[med-svn] r18664 - in trunk/packages/biojava4-live/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Sat Jan 31 12:01:33 UTC 2015
Author: osallou
Date: 2015-01-31 12:01:33 +0000 (Sat, 31 Jan 2015)
New Revision: 18664
Added:
trunk/packages/biojava4-live/trunk/debian/patches/faketest
Modified:
trunk/packages/biojava4-live/trunk/debian/build.xml
trunk/packages/biojava4-live/trunk/debian/changelog
trunk/packages/biojava4-live/trunk/debian/control
trunk/packages/biojava4-live/trunk/debian/patches/series
trunk/packages/biojava4-live/trunk/debian/rules
Log:
add patches and deps to make tests pass
Modified: trunk/packages/biojava4-live/trunk/debian/build.xml
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/build.xml 2015-01-31 11:51:24 UTC (rev 18663)
+++ trunk/packages/biojava4-live/trunk/debian/build.xml 2015-01-31 12:01:33 UTC (rev 18664)
@@ -21,11 +21,12 @@
<property environment="env"/>
<property name="project.jarfile.name" value="BJLIB.jar"/>
- <property name="class.path" value="${lib.dir}/commons-logging.jar ${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 ${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 ${lib.dir}/log4j2.jar ${lib.dir}/json-simple.jar ${lib.dir}/slf4j-api.jar ${lib.dir}/log4j-over-slf4j.jar ${lib.dir}/commons-math.jar"/>
+ <property name="class.path" value="${lib.dir}/commons-logging.jar ${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 ${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 ${lib.dir}/log4j2.jar ${lib.dir}/json-simple.jar ${lib.dir}/slf4j-api.jar ${lib.dir}/log4j-over-slf4j.jar ${lib.dir}/commons-math.jar ${lib.dir}/xmlunit.jar"/>
<path id="compile.classpath">
<fileset dir="${lib.dir}">
<include name="commons-cli.jar"/>
+ <include name="xmlunit.jar"/>
<include name="commons-collections3.jar"/>
<include name="commons-dbcp.jar"/>
<include name="commons-logging.jar"/>
Modified: trunk/packages/biojava4-live/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/changelog 2015-01-31 11:51:24 UTC (rev 18663)
+++ trunk/packages/biojava4-live/trunk/debian/changelog 2015-01-31 12:01:33 UTC (rev 18664)
@@ -1,13 +1,7 @@
biojava4-live (4.0.0+dfsg-1) UNRELEASED; urgency=medium
- * BioJava4 packaging
- [ needs jcolorbrewer from org.biojava, integrate in source code, need to
- add copyright info
+ * BioJava4 packaging
+ [ TODO: test get-orig-source to recreate archive,
+ test generated packages, pbuilder ]
- ]
- [ needs Jmol upgrade? to be confirmed, build of biojava-structure-gui meanwhile ]
- [ failing test :
- commented for the moment, to be investigated
- ]
-
-- Olivier Sallou <osallou at debian.org> Fri, 30 Jan 2015 17:24:21 +0100
Modified: trunk/packages/biojava4-live/trunk/debian/control
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/control 2015-01-31 11:51:24 UTC (rev 18663)
+++ trunk/packages/biojava4-live/trunk/debian/control 2015-01-31 12:01:33 UTC (rev 18664)
@@ -11,7 +11,8 @@
default-jdk (>= 1:1.6), junit4,javahelper (>=0.25),
ant-optional, icedtea-netx, libhamcrest-java,
libjson-simple-java (>=1.1.1),
- liblog4j2-java, libslf4j-java
+ liblog4j2-java, libslf4j-java,
+ libxmlunit-java
Build-Depends: debhelper (>= 9), ant
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava4/trunk/
Added: trunk/packages/biojava4-live/trunk/debian/patches/faketest
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/faketest (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/faketest 2015-01-31 12:01:33 UTC (rev 18664)
@@ -0,0 +1,22 @@
+Subject: empty tst causes failure
+Description: empty test creates failure at compilate, add fake test
+ to allow compilation and global test success
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2015-01-31
+Forwarded: no
+--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/ProfeatPropertiesImplTest.java
++++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/ProfeatPropertiesImplTest.java
+@@ -20,6 +20,13 @@
+ */
+ package org.biojava.nbio.aaproperties;
+
++import org.junit.Test;
++
+ public class ProfeatPropertiesImplTest {
+
++ at Test
++public void testFake() {
++
++}
++
+ }
Modified: trunk/packages/biojava4-live/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/series 2015-01-31 11:51:24 UTC (rev 18663)
+++ trunk/packages/biojava4-live/trunk/debian/patches/series 2015-01-31 12:01:33 UTC (rev 18664)
@@ -1,3 +1,4 @@
fix_itext_class_updates
use_simple_json
fix_import
+faketest
Modified: trunk/packages/biojava4-live/trunk/debian/rules
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/rules 2015-01-31 11:51:24 UTC (rev 18663)
+++ trunk/packages/biojava4-live/trunk/debian/rules 2015-01-31 12:01:33 UTC (rev 18664)
@@ -57,18 +57,18 @@
cd biojava-core && ant test
cd biojava-alignment && ant test
# Investigate test failure
- #cd biojava-aa-prop && ant test
- # Skip, missing dependency
+ cd biojava-aa-prop && ant test
+ # Skip, missing dependency junitx
#cd biojava-genome && ant test
cd biojava-phylo && ant test
# Native errors may cause issue on NFS...; skipping
- #cd biojava-sequencing && ant test
- #cd biojava-modfinder && ant test
+ cd biojava-sequencing && ant test
+ cd biojava-modfinder && ant test
# Investigate test failure
#cd biojava-protein-disorder && ant test
# Requires remote access and tmp directory write access
#cd biojava-structure && ant test
- #cd biojava-structure-gui && ant test
+ cd biojava-structure-gui && ant test
cd biojava-ontology && ant test
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