Author: osallou-guest
Date: 2013-08-06 11:31:55 +0000 (Tue, 06 Aug 2013)
New Revision: 14355
Modified:
trunk/packages/biojava3/trunk/debian/build.xml
trunk/packages/biojava3/trunk/debian/changelog
trunk/packages/biojava3/trunk/debian/control
trunk/packages/biojava3/trunk/debian/get-orig-source
trunk/packages/biojava3/trunk/debian/patches/fix_code_to_support_latest_jmol
trunk/packages/biojava3/trunk/debian/watch
Log:
new upstream release 3.0.6, using github repo
Modified: trunk/packages/biojava3/trunk/debian/build.xml
===================================================================
--- trunk/packages/biojava3/trunk/debian/build.xml 2013-08-05 15:07:14 UTC
(rev 14354)
+++ trunk/packages/biojava3/trunk/debian/build.xml 2013-08-06 11:31:55 UTC
(rev 14355)
@@ -21,13 +21,14 @@
<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 ${lib.dir}/commons-codec.jar
${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar"/>
+ <property name="class.path" value="${lib.dir}/commons-logging.jar
${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}">
<include name="commons-cli.jar"/>
<include name="commons-collections.jar"/>
<include name="commons-dbcp.jar"/>
+ <include name="commons-logging.jar"/>
<include name="commons-pool.jar"/>
<include name="commons-codec.jar"/>
<include name="itext5.jar"/>
Modified: trunk/packages/biojava3/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava3/trunk/debian/changelog 2013-08-05 15:07:14 UTC
(rev 14354)
+++ trunk/packages/biojava3/trunk/debian/changelog 2013-08-06 11:31:55 UTC
(rev 14355)
@@ -1,3 +1,12 @@
+biojava3-live (3.0.6-1) UNRELEASED; urgency=low
+
+ * New upstream release
+ TODO: needs Apache commons logging >= 2.0
+
+ [debian/watch]: use new upstream GitHub repository
+
+ -- Olivier Sallou <[email protected]> Tue, 18 Jun 2013 14:40:39 +0200
+
biojava3-live (3.0.5-3) unstable; urgency=low
* Fix issue wit itext5 >= 5.4.1 related to API change (Closes: #712359)
Modified: trunk/packages/biojava3/trunk/debian/control
===================================================================
--- trunk/packages/biojava3/trunk/debian/control 2013-08-05 15:07:14 UTC
(rev 14354)
+++ trunk/packages/biojava3/trunk/debian/control 2013-08-06 11:31:55 UTC
(rev 14355)
@@ -5,6 +5,7 @@
Uploaders: Olivier Sallou <[email protected]>
Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
+ libcommons-logging-java,
libcommons-cli-java, libguava-java (>= 11.0.1),
libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java,
default-jdk (>= 1:1.6), junit4,javahelper (>=0.25),
@@ -21,6 +22,7 @@
libcommons-pool-java (>= 1.1),
libcommons-collections-java (>= 2.1),
libcommons-dbcp-java (>= 1.1),
+ libcommons-logging-java,
libhsqldb-java,
libbytecode-java,
icedtea-netx,
Modified: trunk/packages/biojava3/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava3/trunk/debian/get-orig-source 2013-08-05
15:07:14 UTC (rev 14354)
+++ trunk/packages/biojava3/trunk/debian/get-orig-source 2013-08-06
11:31:55 UTC (rev 14355)
@@ -12,11 +12,11 @@
cd ../tarballs
#biojava-3.0.4-all.tar.gz
-UTAR="biojava-${VERSION}-all.tar.gz"
+UTAR="biojava-${VERSION}.tar.gz"
mv ../${UTAR} .
tar -xzf ${UTAR}
-mv bj${VERSION} $PKG-${VERSION}.orig # .orig is requested by Developers
Reference 3.4.4 §6.7.8.2
+mv biojava-biojava-${VERSION} $PKG-${VERSION}.orig # .orig is requested by
Developers Reference 3.4.4 §6.7.8.2
cd $PKG-${VERSION}.orig
rm -rf target
Modified:
trunk/packages/biojava3/trunk/debian/patches/fix_code_to_support_latest_jmol
===================================================================
---
trunk/packages/biojava3/trunk/debian/patches/fix_code_to_support_latest_jmol
2013-08-05 15:07:14 UTC (rev 14354)
+++
trunk/packages/biojava3/trunk/debian/patches/fix_code_to_support_latest_jmol
2013-08-06 11:31:55 UTC (rev 14355)
@@ -5,15 +5,7 @@
---
a/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
+++
b/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
-@@ -29,6 +29,7 @@
- import javax.swing.JTextField;
-
- import org.jmol.api.JmolStatusListener;
-+import org.jmol.constant.EnumCallback;
-
- public class MyJmolStatusListener implements JmolStatusListener {
-
-@@ -40,7 +41,17 @@
+@@ -42,7 +42,17 @@
public void setTextField (JTextField statusField) {
status = statusField;
}
Modified: trunk/packages/biojava3/trunk/debian/watch
===================================================================
--- trunk/packages/biojava3/trunk/debian/watch 2013-08-05 15:07:14 UTC (rev
14354)
+++ trunk/packages/biojava3/trunk/debian/watch 2013-08-06 11:31:55 UTC (rev
14355)
@@ -1,4 +1,5 @@
version=3
-http://biojava.org/wiki/BioJava:Download
http://biojava.org/download/bj.*/biojava-(.*)-all\.tar\.gz
+opts=filenamemangle=s/.+\/biojava-?(\d\S*)\.tar\.gz/biojava-$1.tar.gz/ \
+ https://github.com/biojava/biojava/tags .*/biojava-?(\d\S*)\.tar\.gz
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