[Debian-med-packaging] Bug#684172: Bug#684172: picard-tools: Transition package to default java implementation

[Charles Plessy]

Le Wed, Aug 08, 2012 at 08:04:09AM +0200, Andreas Tille a écrit :
> Hi Charles,
> 
> On Wed, Aug 08, 2012 at 01:26:26PM +0900, Charles Plessy wrote:
> > 
> > It may take time to be uploaded as I am still struggling to make picard-tools
> > work with Debian's package for snappy-java...
> 
> Could you refresh our memory what problem you are continue to face here?

Hi Andreas,

Here is how the build fails in my chroot.

 debian/rules build
dh  build
   dh_testdir
   debian/rules override_dh_auto_configure
make[1]: Entering directory `/«PKGBUILDDIR»'
[ -d lib ] || mkdir lib # This empty directory is lost in the packages's Git clone.
dh_auto_configure
make[1]: Leaving directory `/«PKGBUILDDIR»'
   debian/rules override_dh_auto_build
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_auto_build -- -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5
Buildfile: /«PKGBUILDDIR»/build.xml

init:

compile-sam-jdk:
    [mkdir] Created dir: /«PKGBUILDDIR»/classes
    [javac] /«PKGBUILDDIR»/build.xml:98: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 106 source files to /«PKGBUILDDIR»/classes
    [javac] /«PKGBUILDDIR»/src/java/net/sf/samtools/util/SnappyLoader.java:27: cannot find symbol
    [javac] symbol  : class LoadSnappy
    [javac] location: package org.xerial.snappy
    [javac] import org.xerial.snappy.LoadSnappy;
    [javac]                         ^
    [javac] /«PKGBUILDDIR»/src/java/net/sf/samtools/util/SnappyLoader.java:83: cannot find symbol
    [javac] symbol  : variable LoadSnappy
    [javac] location: class net.sf.samtools.util.SnappyLoader
    [javac]             if (!LoadSnappy.load()) {
    [javac]                  ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 2 errors

BUILD FAILED
/«PKGBUILDDIR»/build.xml:98: Compile failed; see the compiler error output for details.

Total time: 1 second
dh_auto_build: ant -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 returned exit code 1


Cheers,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan