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Re: Bug#917655: biojava4-live: FTBFS (cannot find symbol JAXBContext)



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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