[med-svn] [Git][med-team/mauve-aligner][master] 7 commits: Depending on biojava-live 1:1.9.5+dfsg-1, which introduced new jar names
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sun Apr 10 21:52:31 BST 2022
Pierre Gruet pushed to branch master at Debian Med / mauve-aligner
Commits:
836cb722 by Pierre Gruet at 2022-04-10T21:24:43+02:00
Depending on biojava-live 1:1.9.5+dfsg-1, which introduced new jar names
- - - - -
bb898c47 by Pierre Gruet at 2022-04-10T21:24:54+02:00
Refreshing patches
- - - - -
0cd3965c by Pierre Gruet at 2022-04-10T21:25:31+02:00
Setting the package to be 'Architecture: all'
- - - - -
404cf94b by Pierre Gruet at 2022-04-10T21:26:20+02:00
Raising Standards version to 4.6.0 (no change)
- - - - -
81c2b299 by Pierre Gruet at 2022-04-10T21:31:04+02:00
Updating changelog
- - - - -
445eac1d by Pierre Gruet at 2022-04-10T21:54:26+02:00
Remove -1 in versioned build-depend
- - - - -
de562ce9 by Pierre Gruet at 2022-04-10T22:52:02+02:00
Upload to experimental
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/manifest
- debian/patches/debian_classes.patch
- debian/patches/do_not_use_goose_jar.patch
- debian/patches/java17-compatibility.patch
- debian/patches/no_ext_dir_at_all.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+mauve-aligner (2.4.0+4736-5) experimental; urgency=medium
+
+ * Team upload.
+ * Depending on biojava-live 1:1.9.5+dfsg, which introduced new jar names
+ * Refreshing patches
+ * Setting the package to be 'Architecture: all'
+ * Raising Standards version to 4.6.0 (no change)
+
+ -- Pierre Gruet <pgt at debian.org> Sun, 10 Apr 2022 21:54:44 +0200
+
mauve-aligner (2.4.0+4736-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -9,24 +9,24 @@ Build-Depends: debhelper-compat (= 13),
ant,
ant-contrib,
junit,
- libbiojava-java,
+ libbiojava-java (>= 1:1.9.5+dfsg),
libcommons-cli-java,
libdbus-java,
libzeus-jscl-java,
libunixsocket-java,
imagemagick
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/mauve-aligner
Vcs-Git: https://salsa.debian.org/med-team/mauve-aligner.git
Homepage: https://darlinglab.org/mauve/
Rules-Requires-Root: no
Package: mauve-aligner
-Architecture: any
+Architecture: all
Depends: ${java:Depends},
java-wrappers,
${misc:Depends},
- libbiojava-java,
+ libbiojava-java (>= 1:1.9.5+dfsg-1),
progressivemauve
Recommends: ${java:Recommends}
Description: multiple genome alignment
=====================================
debian/manifest
=====================================
@@ -1,2 +1,2 @@
usr/share/java/Mauve.jar:
- Class-Path: /usr/share/java/biojava.jar /usr/share/java/commons-cli.jar /usr/share/icedtea-web/netx.jar /usr/share/java/zeus-jscl.jar /usr/share/java/dbus.jar /usr/share/java/unix.jar
+ Class-Path: /usr/share/java/biojava-core.jar /usr/share/java/biojava-gui.jar /usr/share/java/commons-cli.jar /usr/share/icedtea-web/netx.jar /usr/share/java/zeus-jscl.jar /usr/share/java/dbus.jar /usr/share/java/unix.jar
=====================================
debian/patches/debian_classes.patch
=====================================
@@ -23,7 +23,7 @@ Description: Use Debian packaged classes
</classpath>
</taskdef>
-@@ -77,17 +78,14 @@
+@@ -77,17 +78,15 @@
<!-- Build all java source files -->
<javac
classpath="
@@ -31,7 +31,8 @@ Description: Use Debian packaged classes
- ${ext}/bytecode-1.9.2-SNAPSHOT.jar;
- ${ext}/gui-1.9.2-SNAPSHOT.jar;
- ${ext}/commons-cli-1.2.jar;
-+ ${deblib}/biojava.jar;
++ ${deblib}/biojava-core.jar;
++ ${deblib}/biojava-gui.jar;
+ ${deblib}/commons-cli.jar;
${support}/junit.jar;
- ${ext}/zeus-jscl.jar;
@@ -49,7 +50,7 @@ Description: Use Debian packaged classes
target="1.6"
--- a/.classpath
+++ b/.classpath
-@@ -3,18 +3,14 @@
+@@ -3,18 +3,15 @@
<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"/>
@@ -72,6 +73,7 @@ Description: Use Debian packaged classes
- <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/icedtea-web/netx.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/biojava.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/biojava-core.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/biojava-gui.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
=====================================
debian/patches/do_not_use_goose_jar.patch
=====================================
@@ -11,11 +11,11 @@ Description: Do not use goose.jar since it is not used accorcing to upstream
<classpathentry kind="lib" path="/usr/share/java/unix.jar"/>
- <classpathentry kind="lib" path="ext/goose.jar"/>
<classpathentry kind="lib" path="/usr/share/icedtea-web/netx.jar"/>
- <classpathentry kind="lib" path="/usr/share/java/biojava.jar"/>
- <classpathentry kind="output" path="bin"/>
+ <classpathentry kind="lib" path="/usr/share/java/biojava-core.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/biojava-gui.jar"/>
--- a/build.xml
+++ b/build.xml
-@@ -82,7 +82,6 @@
+@@ -83,7 +83,6 @@
${deblib}/commons-cli.jar;
${support}/junit.jar;
${deblib}/zeus-jscl.jar;
=====================================
debian/patches/java17-compatibility.patch
=====================================
@@ -3,7 +3,7 @@ Author: Emmanuel Bourg <ebourg at apache.org>
Forwarded: no
--- a/build.xml
+++ b/build.xml
-@@ -102,7 +102,7 @@
+@@ -103,7 +103,7 @@
<rmic base="${build}" classname="org.gel.mauve.remote.RemoteControlImpl" />
</target>
=====================================
debian/patches/no_ext_dir_at_all.patch
=====================================
@@ -14,7 +14,7 @@ Description: Some remainings of mentioning ext/ in build.xml were breaking
<property name="deblib" location="/usr/share/java" />
<property name="support" location="/usr/share/java"/>
-@@ -104,18 +103,6 @@
+@@ -105,18 +104,6 @@
</target>
<target name="jar" depends="rmic">
@@ -33,7 +33,7 @@ Description: Some remainings of mentioning ext/ in build.xml were breaking
<!-- Put everything in ${build} into the Mauve.jar file -->
<delete file="Mauve.jar"/>
-@@ -126,7 +113,6 @@
+@@ -127,7 +114,6 @@
<manifest>
<attribute name="Main-Class" value="org.gel.mauve.gui.Mauve"/>
<attribute name="Built-By" value="${user.name}"/>
@@ -41,7 +41,7 @@ Description: Some remainings of mentioning ext/ in build.xml were breaking
<section name="common">
<attribute name="Specification-Title" value="Mauve"/>
<attribute name="Specification-Version" value="${version}"/>
-@@ -161,14 +147,6 @@
+@@ -162,14 +148,6 @@
<signjar jar="mauveApplet.jar" alias="${key.alias}" storepass="${key.password}" keystore="${key.keystore}" />
</target>
@@ -56,7 +56,7 @@ Description: Some remainings of mentioning ext/ in build.xml were breaking
<target name="testdist" depends="signjars">
<copy todir="C:\htdocs" file="Mauve.jar" />
<copy todir="C:\htdocs" file="mauveApplet.jar" />
-@@ -205,7 +183,6 @@
+@@ -206,7 +184,6 @@
<include name="mauveAligner" />
<include name="progressiveMauve" />
</tarfileset>
@@ -64,7 +64,7 @@ Description: Some remainings of mentioning ext/ in build.xml were breaking
</tar>
</target>
-@@ -238,11 +215,6 @@
+@@ -239,11 +216,6 @@
<target name="asapResources">
<pathconvert property="asap.resources" pathsep=" ">
=====================================
debian/rules
=====================================
@@ -9,7 +9,7 @@
JAVA_HOME := /usr/lib/jvm/default-java
DEBJAR := /usr/share/java
-CLASS_PATH := $(DEBJAR)/biojava.jar:$(DEBJAR)/commons-cli.jar:$(DEBJAR)/dbus.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/zeus-jscl.jar
+CLASS_PATH := $(DEBJAR)/biojava-core.jar:$(DEBJAR)/biojava-gui.jar:$(DEBJAR)/commons-cli.jar:$(DEBJAR)/dbus.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/zeus-jscl.jar
## :$(DEBJAR)/postgresql-jdbc4.jar
# to run the test suite
View it on GitLab: https://salsa.debian.org/med-team/mauve-aligner/-/compare/0698f54062f9113494e21fb0cfc6219dd4969f6f...de562ce93d63d0af41658d314effdd546b28262b
--
View it on GitLab: https://salsa.debian.org/med-team/mauve-aligner/-/compare/0698f54062f9113494e21fb0cfc6219dd4969f6f...de562ce93d63d0af41658d314effdd546b28262b
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