[Debian-med-packaging] picard-tools package

[Shaun Jackman]

Hi Charles,

On 22 June 2010 04:11, Charles Plessy <plessy at debian.org> wrote:
...
> ↱picard-tools↲$ fakeroot debian/rules binary
> dh  binary
>   dh_auto_build
> Buildfile: /home/charles/debian/debian-med/picard-tools/build.xml
>
> init:
>
> set_java_home_1.5_correctly:
>
> set_java_home_1.5_to_default_java_home:
>     [echo] JAVA_HOME_1_5=${env.JAVA_HOME}
>
> set_java_home_1.5:
>
> compile-sam-jdk:
>    [javac] /home/charles/debian/debian-med/picard-tools/build.xml:96: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
>    [javac] Compiling 93 source files to /home/charles/debian/debian-med/picard-tools/classes
>
> BUILD FAILED
> /home/charles/debian/debian-med/picard-tools/build.xml:96: Error running ${env.JAVA_HOME}/bin/javac compiler
>
> Total time: 0 seconds
> dh_auto_build: ant returned exit code 1
> make: *** [binary] Error 2
> ---------------------------------------------------------------------

Line 96 of build.xml should be:
               executable="javac"

This portion of debian-changes-1.22-1 is supposed to fix this:

@@ -92,7 +93,7 @@
                sourcepath="" srcdir="${src}"
                includes ="net/sf/samtools/**/*.*"
                excludes = "net/sf/picard/**/*.*"
-               executable="${JAVA_HOME_1_5}/bin/javac"
+               executable="javac"
                compiler="javac1.5" fork="true">
             <!--<compilerarg value="-Xlint:all"/>-->
             <!--<compilerarg value="-Xlint:unchecked"/>-->

Can you check that this patch was applied correctly to your working copy?

Cheers,
Shaun