On Sat, Oct 19, 2013 at 7:06 PM, Charles Plessy <[email protected]> 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
