On Fri, Jan 11, 2019 at 10:26:58PM +0100, Andreas Tille wrote: > Control: tags -1 help upstream > > Hi, > > I've commited a new minor upstream version to Git but the problem exists > also in this version. I've asked at debian-java list for help[1] Hello Andreas, I took a quick look at this and was able to resolve the build problems by dropping the references to the java.se.ee. module and adding jaxb-impl and jaxb-api JARs to the classpath. It might not be the cleanest way - strictly speaking, you should only need the jaxb-api JAR during the build and only the jaxb-impl on the classpath while running tests. Attached are a set of commits that let the package build for me locally. Cheers, tony
From f8f5c72b866718e05811b33f8445ee311228da12 Mon Sep 17 00:00:00 2001
From: tony mancill <tmancill@debian.org>
Date: Fri, 11 Jan 2019 20:17:27 -0800
Subject: [PATCH 1/3] Add build-dep on libjaxb-api-java and libjaxb-java
---
debian/control | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/debian/control b/debian/control
index 1f6cc04..71257a0 100644
--- a/debian/control
+++ b/debian/control
@@ -28,7 +28,9 @@ Build-Depends-Indep: libcommons-dbcp-java,
liblog4j2-java,
libslf4j-java,
libxmlunit-java,
- libjgrapht-java
+ libjgrapht-java,
+ libjaxb-api-java,
+ libjaxb-java
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/biojava4-live
Vcs-Git: https://salsa.debian.org/med-team/biojava4-live.git
--
2.20.1
From ac9fad6e89d9d5ff8501a05da46b26bd158af5f8 Mon Sep 17 00:00:00 2001
From: tony mancill <tmancill@debian.org>
Date: Fri, 11 Jan 2019 20:25:49 -0800
Subject: [PATCH 2/3] Add jaxb-api and jaxb-impl JARs to classpaths in
debian/build.xml
---
debian/build.xml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/debian/build.xml b/debian/build.xml
index 250c143..fae837d 100644
--- a/debian/build.xml
+++ b/debian/build.xml
@@ -28,7 +28,7 @@
<property environment="env"/>
<property name="project.jarfile.name" value="BJLIB.jar"/>
- <property name="class.path" value="${lib.dir}/commons-logging.jar ${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections3.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 ${lib.dir}/log4j2.jar ${lib.dir}/json-simple.jar ${lib.dir}/slf4j-api.jar ${lib.dir}/log4j-over-slf4j.jar ${lib.dir}/commons-math.jar ${lib.dir}/xmlunit.jar ${lib.dir}/vecmath.jar"/>
+ <property name="class.path" value="${lib.dir}/commons-logging.jar ${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections3.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 ${lib.dir}/log4j2.jar ${lib.dir}/json-simple.jar ${lib.dir}/slf4j-api.jar ${lib.dir}/log4j-over-slf4j.jar ${lib.dir}/commons-math.jar ${lib.dir}/xmlunit.jar ${lib.dir}/vecmath.jar ${lib.dir}/jaxb-api.jar ${lib.dir}/jaxb-impl.jar"/>
<path id="compile.classpath">
<fileset dir="${lib.dir}">
@@ -52,6 +52,8 @@
<include name="slf4j-api.jar"/>
<include name="log4j-over-slf4j.jar"/>
<include name="vecmath.jar"/>
+ <include name="jaxb-api.jar"/>
+ <include name="jaxb-impl.jar"/>
</fileset>
<fileset dir="${dist.dir}">
<include name="*.jar"/>
--
2.20.1
From c25549fd76d3378cad50029a6718353858f6cce4 Mon Sep 17 00:00:00 2001
From: tony mancill <tmancill@debian.org>
Date: Fri, 11 Jan 2019 20:36:27 -0800
Subject: [PATCH 3/3] Drop --add-modules java.se.ee from javadoc task
---
debian/build.xml | 16 +++-------------
1 file changed, 3 insertions(+), 13 deletions(-)
diff --git a/debian/build.xml b/debian/build.xml
index fae837d..406f208 100644
--- a/debian/build.xml
+++ b/debian/build.xml
@@ -75,18 +75,9 @@
<target name="javadocs">
<mkdir dir="${docs.dir}"/>
<mkdir dir="${docs.lib.dir}"/>
- <if><equals arg1="${ant.java.version}" arg2="1.8" />
- <then>
- <javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*" encoding="UTF-8" additionalparam="-Xdoclint:none" classpathref="compile.classpath">
- <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
- </javadoc>
- </then>
- <else>
- <javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*" encoding="UTF-8" additionalparam="-Xdoclint:none --add-modules java.se.ee" classpathref="compile.classpath">
- <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
- </javadoc>
- </else>
- </if>
+ <javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*" encoding="UTF-8" additionalparam="-Xdoclint:none" classpathref="compile.classpath">
+ <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
+ </javadoc>
</target>
<target name="compile">
@@ -130,7 +121,6 @@
</then>
<else>
<junit haltonfailure="yes" printsummary="yes" fork="true">
- <jvmarg line="--add-modules java.se.ee"/>
<classpath refid="test.classpath"/>
<formatter type="plain" usefile="false" />
<batchtest>
--
2.20.1
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