Author: osallou-guest Date: 2012-12-04 12:56:48 +0000 (Tue, 04 Dec 2012) New Revision: 12584
Removed: trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue Modified: trunk/packages/biojava3/trunk/debian/build.xml trunk/packages/biojava3/trunk/debian/control trunk/packages/biojava3/trunk/debian/get-orig-source trunk/packages/biojava3/trunk/debian/patches/series Log: update forester source location and dependencies Modified: trunk/packages/biojava3/trunk/debian/build.xml =================================================================== --- trunk/packages/biojava3/trunk/debian/build.xml 2012-12-03 21:09:36 UTC (rev 12583) +++ trunk/packages/biojava3/trunk/debian/build.xml 2012-12-04 12:56:48 UTC (rev 12584) @@ -21,7 +21,7 @@ <property environment="env"/> <property name="project.jarfile.name" value="BJLIB.jar"/> - <property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar"/> + <property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar ${lib.dir}/commons-codec.jar ${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar"/> <path id="compile.classpath"> <fileset dir="${lib.dir}"> @@ -29,10 +29,13 @@ <include name="commons-collections.jar"/> <include name="commons-dbcp.jar"/> <include name="commons-pool.jar"/> + <include name="commons-codec.jar"/> + <include name="itext5.jar"/> + <include name="Jmol.jar"/> <include name="junit4.jar"/> <include name="guava.jar"/> <include name="jgrapht0.8.jar"/> - <include name="Jmol.jar"/> + <include name="JmolApplet.jar"/> <include name="hamcrest.jar"/> <include name="json_simple.jar"/> </fileset> Modified: trunk/packages/biojava3/trunk/debian/control =================================================================== --- trunk/packages/biojava3/trunk/debian/control 2012-12-03 21:09:36 UTC (rev 12583) +++ trunk/packages/biojava3/trunk/debian/control 2012-12-04 12:56:48 UTC (rev 12584) @@ -7,8 +7,9 @@ Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java, libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1), libcommons-cli-java, libguava-java (>= 11.0.1), + libcommons-codec-java, libitext5-java, libjmol-java, jmol-applet, default-jdk (>= 1:1.6), junit4,javahelper (>=0.25), libjgrapht-java, - ant-optional, jmol-applet, icedtea-netx, libhamcrest-java, libjson-simple-java + ant-optional, icedtea-netx, libhamcrest-java, libjson-simple-java Build-Depends: debhelper (>= 9), ant Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava3/trunk/ @@ -24,7 +25,10 @@ libhsqldb-java, libbytecode-java, jmol-applet, icedtea-netx, - libjson-simple-java + libjson-simple-java, + libcommons-codec-java, + libitext5-java, + libjmol-java Suggests: java-virtual-machine, libjgrapht-java, libbiojava3-java, libbiojava3-java-doc Description: Java API to biological data and applications (version 3) This package presents the Open Source Java API to biological databases Modified: trunk/packages/biojava3/trunk/debian/get-orig-source =================================================================== --- trunk/packages/biojava3/trunk/debian/get-orig-source 2012-12-03 21:09:36 UTC (rev 12583) +++ trunk/packages/biojava3/trunk/debian/get-orig-source 2012-12-04 12:56:48 UTC (rev 12584) @@ -24,8 +24,8 @@ mkdir -p biojava3-forester/src/main/java cd biojava3-forester/src/main/java - wget http://www.biojava.org/download/maven/org/forester/1.005/forester-1.005-sources.jar - jar xf forester-1.005-sources.jar + wget http://www.biojava.org/download/maven/org/forester/forester-1.005-sources/1.005/forester-1.005-sources-1.005.jar + jar xf forester-1.005-sources-1.005.jar find . -name *.class | xargs rm -f cd ../../../.. cd .. Deleted: trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue =================================================================== --- trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue 2012-12-03 21:09:36 UTC (rev 12583) +++ trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue 2012-12-04 12:56:48 UTC (rev 12584) @@ -1,16 +0,0 @@ -Subject: ASCII error in pbuilder -Description: unmappable character for encoding ASCII -Author: Olivier Sallou <osal...@debian.org> -Last-Updated: 2012-05-31 - ---- a/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java -+++ b/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java -@@ -44,7 +44,7 @@ - /** - * Method for access REST - * @param query -- * service name¡¢method name and parameter for exection rest -+ * service name method name and parameter for exection rest - * @return - * execution result - * @throws IOException Modified: trunk/packages/biojava3/trunk/debian/patches/series =================================================================== --- trunk/packages/biojava3/trunk/debian/patches/series 2012-12-03 21:09:36 UTC (rev 12583) +++ trunk/packages/biojava3/trunk/debian/patches/series 2012-12-04 12:56:48 UTC (rev 12584) @@ -1,3 +1,2 @@ use_simple_json fix_code_to_support_latest_jmol -fix_ascii_character_issue _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit