Author: tille Date: 2012-01-10 21:34:27 +0000 (Tue, 10 Jan 2012) New Revision: 9245
Added: 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/changelog trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch trunk/packages/beast-mcmc/trunk/debian/patches/series trunk/packages/beast-mcmc/trunk/debian/rules Log: Set explicit CLASSPATH in some scripts to make them run successfully Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install 2012-01-10 19:48:40 UTC (rev 9244) +++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install 2012-01-10 21:34:27 UTC (rev 9245) @@ -1,4 +1,4 @@ release/Linux/scripts/* usr/bin debian/*.xpm usr/share/pixmaps -lib/*.jar usr/share/beast-mcmc/lib -build/dist/*.jar usr/share/beast-mcmc/lib +lib/*.jar usr/share/beast-mcmc +build/dist/*.jar usr/share/beast-mcmc Modified: trunk/packages/beast-mcmc/trunk/debian/changelog =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/changelog 2012-01-10 19:48:40 UTC (rev 9244) +++ trunk/packages/beast-mcmc/trunk/debian/changelog 2012-01-10 21:34:27 UTC (rev 9245) @@ -2,5 +2,4 @@ * Initial release. (Closes: #552101) - -- Andreas Tille <[email protected]> Fri, 04 Feb 2011 19:39:04 +0100 - + -- Andreas Tille <[email protected]> Tue, 10 Jan 2012 22:29:24 +0100 Modified: trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch 2012-01-10 19:48:40 UTC (rev 9244) +++ trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch 2012-01-10 21:34:27 UTC (rev 9245) @@ -27,8 +27,8 @@ - -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 $* -+BEAST_LIB="/usr/share/beast-mcmc/lib" -+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/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 $* --- beast-mcmc-1.6.2.orig/release/Linux/scripts/beauti +++ beast-mcmc-1.6.2/release/Linux/scripts/beauti @@ -1,27 +1,5 @@ @@ -57,7 +57,7 @@ -fi - -BEAST_LIB="$BEAST/lib" -+BEAST_LIB="/usr/share/beast-mcmc/lib" ++BEAST_LIB="/usr/share/beast-mcmc" java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $* --- beast-mcmc-1.6.2.orig/release/Linux/scripts/loganalyser @@ -88,7 +88,7 @@ -fi - -BEAST_LIB="$BEAST/lib" -+BEAST_LIB="/usr/share/beast-mcmc/lib" ++BEAST_LIB="/usr/share/beast-mcmc" java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $* --- beast-mcmc-1.6.2.orig/release/Linux/scripts/logcombiner @@ -119,7 +119,7 @@ -fi - -BEAST_LIB="$BEAST/lib" -+BEAST_LIB="/usr/share/beast-mcmc/lib" ++BEAST_LIB="/usr/share/beast-mcmc" java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $* --- beast-mcmc-1.6.2.orig/release/Linux/scripts/treeannotator @@ -150,7 +150,7 @@ -fi - -BEAST_LIB="$BEAST/lib" -+BEAST_LIB="/usr/share/beast-mcmc/lib" ++BEAST_LIB="/usr/share/beast-mcmc" java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $* --- beast-mcmc-1.6.2.orig/release/Linux/scripts/treestat @@ -181,6 +181,6 @@ -fi - -BEAST_LIB="$BEAST/lib" -+BEAST_LIB="/usr/share/beast-mcmc/lib" ++BEAST_LIB="/usr/share/beast-mcmc" java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.treestat.TreeStatApp $* Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-01-10 19:48:40 UTC (rev 9244) +++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-01-10 21:34:27 UTC (rev 9245) @@ -3,3 +3,4 @@ fix_classpath_in_build_xml.patch patch_tex_docs.patch fix_classpath_in_build_tracer_xml.patch +some_bins_need_explicit_classpath.patch Added: trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch 2012-01-10 21:34:27 UTC (rev 9245) @@ -0,0 +1,42 @@ +Author: Andreas Tille <[email protected]> +Description: The scripts logcombiner, treeannotator and treestat + did not run without explicite CLASSPATH setting. This is done + in this patch + +--- beast-mcmc-1.6.2.orig/release/Linux/scripts/logcombiner ++++ beast-mcmc-1.6.2/release/Linux/scripts/logcombiner +@@ -1,5 +1,7 @@ + #!/bin/sh + + BEAST_LIB="/usr/share/beast-mcmc" +-java -Xms64m -Xmx1024m -Djava.library.path="$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 2012-01-10 19:48:40 UTC (rev 9244) +++ trunk/packages/beast-mcmc/trunk/debian/rules 2012-01-10 21:34:27 UTC (rev 9245) @@ -9,7 +9,7 @@ PACKAGE = beast-mcmc DEBJAR := /usr/share/java -export CLASSPATH := $(DEBJAR)/itext.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar +CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/itext-1.4.5.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar # to run the test suite JAVA := /usr/lib/jvm/java-6-openjdk/bin/java @@ -35,6 +35,7 @@ ant clean override_dh_auto_build: + # CLASSPATH=$(CLASS_PATH) ant build ; \ ant -buildfile build_tracer.xml all ; \ cd native && /bin/sh compileNativeLinux.sh _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
