[med-svn] [mauve] 01/04: Try to get rid of biojava copy. ATTENTION: The copy is from 1.9.2-SNAPSHOT, while Debian has only 1.7.x !!!! (the zeus-jscl attempt was reverted in a separate patch)
Andreas Tille
tille at debian.org
Wed Apr 22 14:23:13 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mauve.
commit c617f66a4ac0f11d844320732ae380cfe82e5430
Author: Andreas Tille <tille at debian.org>
Date: Wed Apr 22 16:18:52 2015 +0200
Try to get rid of biojava copy. ATTENTION: The copy is from 1.9.2-SNAPSHOT, while Debian has only 1.7.x !!!! (the zeus-jscl attempt was reverted in a separate patch)
---
debian/bin/mauve | 2 +-
debian/control | 5 +--
debian/get-orig-source | 2 +-
debian/patches/debian_classes.patch | 37 ++++++++++++++++++++---
debian/patches/revert_zeus-jscl_from_debian.patch | 17 +++++++++++
debian/patches/series | 1 +
debian/rules | 2 +-
7 files changed, 57 insertions(+), 9 deletions(-)
diff --git a/debian/bin/mauve b/debian/bin/mauve
index 33d01a2..cbc9f6a 100644
--- a/debian/bin/mauve
+++ b/debian/bin/mauve
@@ -5,5 +5,5 @@ JAVA_ARGS="-Xms200M -Xmx500M"
DEBJAR="/usr/share/java"
-$JAVA_CMD $JAVA_ARGS -DmauveDir=${DEBJAR}/ -classpath "${CLASSPATH}:${DEBJAR}/bytecode.jar:${DEBJAR}/commons-cli.jar:${DEBJAR}/jebl.jar:${DEBJAR}/zeus-jscl.jar" -jar ${DEBJAR}/Mauve.jar $@
+$JAVA_CMD $JAVA_ARGS -DmauveDir=${DEBJAR}/ -classpath "${CLASSPATH}:${DEBJAR}/biojava.jar:${DEBJAR}/bytecode.jar:${DEBJAR}/commons-cli.jar:${DEBJAR}/jebl.jar:${DEBJAR}/zeus-jscl.jar" -jar ${DEBJAR}/Mauve.jar $@
## :{DEBJAR}/postgresql-jdbc4.jar
diff --git a/debian/control b/debian/control
index 05adf14..ed5dae1 100644
--- a/debian/control
+++ b/debian/control
@@ -9,11 +9,12 @@ Build-Depends: debhelper (>= 9),
default-jdk,
ant,
ant-contrib,
+ libbiojava-java,
libbytecode-java,
libcommons-cli-java,
libdbus-java,
- libjebl2-java,
- libzeus-jscl-java
+ libjebl2-java
+# libzeus-jscl-java
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mauve.git
Vcs-Git: git://anonscm.debian.org/debian-med/mauve.git
diff --git a/debian/get-orig-source b/debian/get-orig-source
index 0d97cff..237fd4b 100755
--- a/debian/get-orig-source
+++ b/debian/get-orig-source
@@ -29,7 +29,7 @@ cd ${TARDIR}
rm -rf osx win32 win64
rm -rf linux-x64/mauveAligner linux-x86/mauveAligner linux-x64/progressiveMauve linux-x86/progressiveMauve
# zeus-jscl should be removable as well but when using libzeus-jscl-java the build fails ...
-for libjava in ant bytecode commons-cli dbus jebl postgres ; do
+for libjava in ant bytecode commons-cli core dbus gui jebl postgres ; do
find . -name "*${libjava}*.jar" -delete
done
rm -rf build_support/retroweaver
diff --git a/debian/patches/debian_classes.patch b/debian/patches/debian_classes.patch
index 7669fb3..8839ba0 100644
--- a/debian/patches/debian_classes.patch
+++ b/debian/patches/debian_classes.patch
@@ -12,14 +12,16 @@ Description: Use Debian packaged classes
<property name="support" location="build_support"/>
<!-- Make datestamp for update checks -->
-@@ -78,15 +79,15 @@
+@@ -77,16 +78,15 @@
+ <!-- Build all java source files -->
<javac
classpath="
- ${ext}/core-1.9.2-SNAPSHOT.jar;
+- ${ext}/core-1.9.2-SNAPSHOT.jar;
- ${ext}/bytecode-1.9.2-SNAPSHOT.jar;
-+ ${deblib}/bytecode.jar;
- ${ext}/gui-1.9.2-SNAPSHOT.jar;
+- ${ext}/gui-1.9.2-SNAPSHOT.jar;
- ${ext}/commons-cli-1.2.jar;
++ ${deblib}/biojava.jar;
++ ${deblib}/bytecode.jar;
+ ${deblib}/commons-cli.jar;
${support}/junit.jar;
- ${ext}/zeus-jscl.jar;
@@ -33,3 +35,30 @@ Description: Use Debian packaged classes
${ext}/unix-0.5.jar"
srcdir="${src}"
destdir="${build}"
+--- a/.classpath
++++ b/.classpath
+@@ -3,18 +3,17 @@
+ <classpathentry kind="src" path="src"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="var" path="JUNIT_HOME/junit.jar" sourcepath="ECLIPSE_HOME/plugins/org.eclipse.jdt.source_3.0.0/src/org.junit_3.8.1/junitsrc.zip"/>
+- <classpathentry kind="lib" path="ext/commons-cli-1.2.jar"/>
+- <classpathentry kind="lib" path="ext/ant-1.7.1.jar"/>
+- <classpathentry kind="lib" path="ext/jebl-0.4.jar" sourcepath="/jebl/src"/>
++ <classpathentry kind="lib" path="/usr/share/java/commons-cli.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/ant.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/jebl.jar" >
+ <classpathentry kind="src" path="test"/>
+ <classpathentry kind="lib" path="ext/zeus-jscl.jar"/>
+- <classpathentry kind="lib" path="ext/dbus-2.6.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/dbus.jar"/>
+ <classpathentry kind="lib" path="ext/unix-0.5.jar"/>
+ <classpathentry kind="lib" path="ext/jsc.jar"/>
+ <classpathentry kind="lib" path="ext/goose.jar"/>
+ <classpathentry kind="lib" path="ext/jnlp.jar"/>
+- <classpathentry kind="lib" path="ext/bytecode-1.9.2-SNAPSHOT.jar"/>
+- <classpathentry kind="lib" path="ext/core-1.9.2-SNAPSHOT.jar"/>
+- <classpathentry kind="lib" path="ext/gui-1.9.2-SNAPSHOT.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/bytecode.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/biojava.jar"/>
+ <classpathentry kind="output" path="bin"/>
+ </classpath>
diff --git a/debian/patches/revert_zeus-jscl_from_debian.patch b/debian/patches/revert_zeus-jscl_from_debian.patch
new file mode 100644
index 0000000..9e70241
--- /dev/null
+++ b/debian/patches/revert_zeus-jscl_from_debian.patch
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Updated: Fri, 17 Apr 2015 15:38:22 +0200
+Description: Since the libzeus-jscl-java package does not (yet)
+ work I revert this patch to enable further development on this package
+ for the moment. It should be disabled before upload.
+
+--- a/build.xml
++++ b/build.xml
+@@ -82,7 +82,7 @@
+ ${deblib}/bytecode.jar;
+ ${deblib}/commons-cli.jar;
+ ${support}/junit.jar;
+- ${deblib}/zeus-jscl.jar;
++ ${ext}/zeus-jscl.jar;
+ ${ext}/goose.jar;
+ ${ext}/ant-1.7.1.jar;
+ ${deblib}/dbus.jar;
diff --git a/debian/patches/series b/debian/patches/series
index a204ff7..71dfd14 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
build_xml.patch
debian_classes.patch
+revert_zeus-jscl_from_debian.patch
diff --git a/debian/rules b/debian/rules
index c649bb4..ea279b3 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,7 +11,7 @@ PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
JAVA_HOME := /usr/lib/jvm/default-java
DEBJAR := /usr/share/java
-CLASS_PATH := $(DEBJAR)/bytecode.jar:$(DEBJAR)/commons-cli.jar:$(DEBJAR)/dbus.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/zeus-jscl.jar
+CLASS_PATH := $(DEBJAR)/biojava.jar:$(DEBJAR)/bytecode.jar:$(DEBJAR)/commons-cli.jar:$(DEBJAR)/dbus.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/zeus-jscl.jar
## :$(DEBJAR)/postgresql-jdbc4.jar
# to run the test suite
--
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