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 <[email protected]> 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; ${deblib}/zeus-jscl.jar; ===================================== debian/patches/java17-compatibility.patch ===================================== @@ -3,7 +3,7 @@ Author: Emmanuel Bourg <[email protected]> Forwarded: no --- a/build.xml +++ b/build.xml -@@ -102,7 +102,7 @@ +@@ -103,7 +103,7 @@ <rmic base="${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 You're receiving this email because of your account on salsa.debian.org.
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