[med-svn] r9430 - in trunk/packages/beast-mcmc/trunk/debian: . bin patches
Andreas Tille
tille at alioth.debian.org
Wed Jan 25 12:53:26 UTC 2012
Author: tille
Date: 2012-01-25 12:53:26 +0000 (Wed, 25 Jan 2012)
New Revision: 9430
Modified:
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu
trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc
trunk/packages/beast-mcmc/trunk/debian/control
trunk/packages/beast-mcmc/trunk/debian/copyright
trunk/packages/beast-mcmc/trunk/debian/get-orig-source
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
Log:
Ironed out two further binary JAR files in the source tarball; so only one binary is left which should be kicked as well by creating a libmtj-java package (which does require some more work unfortunately)
Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2012-01-25 08:14:08 UTC (rev 9429)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2012-01-25 12:53:26 UTC (rev 9430)
@@ -2,7 +2,7 @@
needs="x11"\
section="Applications/Science/Biology"\
title="BEAST"\
- command="x-terminal-emulator -e sh -c \"/usr/bin/beast-mcmc; read\""\
+ command="/usr/bin/beast-mcmc"\
hints="Bayesian evolutionary analysis sampling trees"\
icon="/usr/share/pixmaps/beast.xpm"
Modified: trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc 2012-01-25 08:14:08 UTC (rev 9429)
+++ trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc 2012-01-25 12:53:26 UTC (rev 9430)
@@ -11,5 +11,5 @@
BEAST_LIB="/usr/share/beast-mcmc"
DEBJAR="/usr/share/java"
java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB:/usr/lib" \
- -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/commons-math.jar:${DEBJAR}/treeview.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/beast-beagle.jar" \
+ -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${DEBJAR}/commons-math.jar:${DEBJAR}/treeview.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/beast-beagle.jar" \
dr.app.beast.BeastMain $*
Modified: trunk/packages/beast-mcmc/trunk/debian/control
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/control 2012-01-25 08:14:08 UTC (rev 9429)
+++ trunk/packages/beast-mcmc/trunk/debian/control 2012-01-25 12:53:26 UTC (rev 9430)
@@ -8,7 +8,7 @@
Build-Depends: debhelper (>= 8), javahelper (>=0.25),
ant, ant-optional, openjdk-6-jdk, default-jdk,
libjebl2-java, libjam-java, figtree, liboptions-java, libhmsbeagle-java,
- r-cran-rjava, libcommons-math-java, libjdom1-java, junit4,
+ libcolt-java, libmpj-java, r-cran-rjava, libcommons-math-java, libjdom1-java, junit4,
libitext1-java, texlive-latex-base
Standards-Version: 3.9.2
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/beast-mcmc/trunk/
@@ -88,4 +88,3 @@
analyses and a suit of programs for analysing the results.
.
This package contains the documentation.
-
Modified: trunk/packages/beast-mcmc/trunk/debian/copyright
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/copyright 2012-01-25 08:14:08 UTC (rev 9429)
+++ trunk/packages/beast-mcmc/trunk/debian/copyright 2012-01-25 12:53:26 UTC (rev 9430)
@@ -1,4 +1,4 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+Format: http://dep.debian.net/deps/dep5/
Upstream-Name: BEAST-MCMC
Upstream-Contact: Alexei Drummond <alexei at cs.auckland.ac.nz>,
Andrew Rambaut <a.rambaut at ed.ac.uk>
@@ -23,98 +23,7 @@
in the file ‘/usr/share/common-licenses/LGPL-3’, and the GNU GPL license
version 3 is included in the file ‘/usr/share/common-licenses/GPL-3’.
-Files: lib/beagle.jar
-Copyright: 2007-2011 Brian L. Browning
-License:
- You may download and use the BEAGLE executable file for non-commercial
- and commercial research. BEAGLE is distributed on an "AS IS" basis.
-Remark: http://lists.debian.org/debian-med/2011/03/msg00098.html
- From: Brian Browning <browning at u.washington.edu>
- Subject: RE: BEAGLE Genetic Analysis for Debian Med
- Date: Fri, 11 Mar 2011 08:07:25 -0800
- Dear Andreas,
- Thank you for your e-mail. Beagle will ultimately be open source. It is
- not yet open source because the program is still being intensively
- developed, and the source code and includes unpublished research
- (statistical methods and computational methods that are undergoing
- continuous development and that are not yet published). I will probably
- make source code for older versions of Beagle open source later this year,
- and this would probably serve your purpose. If you e-mail me in August, I
- could give you an update then.
-
- Best regards,
-
- Brian
-
-Files: lib/colt.jar
-Copyright: 1999 CERN - European Organization for Nuclear Research.
-License: Colt License Agreement
- Packages cern.colt* , cern.jet*, cern.clhep
- .
- Permission to use, copy, modify, distribute and sell this software and its
- documentation for any purpose is hereby granted without fee, provided that
- the above copyright notice appear in all copies and that both that
- copyright notice and this permission notice appear in supporting
- documentation. CERN makes no representations about the suitability of this
- software for any purpose. It is provided "as is" without expressed or
- implied warranty.
- .
- Packages hep.aida.*
- .
- Written by Pavel Binko, Dino Ferrero Merlino, Wolfgang Hoschek, Tony
- Johnson, Andreas Pfeiffer, and others. Check the FreeHEP home page for more
- info. Permission to use and/or redistribute this work is granted under the
- terms of the LGPL License, with the exception that any usage related to
- military applications is expressly forbidden. The software and
- documentation made available under the terms of this license are provided
- with no warranty.
-Comment: Needs to be packaged separately from source
- The source of the jar is available at
- http://acs.lbl.gov/software/colt/
- and needs separate packaging for Debian. This is planed to be done in
- the future.
-
-Files: lib/mpj.jar
-Copyright: 2005 - 2007
- 1. Distributed Systems Group, University of Portsmouth (2005)
- 2. Aamir Shafi (2005 - 2007)
- 3. Bryan Carpenter (2005 - 2007)
- 4. Mark Baker (2005 - 2007)
-License: The MIT License
- The bulk of code in this distribution was developed by the Distributed Systems
- Group at the University of Portsmouth. Some sections of the code like
- the buffering API and derived datatypes include contributions developed at
- the Community Grids Lab at Indiana University.
- .
- 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.
- .
- 2. MPJ uses two third party softwares: Jetty and Java Service Wrapper project.
- The licenses for these two projects can be seen in
- $MPJ_HOME/THIRDPARTYLICENSES file.
-Comment: Needs to be packaged separately from source
- The source of the jar is available at
- http://sourceforge.net/projects/mpjexpress/
- and needs separate packaging for Debian. This is planed to be done in
- the future.
-
Files: lib/mtj.jar
Copyright: 2003-2006 Bjørn-Ove Heimsund
License: LGPL-3+
Modified: trunk/packages/beast-mcmc/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2012-01-25 08:14:08 UTC (rev 9429)
+++ trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2012-01-25 12:53:26 UTC (rev 9430)
@@ -29,6 +29,7 @@
for jar in \
JRI.jar \
beagle.jar \
+ colt.jar \
commons-math-2.0.jar \
figtreepanel.jar \
itext-1.4.5.jar \
@@ -37,6 +38,7 @@
jebl.jar \
junit-4.4.jar \
libjri.jnilib \
+ mpj.jar \
options.jar \
org.boehn.kmlframework_20090320.jar \
; do
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-01-25 08:14:08 UTC (rev 9429)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-01-25 12:53:26 UTC (rev 9430)
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Tue, 10 Jan 2012 22:29:24 +0100
+Description: Make sure package builds with Debian packages JARs
+
--- beast-mcmc-1.6.2.orig/build.xml
+++ beast-mcmc-1.6.2/build.xml
@@ -9,6 +9,7 @@
@@ -8,11 +12,12 @@
<property name="dist" location="${build}/dist" />
<property name="main_class_BEAST" value="dr.app.beast.BeastMain" />
-@@ -20,6 +21,16 @@
+@@ -20,6 +21,18 @@
<path id="classpath">
<fileset dir="${lib}" includes="**/*.jar"/>
+ <fileset dir="${deblib}" includes="beagle.jar"/>
++ <fileset dir="${deblib}" includes="colt.jar"/>
+ <fileset dir="${deblib}" includes="commons-math.jar"/>
+ <fileset dir="${deblib}" includes="figtree.jar"/>
+ <fileset dir="${deblib}" includes="itext1.jar"/>
@@ -21,11 +26,12 @@
+ <fileset dir="${deblib}" includes="jebl.jar"/>
+ <fileset dir="/usr/lib/R/site-library/rJava/jri/" includes="JRI.jar"/>
+ <fileset dir="${deblib}" includes="junit4.jar"/>
++ <fileset dir="${deblib}" includes="mpj.jar"/>
+ <fileset dir="${deblib}" includes="options.jar"/>
</path>
<!-- start -->
-@@ -130,14 +141,8 @@
+@@ -130,14 +143,6 @@
<include name="org/virion/jam/**/*.png" />
<include name="dr/**/*.properties" />
</fileset>
@@ -33,9 +39,9 @@
- <zipgroupfileset dir="${lib}" includes="jam.jar" />
- <zipgroupfileset dir="${lib}" includes="jdom.jar" />
- <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar" />
- <zipgroupfileset dir="${lib}" includes="mtj.jar" />
+- <zipgroupfileset dir="${lib}" includes="mtj.jar" />
- <zipgroupfileset dir="${lib}" includes="JRI.jar" />
- <zipgroupfileset dir="${lib}" includes="colt.jar" />
+- <zipgroupfileset dir="${lib}" includes="colt.jar" />
- <zipgroupfileset dir="${lib}" includes="beagle.jar" />
</jar>
@@ -57,8 +63,7 @@
<classpath>
<classpathentry kind="src" path="src"/>
- <classpathentry kind="lib" path="lib/beagle.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/beagle.jar"/>
- <classpathentry kind="lib" path="lib/colt.jar"/>
+- <classpathentry kind="lib" path="lib/colt.jar"/>
- <classpathentry kind="lib" path="lib/figtreepanel.jar"/>
- <classpathentry kind="lib" path="lib/itext-1.4.5.jar"/>
- <classpathentry kind="lib" path="lib/jam.jar"/>
@@ -66,6 +71,9 @@
- <classpathentry kind="lib" path="lib/jebl.jar"/>
- <classpathentry kind="lib" path="lib/JRI.jar"/>
- <classpathentry kind="lib" path="lib/junit-4.4.jar"/>
+- <classpathentry kind="lib" path="lib/mpj.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/beagle.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/colt.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/figtree.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/itext1.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/jam.jar"/>
@@ -73,7 +81,7 @@
+ <classpathentry kind="lib" path="/usr/share/java/jebl.jar"/>
+ <classpathentry kind="lib" path="/usr/lib/R/site-library/rJava/jri/JRI.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/junit4.jar"/>
- <classpathentry kind="lib" path="lib/mpj.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/mpj.jar"/>
<classpathentry kind="lib" path="lib/mtj.jar"/>
- <classpathentry kind="lib" path="lib/options.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/options.jar"/>
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