[med-svn] r9252 - in trunk/packages/beast-mcmc/trunk/debian: . bin patches
Andreas Tille
tille at alioth.debian.org
Wed Jan 11 16:11:15 UTC 2012
Author: tille
Date: 2012-01-11 16:11:15 +0000 (Wed, 11 Jan 2012)
New Revision: 9252
Added:
trunk/packages/beast-mcmc/trunk/debian/bin/
trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc
trunk/packages/beast-mcmc/trunk/debian/bin/beauti
trunk/packages/beast-mcmc/trunk/debian/bin/loganalyser
trunk/packages/beast-mcmc/trunk/debian/bin/logcombiner
trunk/packages/beast-mcmc/trunk/debian/bin/treeannotator
trunk/packages/beast-mcmc/trunk/debian/bin/treestat
Removed:
trunk/packages/beast-mcmc/trunk/debian/README.source
trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch
trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch
Modified:
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest
trunk/packages/beast-mcmc/trunk/debian/control
trunk/packages/beast-mcmc/trunk/debian/patches/series
trunk/packages/beast-mcmc/trunk/debian/rules
Log:
Do not try to patch singular upstream wrappers if we need to do massive changes to work around stupid manifest problems anyway it makes sense to provide them directly in debian/bin
Deleted: trunk/packages/beast-mcmc/trunk/debian/README.source
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/README.source 2012-01-11 15:52:48 UTC (rev 9251)
+++ trunk/packages/beast-mcmc/trunk/debian/README.source 2012-01-11 16:11:15 UTC (rev 9252)
@@ -1,10 +0,0 @@
-The beast-mcmc source is not provided as tarball but only in SVN.
-The SVN revision was tagged a 1.6.1 as it can be seen at
-
- http://code.google.com/p/beast-mcmc/source/detail?r=3660
-
-The script debian/get-orig-source fetches exactly this revision.
-In addition it removes some binary jars which are packaged for
-Debian and do not need to be shipped with the original tarball.
-
- -- Andreas Tille <tille at debian.org> Tue, 15 Feb 2011 12:39:04 +0100
\ No newline at end of file
Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install 2012-01-11 15:52:48 UTC (rev 9251)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install 2012-01-11 16:11:15 UTC (rev 9252)
@@ -1,4 +1,4 @@
-release/Linux/scripts/* usr/bin
-debian/*.xpm usr/share/pixmaps
-lib/*.jar usr/share/beast-mcmc
-build/dist/*.jar usr/share/beast-mcmc
+debian/bin usr
+debian/*.xpm usr/share/pixmaps
+lib/*.jar usr/share/beast-mcmc
+build/dist/*.jar usr/share/beast-mcmc
Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest 2012-01-11 15:52:48 UTC (rev 9251)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest 2012-01-11 16:11:15 UTC (rev 9252)
@@ -1,6 +1,6 @@
/usr/share/beast-mcmc/beast.jar:
Main-Class: dr.app.beast.BeastMain
- Class-Path: /usr/share/beast-mcmc/beagle.jar /usr/share/java/jebl.jar /usr/share/java/jam.jar /usr/share/java/treeview.jar
+ Class-Path: /usr/share/beast-mcmc/beagle.jar /usr/share/java/commons-math.jar /usr/share/java/jdom1.jar /usr/share/java/jebl.jar /usr/share/java/jam.jar /usr/share/java/treeview.jar
/usr/share/beast-mcmc/beauti.jar:
Main-Class: dr.app.beauti.BeautiApp
Added: trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/bin/beast-mcmc 2012-01-11 16:11:15 UTC (rev 9252)
@@ -0,0 +1,15 @@
+#!/bin/sh
+
+# upstream has set 1024
+# I had use cases that required more than 2048
+MAXMEM=3072
+
+# Remark: There should be no need to specify CLASSPATH
+# explicitely because it is set in manifest - however, this
+# does not work
+
+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" \
+ dr.app.beast.BeastMain $*
Added: trunk/packages/beast-mcmc/trunk/debian/bin/beauti
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/bin/beauti (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/bin/beauti 2012-01-11 16:11:15 UTC (rev 9252)
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+BEAST_LIB="/usr/share/beast-mcmc"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $*
+
Added: trunk/packages/beast-mcmc/trunk/debian/bin/loganalyser
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/bin/loganalyser (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/bin/loganalyser 2012-01-11 16:11:15 UTC (rev 9252)
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+BEAST_LIB="/usr/share/beast-mcmc"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $*
+
Added: trunk/packages/beast-mcmc/trunk/debian/bin/logcombiner
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/bin/logcombiner (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/bin/logcombiner 2012-01-11 16:11:15 UTC (rev 9252)
@@ -0,0 +1,7 @@
+#!/bin/sh
+
+BEAST_LIB="/usr/share/beast-mcmc"
+DEBJAR="/usr/share/java"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
+ dr.app.tools.LogCombiner $*
Added: trunk/packages/beast-mcmc/trunk/debian/bin/treeannotator
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/bin/treeannotator (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/bin/treeannotator 2012-01-11 16:11:15 UTC (rev 9252)
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+BEAST_LIB="/usr/share/beast-mcmc"
+DEBJAR="/usr/share/java"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
+ dr.app.tools.TreeAnnotator $*
+
+
Added: trunk/packages/beast-mcmc/trunk/debian/bin/treestat
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/bin/treestat (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/bin/treestat 2012-01-11 16:11:15 UTC (rev 9252)
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+BEAST_LIB="/usr/share/beast-mcmc"
+DEBJAR="/usr/share/java"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar:${DEBJAR}/jdom1.jar \
+ dr.app.treestat.TreeStatApp $*
+
Modified: trunk/packages/beast-mcmc/trunk/debian/control
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/control 2012-01-11 15:52:48 UTC (rev 9251)
+++ trunk/packages/beast-mcmc/trunk/debian/control 2012-01-11 16:11:15 UTC (rev 9252)
@@ -18,7 +18,8 @@
Package: beast-mcmc
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, openjdk-6-jre | java-jre, beast-mcmc-lib, xterm | x-terminal-emulator
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, openjdk-6-jre | java-jre,
+ beast-mcmc-lib, xterm | x-terminal-emulator
Suggests: beast-doc
Description: Bayesian MCMC phylogenetic inference
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
@@ -87,4 +88,3 @@
analyses and a suit of programs for analysing the results.
.
This package contains the documentation.
-
Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch 2012-01-11 15:52:48 UTC (rev 9251)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch 2012-01-11 16:11:15 UTC (rev 9252)
@@ -1,186 +0,0 @@
---- beast-mcmc-1.6.2.orig/release/Linux/scripts/beast
-+++ beast-mcmc-1.6.2/release/Linux/scripts/beast
-@@ -1,26 +1,4 @@
- #!/bin/sh
-
--if [ -z "$BEAST" ]; then
-- ## resolve links - $0 may be a link to application
-- PRG="$0"
--
-- # need this for relative symlinks
-- while [ -h "$PRG" ] ; do
-- ls=`ls -ld "$PRG"`
-- link=`expr "$ls" : '.*-> \(.*\)$'`
-- if expr "$link" : '/.*' > /dev/null; then
-- PRG="$link"
-- else
-- PRG="`dirname "$PRG"`/$link"
-- fi
-- done
--
-- # make it fully qualified
-- saveddir=`pwd`
-- BEAST0=`dirname "$PRG"`/..
-- BEAST=`cd "$BEAST0" && pwd`
-- cd "$saveddir"
--fi
--
--BEAST_LIB="$BEAST/lib"
--java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/local/lib" -cp "$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
-+BEAST_LIB="/usr/share/beast-mcmc"
-+java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB:/usr/lib" -cp "$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
---- beast-mcmc-1.6.2.orig/release/Linux/scripts/beauti
-+++ beast-mcmc-1.6.2/release/Linux/scripts/beauti
-@@ -1,27 +1,5 @@
- #!/bin/sh
-
--if [ -z "$BEAST" ]; then
-- ## resolve links - $0 may be a link to application
-- PRG="$0"
--
-- # need this for relative symlinks
-- while [ -h "$PRG" ] ; do
-- ls=`ls -ld "$PRG"`
-- link=`expr "$ls" : '.*-> \(.*\)$'`
-- if expr "$link" : '/.*' > /dev/null; then
-- PRG="$link"
-- else
-- PRG="`dirname "$PRG"`/$link"
-- fi
-- done
--
-- # make it fully qualified
-- saveddir=`pwd`
-- BEAST0=`dirname "$PRG"`/..
-- BEAST=`cd "$BEAST0" && pwd`
-- cd "$saveddir"
--fi
--
--BEAST_LIB="$BEAST/lib"
-+BEAST_LIB="/usr/share/beast-mcmc"
- java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $*
-
---- beast-mcmc-1.6.2.orig/release/Linux/scripts/loganalyser
-+++ beast-mcmc-1.6.2/release/Linux/scripts/loganalyser
-@@ -1,27 +1,5 @@
- #!/bin/sh
-
--if [ -z "$BEAST" ]; then
-- ## resolve links - $0 may be a link to application
-- PRG="$0"
--
-- # need this for relative symlinks
-- while [ -h "$PRG" ] ; do
-- ls=`ls -ld "$PRG"`
-- link=`expr "$ls" : '.*-> \(.*\)$'`
-- if expr "$link" : '/.*' > /dev/null; then
-- PRG="$link"
-- else
-- PRG="`dirname "$PRG"`/$link"
-- fi
-- done
--
-- # make it fully qualified
-- saveddir=`pwd`
-- BEAST0=`dirname "$PRG"`/..
-- BEAST=`cd "$BEAST0" && pwd`
-- cd "$saveddir"
--fi
--
--BEAST_LIB="$BEAST/lib"
-+BEAST_LIB="/usr/share/beast-mcmc"
- java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $*
-
---- beast-mcmc-1.6.2.orig/release/Linux/scripts/logcombiner
-+++ beast-mcmc-1.6.2/release/Linux/scripts/logcombiner
-@@ -1,27 +1,5 @@
- #!/bin/sh
-
--if [ -z "$BEAST" ]; then
-- ## resolve links - $0 may be a link to application
-- PRG="$0"
--
-- # need this for relative symlinks
-- while [ -h "$PRG" ] ; do
-- ls=`ls -ld "$PRG"`
-- link=`expr "$ls" : '.*-> \(.*\)$'`
-- if expr "$link" : '/.*' > /dev/null; then
-- PRG="$link"
-- else
-- PRG="`dirname "$PRG"`/$link"
-- fi
-- done
--
-- # make it fully qualified
-- saveddir=`pwd`
-- BEAST0=`dirname "$PRG"`/..
-- BEAST=`cd "$BEAST0" && pwd`
-- cd "$saveddir"
--fi
--
--BEAST_LIB="$BEAST/lib"
-+BEAST_LIB="/usr/share/beast-mcmc"
- java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $*
-
---- beast-mcmc-1.6.2.orig/release/Linux/scripts/treeannotator
-+++ beast-mcmc-1.6.2/release/Linux/scripts/treeannotator
-@@ -1,27 +1,5 @@
- #!/bin/sh
-
--if [ -z "$BEAST" ]; then
-- ## resolve links - $0 may be a link to application
-- PRG="$0"
--
-- # need this for relative symlinks
-- while [ -h "$PRG" ] ; do
-- ls=`ls -ld "$PRG"`
-- link=`expr "$ls" : '.*-> \(.*\)$'`
-- if expr "$link" : '/.*' > /dev/null; then
-- PRG="$link"
-- else
-- PRG="`dirname "$PRG"`/$link"
-- fi
-- done
--
-- # make it fully qualified
-- saveddir=`pwd`
-- BEAST0=`dirname "$PRG"`/..
-- BEAST=`cd "$BEAST0" && pwd`
-- cd "$saveddir"
--fi
--
--BEAST_LIB="$BEAST/lib"
-+BEAST_LIB="/usr/share/beast-mcmc"
- java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $*
-
---- beast-mcmc-1.6.2.orig/release/Linux/scripts/treestat
-+++ beast-mcmc-1.6.2/release/Linux/scripts/treestat
-@@ -1,27 +1,5 @@
- #!/bin/sh
-
--if [ -z "$BEAST" ]; then
-- ## resolve links - $0 may be a link to application
-- PRG="$0"
--
-- # need this for relative symlinks
-- while [ -h "$PRG" ] ; do
-- ls=`ls -ld "$PRG"`
-- link=`expr "$ls" : '.*-> \(.*\)$'`
-- if expr "$link" : '/.*' > /dev/null; then
-- PRG="$link"
-- else
-- PRG="`dirname "$PRG"`/$link"
-- fi
-- done
--
-- # make it fully qualified
-- saveddir=`pwd`
-- BEAST0=`dirname "$PRG"`/..
-- BEAST=`cd "$BEAST0" && pwd`
-- cd "$saveddir"
--fi
--
--BEAST_LIB="$BEAST/lib"
-+BEAST_LIB="/usr/share/beast-mcmc"
- java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.treestat.TreeStatApp $*
-
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-01-11 15:52:48 UTC (rev 9251)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-01-11 16:11:15 UTC (rev 9252)
@@ -1,6 +1,4 @@
-beast.patch
fix_gcc_options.patch
fix_classpath_in_build_xml.patch
patch_tex_docs.patch
fix_classpath_in_build_tracer_xml.patch
-some_bins_need_explicit_classpath.patch
Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch 2012-01-11 15:52:48 UTC (rev 9251)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch 2012-01-11 16:11:15 UTC (rev 9252)
@@ -1,42 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Description: The scripts logcombiner, treeannotator and treestat
- did not run without explicite CLASSPATH setting. This is done
- in this patch
-
---- beast-mcmc-1.6.2.orig/release/Linux/scripts/logcombiner
-+++ beast-mcmc-1.6.2/release/Linux/scripts/logcombiner
-@@ -1,5 +1,7 @@
- #!/bin/sh
-
- BEAST_LIB="/usr/share/beast-mcmc"
--java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $*
--
-+DEBJAR="/usr/share/java"
-+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
-+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
-+ dr.app.tools.LogCombiner $*
---- beast-mcmc-1.6.2.orig/release/Linux/scripts/treeannotator
-+++ beast-mcmc-1.6.2/release/Linux/scripts/treeannotator
-@@ -1,5 +1,9 @@
- #!/bin/sh
-
- BEAST_LIB="/usr/share/beast-mcmc"
--java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $*
-+DEBJAR="/usr/share/java"
-+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
-+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
-+ dr.app.tools.TreeAnnotator $*
-+
-
---- beast-mcmc-1.6.2.orig/release/Linux/scripts/treestat
-+++ beast-mcmc-1.6.2/release/Linux/scripts/treestat
-@@ -1,5 +1,8 @@
- #!/bin/sh
-
- BEAST_LIB="/usr/share/beast-mcmc"
--java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.treestat.TreeStatApp $*
-+DEBJAR="/usr/share/java"
-+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
-+ -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar:${DEBJAR}/jdom1.jar \
-+ dr.app.treestat.TreeStatApp $*
-
Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules 2012-01-11 15:52:48 UTC (rev 9251)
+++ trunk/packages/beast-mcmc/trunk/debian/rules 2012-01-11 16:11:15 UTC (rev 9252)
@@ -65,11 +65,6 @@
#
# $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml junit
-override_dh_install:
- dh_install
- # rename beast to beast-mcmc
- mv $(CURDIR)/debian/$(PACKAGE)/usr/bin/beast $(CURDIR)/debian/$(PACKAGE)/usr/bin/beast-mcmc
-
override_dh_compress:
dh_compress --exclude=.pdf
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