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Re: Could not build picard-tools version 1.100



On Sat, Oct 19, 2013 at 7:06 PM, Charles Plessy <plessy@debian.org> wrote:
Hello everybody,

I tried to update picard-tools to version 1.100, unfortunately, it makes an
error.  It may be trivial for people knowing Java, so please let me know of a
workaround (or commit it directly).

The update made the following change in the build.xml file.

     <property environment="env"/>
+    <property name="java6.home" value="${env.JAVA6_HOME}"/>

     <condition  property="isUnix">
         <os family="unix"/>
@@ -75,6 +77,10 @@
             <pathelement path="${classpath}"/>
             <pathelement location="${classes}"/>
         </path>
+
+        <path id="java6.lib.ref">
+            <fileset dir="${java6.home}/lib" includes="*.jar"/>
+        </path>
     </target>

And it leads to the following error.

compile-sam-jdk:
    [mkdir] Created dir: /«PKGBUILDDIR»/classes

BUILD FAILED
/«PKGBUILDDIR»/build.xml:109: The following error occurred while executing this line:
/«PKGBUILDDIR»/build.xml:476: /«PKGBUILDDIR»/${env.JAVA6_HOME}/lib does not exist.

Cheers,

Charles

Hi everyone,

The Picard team left a note in the 1.97 release about how they're currently handling the Java 6 to 7 transition:
http://sourceforge.net/projects/picard/files/picard-tools/1.97/

"IMPORTANT NOTE: build.xml now force compilers to use Java 6 bootclasspath even if JAVA_HOME is Java 7. In order to do this, either the environment variable JAVA6_HOME must point to Java 6 JAVA_HOME, or -Djava6.home=<path> must be put on the ant command line. This ensures maximum Java 6 JVM compatibility. If you do not have a Java 6 JVM on your build machine, you can set JAVA6_HOME to point to your Java 7 installation, but there may be problems running this code in a Jav 6 JVM."

Also, from version 1.96:
http://sourceforge.net/projects/picard/files/picard-tools/1.96/

"Various changes have been made so that Picard programs and libraries will work properly with Java 7. However, Picard will continue to be compiled with Java 6."

In practice there are still sometimes problems when running Picard tools in Java 7, despite recent progress.

Hope that helps,
Eric

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