[med-svn] r19988 - trunk/packages/biojava/trunk/debian

Olivier Sallou osallou at moszumanska.debian.org
Fri Aug 21 16:48:35 UTC 2015 

Author: osallou
Date: 2015-08-21 16:48:34 +0000 (Fri, 21 Aug 2015)
New Revision: 19988

Added:
   trunk/packages/biojava/trunk/debian/libbiojava1.9-java.jlibs
Removed:
   trunk/packages/biojava/trunk/debian/libbiojava1.8-java.jlibs
Modified:
   trunk/packages/biojava/trunk/debian/build.xml
   trunk/packages/biojava/trunk/debian/changelog
   trunk/packages/biojava/trunk/debian/control
   trunk/packages/biojava/trunk/debian/copyright
   trunk/packages/biojava/trunk/debian/get-orig-source
   trunk/packages/biojava/trunk/debian/rules
   trunk/packages/biojava/trunk/debian/watch
Log:
prepare release 1.9.2, not yet ready for upload due to failing tests

Modified: trunk/packages/biojava/trunk/debian/build.xml
===================================================================
--- trunk/packages/biojava/trunk/debian/build.xml	2015-08-21 12:36:47 UTC (rev 19987)
+++ trunk/packages/biojava/trunk/debian/build.xml	2015-08-21 16:48:34 UTC (rev 19988)
@@ -21,15 +21,15 @@
 	<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}/junit.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar"/>
+	<property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections3.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar"/>
 								
 	<path id="compile.classpath">
                         <fileset dir="${lib.dir}">
 				<include name="commons-cli.jar"/>
-				<include name="commons-collections.jar"/>
+				<include name="commons-collections3.jar"/>
 				<include name="commons-dbcp.jar"/>
 				<include name="commons-pool.jar"/>
-				<include name="junit.jar"/>
+				<include name="junit4.jar"/>
 				<include name="guava.jar"/>
 				<include name="jgrapht0.8.jar"/>
 			</fileset>

Modified: trunk/packages/biojava/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava/trunk/debian/changelog	2015-08-21 12:36:47 UTC (rev 19987)
+++ trunk/packages/biojava/trunk/debian/changelog	2015-08-21 16:48:34 UTC (rev 19988)
@@ -1,15 +1,13 @@
-biojava-live (1:1.8.2-1) UNRELEASED; urgency=low
+biojava-live (1:1.9.2+dfsg-1) UNRELEASED; urgency=low
 
   * New upstream version
-    Closes: #659824 
+    (Closes: #659824) 
+  * d/watch: get from github
 
-  * TODO fix DAS compilation, check doc and lib setup in packages: missing files
-  related to biojava3-structure, need to integrate in upstream all required code.
-  Mail sent upstream for information.
-  * TODO issue with watch to detect latest release, organized in sub directories
-  * TODO: Upstream seems to have droped the habit of shiping jar files - may be
-    the get-orig-source script can be dropped
+  [ ISSUES]
+  Several tests are failing, some randomly. I have contacted upstream for analysis.
 
+
  -- Olivier Sallou <osallou at debian.org>  Sat, 01 Feb 2014 11:28:20 +0100
 
 biojava-live (1:1.7.1-4) unstable; urgency=low

Modified: trunk/packages/biojava/trunk/debian/control
===================================================================
--- trunk/packages/biojava/trunk/debian/control	2015-08-21 12:36:47 UTC (rev 19987)
+++ trunk/packages/biojava/trunk/debian/control	2015-08-21 16:48:34 UTC (rev 19988)
@@ -6,9 +6,9 @@
  Andreas Tille <tille at debian.org>,
  Olivier Sallou <osallou at debian.org>
 Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
- libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
+ libcommons-collections3-java (>= 2.1), libcommons-pool-java (>= 1.1),
  libcommons-cli-java, libguava-java (>= 11.0.1),
- default-jdk, junit4,javahelper (>=0.25), libjgrapht-java,
+ default-jdk, junit4,javahelper (>=0.25), libjgrapht0.8-java,
  ant-optional
 Build-Depends: debhelper (>= 9), cdbs, ant
 Standards-Version: 3.9.5
@@ -16,7 +16,7 @@
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava/trunk/
 Homepage: http://www.biojava.org
 
-Package: libbiojava1.8-java
+Package: libbiojava1.9-java
 Architecture: all
 Depends: ${shlibs:Depends}, ${misc:Depends},
  libcommons-pool-java (>= 1.1),

Modified: trunk/packages/biojava/trunk/debian/copyright
===================================================================
--- trunk/packages/biojava/trunk/debian/copyright	2015-08-21 12:36:47 UTC (rev 19987)
+++ trunk/packages/biojava/trunk/debian/copyright	2015-08-21 16:48:34 UTC (rev 19988)
@@ -1,7 +1,13 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: BioJava
 Source: http://www.biojava.org/download/source
+Files-Excluded: core/src/test/resources/org/biojava/bio/program/indexdb/*.swiss
+                core/src/test/resources/AAC4_HUMAN.sp
 
+Files: core/src/main/java/org/biojava/bio/program/phred/PhredTools.java
+Copyright: 2001 AgResearch
+License: LGPL-2.1+
+
 Files: *
 Copyright: 1999-2008 the Individual authors who contributed the code,
     as identified by the @authors tag of the respective source file.

Modified: trunk/packages/biojava/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava/trunk/debian/get-orig-source	2015-08-21 12:36:47 UTC (rev 19987)
+++ trunk/packages/biojava/trunk/debian/get-orig-source	2015-08-21 16:48:34 UTC (rev 19988)
@@ -8,6 +8,8 @@
     head -n 1 |
     sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
 
+print "VERSION="$VERSION
+
 mkdir -p ../tarballs
 
 cd ../tarballs

Deleted: trunk/packages/biojava/trunk/debian/libbiojava1.8-java.jlibs
===================================================================
--- trunk/packages/biojava/trunk/debian/libbiojava1.8-java.jlibs	2015-08-21 12:36:47 UTC (rev 19987)
+++ trunk/packages/biojava/trunk/debian/libbiojava1.8-java.jlibs	2015-08-21 16:48:34 UTC (rev 19988)
@@ -1,9 +0,0 @@
-dist/biojava-alignment.jar
-dist/biojava-biosql.jar
-dist/biojava-blast.jar
-dist/biojava-bytecode.jar
-dist/biojava-core.jar
-dist/biojava-das.jar
-dist/biojava-gui.jar
-dist/biojava-phylo.jar
-dist/biojava-sequencing.jar

Added: trunk/packages/biojava/trunk/debian/libbiojava1.9-java.jlibs
===================================================================
--- trunk/packages/biojava/trunk/debian/libbiojava1.9-java.jlibs	                        (rev 0)
+++ trunk/packages/biojava/trunk/debian/libbiojava1.9-java.jlibs	2015-08-21 16:48:34 UTC (rev 19988)
@@ -0,0 +1,8 @@
+dist/biojava-alignment.jar
+dist/biojava-biosql.jar
+dist/biojava-blast.jar
+dist/biojava-bytecode.jar
+dist/biojava-core.jar
+dist/biojava-gui.jar
+dist/biojava-phylo.jar
+dist/biojava-sequencing.jar

Modified: trunk/packages/biojava/trunk/debian/rules
===================================================================
--- trunk/packages/biojava/trunk/debian/rules	2015-08-21 12:36:47 UTC (rev 19987)
+++ trunk/packages/biojava/trunk/debian/rules	2015-08-21 16:48:34 UTC (rev 19988)
@@ -17,7 +17,6 @@
 	sed -e 's/BJLIB/biojava-alignment/g' debian/build.xml > alignment/build.xml
 	sed -e 's/BJLIB/biojava-biosql/g' debian/build.xml > biosql/build.xml
 	sed -e 's/BJLIB/biojava-blast/g' debian/build.xml > blast/build.xml
-	sed -e 's/BJLIB/biojava-das/g' debian/build.xml > das/build.xml
 	sed -e 's/BJLIB/biojava-gui/g' debian/build.xml > gui/build.xml
 	sed -e 's/BJLIB/biojava-phylo/g' debian/build.xml > phylo/build.xml
 	sed -e 's/BJLIB/biojava-sequencing/g' debian/build.xml > sequencing/build.xml
@@ -31,7 +30,6 @@
 	cd phylo && ant jar
 	cd sequencing && ant jar
 	cd gui && ant jar
-	cd das && ant jar
 	# make doc
 	rm -rf biojavadoc
 	mkdir biojavadoc
@@ -43,21 +41,17 @@
 	cp -r phylo/* biojavadoc/
 	cp -r sequencing/* biojavadoc/
 	cp -r gui/* biojavadoc/
-	cp -r das/* biojavadoc/
 	sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml
 	cd biojavadoc && ant javadocs
 	rm -rf biojavadoc
 
 override_dh_auto_test:
-	cd bytecode && ant test
 	cd core && ant test
 	cd alignment && ant test
 	cd biosql && ant test
 	cd blast && ant test
 	cd phylo && ant test
 	cd sequencing && ant test
-	cd gui && ant test
-	cd das && ant test
 
 
 

Modified: trunk/packages/biojava/trunk/debian/watch
===================================================================
--- trunk/packages/biojava/trunk/debian/watch	2015-08-21 12:36:47 UTC (rev 19987)
+++ trunk/packages/biojava/trunk/debian/watch	2015-08-21 16:48:34 UTC (rev 19988)
@@ -2,4 +2,7 @@
 #http://biojava.org/wiki/BioJava:Download http://biojava.org/download/bj.*/biojava-([0-9.]+)-all\.tar\.gz
 
 #http://biojava.org/wiki/BioJava:Download http://biojava.org/wiki/BioJava:Download_(1\.[0-9.]+)
-http://biojava.org/wiki/BioJava:Download_(1\.[0-9.]+)
+#http://biojava.org/wiki/BioJava:Download_(1\.[0-9.]+)
+
+opts=filenamemangle=s/.+\/biojava-legacy-(\d\S*)\.tar\.gz/biojava-legacy-$1\.tar\.gz/ \
+  https://github.com/biojava/biojava-legacy/tags .*/biojava-legacy-(\d\S*)\.tar\.gz

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