[Debian-med-packaging] Bug#697158:

[olivier sallou]

Hi,
it is strange because picard-tools is packaged and build on Debian (using
snappy package).

Looking at package content of libsnappy:

lrwxrwxrwx root/root         0 2013-01-04 10:10
./usr/share/java/snappy1.0.3-java.jar ->
../maven-repo/org/xerial/snappy/snappy1.0.3-java/1.0.3-rc3/snappy1.0.3-java-1.0.3-rc3.jar

/usr/share/java/snappy...  file is a symlink to file to maven-repo
directory. Jar file is present in the maven-repo as you can see:

http://packages.debian.org/sid/all/libsnappy1.0.3-java/filelist


I have patched the build.xml for picard-tools to use the snappy jar file.
Maybe your picard-tools package is not correctly patched.


Here is an extract of my picard-tools build using my snappy package.

init:

compile-sam-jdk:
    [mkdir] Created dir:
/home/osallou/DEBIAN-MED/picard-tools/picard-tools/classes
    [javac]
/home/osallou/DEBIAN-MED/picard-tools/picard-tools/build.xml:101: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
to false for repeatable builds
    [javac] Compiling 112 source files to
/home/osallou/DEBIAN-MED/picard-tools/picard-tools/classes
    [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.

sam-jar:
    [mkdir] Created dir:
/home/osallou/DEBIAN-MED/picard-tools/picard-tools/dist
      [jar] Building jar:
/home/osallou/DEBIAN-MED/picard-tools/picard-tools/dist/sam-1.82.jar

compile-picard:
    [javac]
/home/osallou/DEBIAN-MED/picard-tools/picard-tools/build.xml:113: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
to false for repeatable builds
As you can see it is successful.

Olivier
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