov.jar /usr/share/java/jgrapht0.8.jar /usr/share/java/jide-oss.jar /usr/share/java/commons-io.jar /usr/share/java/cofoja.jar /usr/share/java/jaxb-api.jar
+ Class-Path: /usr/share/java/log4j-api.jar /usr/share/java/log4j-core.jar /usr/share/java/htsjdk.jar /usr/share/java/batik-awt-util.jar /usr/share/java/batik-css.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-gui-util.jar /usr/share/java/batik-gvt.jar /usr/share/java/batik-parser.jar /usr/share/java/batik-svg-dom.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-transcoder.jar /usr/share/java/batik-util.jar /usr/share/java/batik-xml.jar /usr/share/java/commons-io.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/gson.jar /usr/share/java/guava.jar /usr/share/java/jcommon.jar /usr/share/java/jfreechart.jar /usr/share/java/log4j-1.2.jar /usr/share/java/swing-layout.jar /usr/share/java/xml-apis-ext.jar /usr/share/java/AbsoluteLayout.jar /usr/share/java/jgrapht0.8.jar /usr/share/java/jide-oss.jar /usr/share/java/jaxb-api.jar /usr/share/java/AbsoluteLayout.jar
View it on GitLab: https://salsa.debian.org/med-team/igv/-/compare/6ca00eaf2bee5ef481112b6cb8ce7943f96e424f...321165093ecb74913a67170352812dba39f7d1cd
--
View it on GitLab: https://salsa.debian.org/med-team/igv/-/compare/6ca00eaf2bee5ef481112b6cb8ce7943f96e424f...321165093ecb74913a67170352812dba39f7d1cd
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