Hello everyone,
Recently I worked on biojava-live (locally, pushed nothing to Salsa), which currently has version 1.7.1. Upstream is active and published version 1.9.5 of this "legacy" biojava, which is still used by many software: four reverse dependencies in Debian (alien-hunter, artemis, logol, mauve-aligner), which cannot depend on modern biojava5-live because classes have changed so much in between.
I would like to upgrade to version 1.9.5, which would mean:- keeping the same source package but pushing new binary package libbiojava1.9-java to NEW, conflicting with and replacing libbiojava1.7-java;
- making a source upload of the four reverse dependencies afterwards.About this last point: I am able to build the four reverse dependencies against this biojava 1.9.5, few changes are necessary: mainly the names of the jars, which have changed between 1.7.1 and 1.9.5. Enclosed are the source debdiffs of the needed changes for the four reverse dependencies.
Is it OK for you if I upgrade to 1.9.5 and then I take care of the reverse dependencies?
I am explicitly CC-ing the current uploaders of biojava-live, and I plan to add myself to this list of uploaders.
Best regards, -- Pierre
diff -Nru artemis-18.1.0+dfsg/debian/artemis.manifest
artemis-18.1.0+dfsg/debian/artemis.manifest
--- artemis-18.1.0+dfsg/debian/artemis.manifest 2021-11-06 14:44:49.000000000
+0100
+++ artemis-18.1.0+dfsg/debian/artemis.manifest 2022-02-28 18:24:58.000000000
+0100
@@ -1,15 +1,15 @@
usr/share/java/artemis.jar:
- Class-Path: /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar
/usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar
/usr/share/java/batik-util.jar /usr/share/java/biojava.jar
/usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar
/usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar
/usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar
/usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar
/usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar
+ Class-Path: /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar
/usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar
/usr/share/java/batik-util.jar /usr/share/java/biojava-core.jar
/usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar
/usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar
/usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar
/usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar
/usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar
Main-Class: uk.ac.sanger.artemis.components.ArtemisMain
usr/share/java/act.jar:
- Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar
/usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar
/usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar
/usr/share/java/biojava.jar /usr/share/java/cglib.jar
/usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar
/usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar
/usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar
/usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar
/usr/share/java/postgresql-jdbc.jar
+ Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar
/usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar
/usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar
/usr/share/java/biojava-core.jar /usr/share/java/cglib.jar
/usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar
/usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar
/usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar
/usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar
/usr/share/java/postgresql-jdbc.jar
Main-Class: uk.ac.sanger.artemis.components.ActMain
usr/share/java/bamview.jar:
- Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar
/usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar
/usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar
/usr/share/java/biojava.jar /usr/share/java/cglib.jar
/usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar
/usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar
/usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar
/usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar
/usr/share/java/postgresql-jdbc.jar
+ Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar
/usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar
/usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar
/usr/share/java/biojava-core.jar /usr/share/java/cglib.jar
/usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar
/usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar
/usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar
/usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar
/usr/share/java/postgresql-jdbc.jar
Main-Class: uk.ac.sanger.artemis.components.alignment.BamView
usr/share/java/dnaplotter.jar:
- Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar
/usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar
/usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar
/usr/share/java/biojava.jar /usr/share/java/cglib.jar
/usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar
/usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar
/usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar
/usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar
/usr/share/java/postgresql-jdbc.jar
+ Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar
/usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar
/usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar
/usr/share/java/biojava-core.jar /usr/share/java/cglib.jar
/usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar
/usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar
/usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar
/usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar
/usr/share/java/postgresql-jdbc.jar
Main-Class: uk.ac.sanger.artemis.circular.DNADraw
diff -Nru artemis-18.1.0+dfsg/debian/changelog
artemis-18.1.0+dfsg/debian/changelog
--- artemis-18.1.0+dfsg/debian/changelog 2021-11-07 15:25:19.000000000
+0100
+++ artemis-18.1.0+dfsg/debian/changelog 2022-02-28 18:24:58.000000000
+0100
@@ -1,3 +1,9 @@
+artemis (18.1.0+dfsg-7) UNRELEASED; urgency=medium
+
+ * Changing coordinates of biojava, which is now Maven-packaged
+
+ -- Pierre Gruet <p...@debian.org> Mon, 28 Feb 2022 18:24:58 +0100
+
artemis (18.1.0+dfsg-6) unstable; urgency=medium
* Using -Xmx1946m instead of -Xm4g in the autopkgtest, so that it runs on
diff -Nru artemis-18.1.0+dfsg/debian/control artemis-18.1.0+dfsg/debian/control
--- artemis-18.1.0+dfsg/debian/control 2021-11-05 20:52:28.000000000 +0100
+++ artemis-18.1.0+dfsg/debian/control 2022-02-28 18:24:58.000000000 +0100
@@ -43,23 +43,8 @@
Package: artemis
Architecture: all
Depends: ${misc:Depends},
- ${java:Depends},
-# java:Depends adds a dependency on a versioned biojava, but that does not
-# contain the required biojava.jar file
- libbiojava-java,
- libhtsjdk-java,
- libcommons-net-java,
- libcommons-lang3-java,
- libcommons-logging-java,
- libbatik-java,
- libj2ssh-java,
- libibatis-java,
- liblog4j1.2-java,
- libpostgresql-jdbc-java,
- libpicard-java,
- jemboss,
- libcglib-java,
- default-jre
+ ${maven:Depends}
+Suggests: ${maven:OptionalDepends}
Description: genome browser and annotation tool
Artemis is a genome browser and annotation tool that allows visualisation of
sequence features, next generation data and the results of analyses within the
diff -Nru artemis-18.1.0+dfsg/debian/maven.rules
artemis-18.1.0+dfsg/debian/maven.rules
--- artemis-18.1.0+dfsg/debian/maven.rules 2020-09-05 15:02:32.000000000
+0200
+++ artemis-18.1.0+dfsg/debian/maven.rules 2022-02-28 18:24:58.000000000
+0100
@@ -15,3 +15,4 @@
junit junit jar s/.*/4.x/ * *
slf4j slf4j-nop jar s/.*/debian/ * *
org.mockito mockito-core jar s/.*/debian/ * *
+org.biojava s/biojava/core/ jar s/1.*/1.x/ * *
diff -Nru
artemis-18.1.0+dfsg/debian/patches/missing_htsjdk_dependency_in_pom.patch
artemis-18.1.0+dfsg/debian/patches/missing_htsjdk_dependency_in_pom.patch
--- artemis-18.1.0+dfsg/debian/patches/missing_htsjdk_dependency_in_pom.patch
2021-04-26 17:29:15.000000000 +0200
+++ artemis-18.1.0+dfsg/debian/patches/missing_htsjdk_dependency_in_pom.patch
2022-02-28 18:22:16.000000000 +0100
@@ -5,7 +5,7 @@
--- a/pom.xml
+++ b/pom.xml
-@@ -298,7 +298,13 @@
+@@ -296,7 +296,13 @@
</dependency>
<!-- End of Picard jars -->
diff -Nru artemis-18.1.0+dfsg/debian/patches/no_install_of_provided_jars.patch
artemis-18.1.0+dfsg/debian/patches/no_install_of_provided_jars.patch
--- artemis-18.1.0+dfsg/debian/patches/no_install_of_provided_jars.patch
2021-04-26 17:29:03.000000000 +0200
+++ artemis-18.1.0+dfsg/debian/patches/no_install_of_provided_jars.patch
2022-02-28 18:22:20.000000000 +0100
@@ -7,7 +7,7 @@
--- a/pom.xml
+++ b/pom.xml
-@@ -415,76 +415,6 @@
+@@ -413,76 +413,6 @@
</executions>
</plugin>
diff -Nru artemis-18.1.0+dfsg/debian/patches/running_build_tests.patch
artemis-18.1.0+dfsg/debian/patches/running_build_tests.patch
--- artemis-18.1.0+dfsg/debian/patches/running_build_tests.patch
2021-04-26 17:30:25.000000000 +0200
+++ artemis-18.1.0+dfsg/debian/patches/running_build_tests.patch
2022-02-28 18:22:23.000000000 +0100
@@ -10,7 +10,7 @@
--- a/pom.xml
+++ b/pom.xml
-@@ -510,28 +510,6 @@
+@@ -508,28 +508,6 @@
</configuration>
</plugin>
@@ -39,7 +39,7 @@
<!-- ======================================= Surefire
Unit tests ==========================================-->
<!-- Only currently runs default unit tests because of
bug in Evosuite on Java 9+. -->
-@@ -540,11 +518,9 @@
+@@ -538,11 +516,9 @@
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.1</version>
<configuration>
@@ -51,7 +51,7 @@
<argLine>@{surefireArgLine}</argLine>
<excludes>
<!-- Exclude Evosuite tests -->
-@@ -554,6 +530,9 @@
+@@ -552,6 +528,9 @@
<exclude>**/RunBlastAtNCBITest.*</exclude>
<exclude>**/TestIbatisDAO.*</exclude>
<exclude>**/TestJdbcDAO.*</exclude>
@@ -119,4 +119,3 @@
-}
\ No newline at end of file
+}
-
diff -Nru artemis-18.1.0+dfsg/debian/patches/using_system_jars_in_pom.patch
artemis-18.1.0+dfsg/debian/patches/using_system_jars_in_pom.patch
--- artemis-18.1.0+dfsg/debian/patches/using_system_jars_in_pom.patch
2021-04-26 17:28:51.000000000 +0200
+++ artemis-18.1.0+dfsg/debian/patches/using_system_jars_in_pom.patch
2022-02-28 18:22:11.000000000 +0100
@@ -16,16 +16,7 @@
</dependency>
<!-- Very out of date, but using the latest v3 will not
compile atm -->
-@@ -278,6 +280,8 @@
- <groupId>org.biojava</groupId>
- <artifactId>biojava</artifactId>
- <version>1.6</version>
-+ <scope>system</scope>
-+ <systemPath>/usr/share/java/biojava.jar</systemPath>
- </dependency>
-
- <!-- Start of Picard jars -->
-@@ -289,6 +293,8 @@
+@@ -289,6 +291,8 @@
<groupId>com.github.broadinstitute</groupId>
<artifactId>picard</artifactId>
<version>2.18.14</version>
diff -Nru logol-1.7.9+dfsg/debian/changelog logol-1.7.9+dfsg/debian/changelog
--- logol-1.7.9+dfsg/debian/changelog 2022-03-04 07:29:09.000000000 +0100
+++ logol-1.7.9+dfsg/debian/changelog 2022-02-28 21:57:06.000000000 +0100
@@ -1,3 +1,11 @@
+logol (1.7.9+dfsg-4) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Using biojava-core.jar and biojava-bytecode.jar which are now shipped by
+ libbiojava-java instead of former biojava.jar
+
+ -- Pierre Gruet <p...@debian.org> Mon, 28 Feb 2022 21:57:06 +0100
+
logol (1.7.9+dfsg-3) unstable; urgency=medium
* d/control: add dep on swi-prolog ABI via swi-prolog-abi-binary-68
diff -Nru logol-1.7.9+dfsg/debian/patches/fix_biojava_paths_in_scripts.patch
logol-1.7.9+dfsg/debian/patches/fix_biojava_paths_in_scripts.patch
--- logol-1.7.9+dfsg/debian/patches/fix_biojava_paths_in_scripts.patch
1970-01-01 01:00:00.000000000 +0100
+++ logol-1.7.9+dfsg/debian/patches/fix_biojava_paths_in_scripts.patch
2022-02-28 21:57:06.000000000 +0100
@@ -0,0 +1,61 @@
+Description: biojava has been split into several jars, starting from version
1.9
+Author: Pierre Gruet <p...@debian.org>
+Forwarded: not-needed
+Last-Update: 2022-02-28
+
+--- a/LogolExec.rb
++++ b/LogolExec.rb
+@@ -10,7 +10,7 @@
+
+ #puts "calling logol with parameters "+args
+
+-cmd="java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath
$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar
org.irisa.genouest.logol.Logol "+args.to_s
++cmd="java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath
/usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar
org.irisa.genouest.logol.Logol "+args.to_s
+ cmd=cmd.gsub(":",";")
+ cmd=cmd.gsub("file;","file:")
+ cmd=cmd.gsub("$LOGOL_HOME",LOGOL_HOME)
+--- a/LogolMultiExec.rb
++++ b/LogolMultiExec.rb
+@@ -10,7 +10,7 @@
+
+ #puts "calling logol with parameters "+args
+
+-cmd="java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath
$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar
org.irisa.genouest.logol.dispatcher.Dispatch "+args.to_s
++cmd="java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath
/usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar
org.irisa.genouest.logol.dispatcher.Dispatch "+args.to_s
+ cmd=cmd.gsub(":",";")
+ cmd=cmd.gsub("file;","file:")
+ cmd=cmd.gsub("$LOGOL_HOME",LOGOL_HOME)
+--- a/MatchToModel.sh
++++ b/MatchToModel.sh
+@@ -16,7 +16,7 @@
+ echo "calling logol with parameters "$*
+
+ java -Xms512m -Xmx4096m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -
+-classpath
$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/li
+-b/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_
+-HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL
+-_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar
org.irisa.genouest.logol.utils.model.MatchToModel $*
+\ No newline at end of file
++classpath
/usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.ja
++r:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5
++.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL
++_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar
org.irisa.genouest.logol.utils.model.MatchToModel $*
+--- a/Model2Grammar.sh
++++ b/Model2Grammar.sh
+@@ -14,5 +14,5 @@
+
+ echo "calling logol with parameters "$*
+
+-java -Xms512m -Xmx4096m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath
$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar
org.irisa.genouest.logol.utils.model.ModelConverter $*
++java -Xms512m -Xmx4096m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath
/usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar
org.irisa.genouest.logol.utils.model.ModelConverter $*
+
+--- a/logolTest.sh
++++ b/logolTest.sh
+@@ -11,6 +11,6 @@
+
+ echo "calling logol with parameters "$*
+
+-java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME
-Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath
$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/junit.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar
org.irisa.genouest.logol.test.TestSuite $*
++java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME
-Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath
/usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/junit.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar
org.irisa.genouest.logol.test.TestSuite $*
+
+
diff -Nru logol-1.7.9+dfsg/debian/patches/fixLibPath
logol-1.7.9+dfsg/debian/patches/fixLibPath
--- logol-1.7.9+dfsg/debian/patches/fixLibPath 2022-03-04 07:29:09.000000000
+0100
+++ logol-1.7.9+dfsg/debian/patches/fixLibPath 2022-02-28 21:57:06.000000000
+0100
@@ -39,12 +39,13 @@
<exec executable="swipl">
<arg line=" -f ${basedir}/prolog/unitTest/swi-unit.pl
-- ${basedir}/prolog/unitTest/sampleUnit.pro ${basedir}/prolog/sicstus.pl
${work.dir}/SwiLogolSelfTest-PUnit-${build.nb}.xml
${basedir}/prolog/unitTest/plunittest.pro ${basedir}/prolog/logol.pl
${basedir}/test/test.fasta" />
</exec>
-@@ -148,6 +153,25 @@
+@@ -148,6 +153,26 @@
<fileset dir="${basedir}/lib">
<include name="**/*.jar" />
</fileset>
+ <fileset dir="/usr/share/java" >
-+ <include name="biojava.jar"/>
++ <include name="biojava-bytecode.jar"/>
++ <include name="biojava-core.jar"/>
+ <include name="activation.jar"/>
+ <include name="bytecode.jar"/>
+ <include name="drmaa.jar"/>
@@ -65,11 +66,11 @@
</classpath>
<sysproperty key="logol.install" value="${basedir}" />
<sysproperty key="log4j.configuration"
value="file://${basedir}/log4j.properties" />
-@@ -210,6 +234,7 @@
+@@ -210,6 +235,7 @@
<attribute name="Main-Class"
value="org.irisa.genouest.logol.Logol" />
<attribute name="Implementation-Version"
value="${version}" />
<attribute name="Implementation-Build"
value="${build.nb}" />
-+ <attribute name="Class-Path"
value="/usr/share/java/biojava.jar /usr/share/java/activation.jar
/usr/share/java/bytecode.jar /usr/share/java/serializer.jar
/usr/share/java/antlr3-runtime.jar /usr/share/java/drmaa.jar
/usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar
/usr/share/java/commons-configuration.jar /usr/share/java/commons-lang.jar
/usr/share/java/commons-logging.jar /usr/share/java/xalan2.jar
/usr/share/java/xercesImpl.jar /usr/share/java/javax.mail.jar
/usr/share/java/log4j1.2.jar /usr/share/java/xml-apis.jar" />
++ <attribute name="Class-Path"
value="/usr/share/java/biojava-bytecode.jar /usr/share/java/biojava-core.jar
/usr/share/java/activation.jar /usr/share/java/bytecode.jar
/usr/share/java/serializer.jar /usr/share/java/antlr3-runtime.jar
/usr/share/java/drmaa.jar /usr/share/java/commons-cli.jar
/usr/share/java/commons-collections3.jar
/usr/share/java/commons-configuration.jar /usr/share/java/commons-lang.jar
/usr/share/java/commons-logging.jar /usr/share/java/xalan2.jar
/usr/share/java/xercesImpl.jar /usr/share/java/javax.mail.jar
/usr/share/java/log4j1.2.jar /usr/share/java/xml-apis.jar" />
</manifest>
</jar>
</target>
diff -Nru logol-1.7.9+dfsg/debian/patches/series
logol-1.7.9+dfsg/debian/patches/series
--- logol-1.7.9+dfsg/debian/patches/series 2022-03-04 07:29:09.000000000
+0100
+++ logol-1.7.9+dfsg/debian/patches/series 2022-02-28 21:57:06.000000000
+0100
@@ -7,3 +7,4 @@
fix_swipl_declarations
fix_swipl_foreign_load
remove_test
+fix_biojava_paths_in_scripts.patch
diff -Nru logol-1.7.9+dfsg/debian/patches/setDebianDirs
logol-1.7.9+dfsg/debian/patches/setDebianDirs
--- logol-1.7.9+dfsg/debian/patches/setDebianDirs 2022-03-04
07:29:09.000000000 +0100
+++ logol-1.7.9+dfsg/debian/patches/setDebianDirs 2022-02-28
21:57:06.000000000 +0100
@@ -30,7 +30,7 @@
fi
-java $JAVA_OPTS -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_LOG4J -classpath
$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar
org.irisa.genouest.logol.Logol $*
-+java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_LOG4J -classpath
$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar
org.irisa.genouest.logol.Logol $*
++java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_LOG4J -classpath
/usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar
org.irisa.genouest.logol.Logol $*
--- a/LogolMultiExec.sh
+++ b/LogolMultiExec.sh
@@ -39,5 +39,5 @@
echo "calling logol with parameters "$*
-java $JAVA_OPTS -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_LOG4J -classpath
$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar
org.irisa.genouest.logol.dispatcher.Dispatch $*
-+java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_LOG4J -classpath
$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar
org.irisa.genouest.logol.dispatcher.Dispatch $*
++java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME
-Dlogol.conf=$LOGOL_HOME/prolog/logol.properties
-Dlog4j.configuration=file://$LOGOL_LOG4J -classpath
$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:/usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar
org.irisa.genouest.logol.dispatcher.Dispatch $*
diff -Nru alien-hunter-1.7/debian/changelog alien-hunter-1.7/debian/changelog
--- alien-hunter-1.7/debian/changelog 2020-11-26 08:05:33.000000000 +0100
+++ alien-hunter-1.7/debian/changelog 2022-02-28 21:32:10.000000000 +0100
@@ -1,3 +1,11 @@
+alien-hunter (1.7-9) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Using biojava-core.jar, now shipped by libbiojava-java, instead of former
+ biojava.jar
+
+ -- Pierre Gruet <p...@debian.org> Mon, 28 Feb 2022 21:32:10 +0100
+
alien-hunter (1.7-8) unstable; urgency=medium
* Standards-Version: 4.5.1 (routine-update)
diff -Nru alien-hunter-1.7/debian/patches/20_type_StatePath_States.patch
alien-hunter-1.7/debian/patches/20_type_StatePath_States.patch
--- alien-hunter-1.7/debian/patches/20_type_StatePath_States.patch
1970-01-01 01:00:00.000000000 +0100
+++ alien-hunter-1.7/debian/patches/20_type_StatePath_States.patch
2022-02-28 21:32:10.000000000 +0100
@@ -0,0 +1,27 @@
+Description: casting an Object to String to comply to biojava 1.9
implementation
+Author: Pierre Gruet <p...@debian.org>
+Forwarded: not-needed
+Last-Update: 2022-02-28
+
+--- a/ChangepointLeft.java
++++ b/ChangepointLeft.java
+@@ -128,7 +128,7 @@
+
+ for(int j = i*60; j < Math.min((i+1)*60,
statePath.length()); j++) {
+
//System.out.print(statePath.symbolAt(StatePath.STATES,
j+1).getName().charAt(0));
+- char state=statePath.symbolAt(StatePath.STATES,
j+1).getName().charAt(0);
++ char
state=statePath.symbolAt((String)(StatePath.STATES), j+1).getName().charAt(0);
+ count++;
+ //it prints the states in binary mode for art
user_graph
+ if(state == 'a'){
+--- a/ChangepointRight.java
++++ b/ChangepointRight.java
+@@ -130,7 +130,7 @@
+
+ for(int j = i*60; j < Math.min((i+1)*60,
statePath.length()); j++) {
+
//System.out.print(statePath.symbolAt(StatePath.STATES,
j+1).getName().charAt(0));
+- char state=statePath.symbolAt(StatePath.STATES,
j+1).getName().charAt(0);
++ char
state=statePath.symbolAt((String)(StatePath.STATES), j+1).getName().charAt(0);
+ count++;
+ //it prints the states in binary mode for art
user_graph
+ if(state == 'a'){
diff -Nru alien-hunter-1.7/debian/patches/series
alien-hunter-1.7/debian/patches/series
--- alien-hunter-1.7/debian/patches/series 2020-11-26 08:05:33.000000000
+0100
+++ alien-hunter-1.7/debian/patches/series 2022-02-28 21:32:10.000000000
+0100
@@ -1,2 +1,3 @@
10_fix_classpath.patch
10_location_of_perl.patch
+20_type_StatePath_States.patch
diff -Nru alien-hunter-1.7/debian/rules alien-hunter-1.7/debian/rules
--- alien-hunter-1.7/debian/rules 2020-11-26 08:05:33.000000000 +0100
+++ alien-hunter-1.7/debian/rules 2022-02-28 21:28:51.000000000 +0100
@@ -6,7 +6,7 @@
dh $@
override_dh_auto_build:
- CLASSPATH=/usr/share/java/biojava.jar javac -Xlint:deprecation
-Xlint:unchecked *.java
+ CLASSPATH=/usr/share/java/biojava-core.jar javac -Xlint:deprecation
-Xlint:unchecked *.java
override_dh_auto_clean:
rm -f *.class $(executable).1
diff -Nru mauve-aligner-2.4.0+4736/debian/changelog
mauve-aligner-2.4.0+4736/debian/changelog
--- mauve-aligner-2.4.0+4736/debian/changelog 2021-04-17 21:49:20.000000000
+0200
+++ mauve-aligner-2.4.0+4736/debian/changelog 2022-02-28 20:13:37.000000000
+0100
@@ -1,3 +1,10 @@
+mauve-aligner (2.4.0+4736-5) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * New jar biojava-core.jar from libbiojava-java
+
+ -- Pierre Gruet <p...@debian.org> Mon, 28 Feb 2022 21:13:37 +0200
+
mauve-aligner (2.4.0+4736-4) unstable; urgency=medium
* Team upload.
diff -Nru mauve-aligner-2.4.0+4736/debian/manifest
mauve-aligner-2.4.0+4736/debian/manifest
--- mauve-aligner-2.4.0+4736/debian/manifest 2021-04-17 21:37:05.000000000
+0200
+++ mauve-aligner-2.4.0+4736/debian/manifest 2022-02-28 20:13:37.000000000
+0100
@@ -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
diff -Nru mauve-aligner-2.4.0+4736/debian/patches/debian_classes.patch
mauve-aligner-2.4.0+4736/debian/patches/debian_classes.patch
--- mauve-aligner-2.4.0+4736/debian/patches/debian_classes.patch
2021-04-17 21:37:05.000000000 +0200
+++ mauve-aligner-2.4.0+4736/debian/patches/debian_classes.patch
2022-02-28 20:13:37.000000000 +0100
@@ -23,7 +23,7 @@
</classpath>
</taskdef>
-@@ -77,17 +78,14 @@
+@@ -77,17 +78,15 @@
<!-- Build all java source files -->
<javac
classpath="
@@ -31,7 +31,8 @@
- ${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 @@
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 @@
- <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>
diff -Nru mauve-aligner-2.4.0+4736/debian/patches/do_not_use_goose_jar.patch
mauve-aligner-2.4.0+4736/debian/patches/do_not_use_goose_jar.patch
--- mauve-aligner-2.4.0+4736/debian/patches/do_not_use_goose_jar.patch
2021-04-17 21:37:05.000000000 +0200
+++ mauve-aligner-2.4.0+4736/debian/patches/do_not_use_goose_jar.patch
2022-02-28 20:13:37.000000000 +0100
@@ -11,11 +11,11 @@
<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;
${deblib}/zeus-jscl.jar;
diff -Nru mauve-aligner-2.4.0+4736/debian/patches/java17-compatibility.patch
mauve-aligner-2.4.0+4736/debian/patches/java17-compatibility.patch
--- mauve-aligner-2.4.0+4736/debian/patches/java17-compatibility.patch
2021-04-17 21:48:47.000000000 +0200
+++ mauve-aligner-2.4.0+4736/debian/patches/java17-compatibility.patch
2022-02-28 20:13:37.000000000 +0100
@@ -3,7 +3,7 @@
Forwarded: no
--- a/build.xml
+++ b/build.xml
-@@ -102,7 +102,7 @@
+@@ -103,7 +103,7 @@
<rmic base="${build}"
classname="org.gel.mauve.remote.RemoteControlImpl" />
</target>
diff -Nru mauve-aligner-2.4.0+4736/debian/patches/no_ext_dir_at_all.patch
mauve-aligner-2.4.0+4736/debian/patches/no_ext_dir_at_all.patch
--- mauve-aligner-2.4.0+4736/debian/patches/no_ext_dir_at_all.patch
2021-04-17 21:37:05.000000000 +0200
+++ mauve-aligner-2.4.0+4736/debian/patches/no_ext_dir_at_all.patch
2022-02-28 20:13:37.000000000 +0100
@@ -14,7 +14,7 @@
<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 @@
<!-- 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 @@
<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 @@
<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 @@
</tar>
</target>
-@@ -238,11 +215,6 @@
+@@ -239,11 +216,6 @@
<target name="asapResources">
<pathconvert property="asap.resources" pathsep=" ">
diff -Nru mauve-aligner-2.4.0+4736/debian/rules
mauve-aligner-2.4.0+4736/debian/rules
--- mauve-aligner-2.4.0+4736/debian/rules 2021-04-17 21:37:05.000000000
+0200
+++ mauve-aligner-2.4.0+4736/debian/rules 2022-02-28 20:13:37.000000000
+0100
@@ -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
OpenPGP_signature
Description: OpenPGP digital signature
