Cant compile jai-imageio-bioformats ( resume work on bioformats)

[Mathieu Malaterre <mathieu.malaterre@gmail.com>]

Hi Melissa,

On Fri, May 25, 2012 at 4:17 PM, Melissa Linkert
<melissa@glencoesoftware.com> wrote:
> Hi Mathieu,
>
>> What I still do not really understand is that after a git clone of
>> bioformat I can see I am getting the non-free
>> ./jar/clibwrapper_jiio.jar; but I cannot find the shared lib anywhere.
>> Should use download/install it separately ?
>
> The shared library is not required by Bio-Formats, and in fact having it
> does not even improve functionality.  So it is expected that the user
> will download and install it themselves, if they feel that they need it.

I think I misunderstood your comment. Here is what I am doing:

  wget https://github.com/openmicroscopy/bioformats/tarball/v4.4.1
  tar xvfz v4.4.1
  cd openmicroscopy-bioformats-68cf74c
  find . -name \*.jar -delete
  export ANT_OPTS=-Dbuild.sysclasspath=first
  export CLASSPATH=/usr/share/java/velocity.jar:/usr/share/java/forms.jar:/usr/share/java/commons-logging.jar:/usr/share/java/ij.jar:/usr/share/java/slf4j-api.jar:/usr/share/java/bnd.jar:/usr/share/java/net.luminis.build.plugin.jar:/usr/share/java/testng.jar:/usr/share/java/ncCore-4.3.jar:/usr/share/java/ant-contrib.jar
  ant -f build.xml jar-jai

which leads to error like:

    [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/common/PackageUtil.java:85:
package com.sun.medialib.codec.jiio does not exist
    [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/clib/CLibImageReader.java:114:
package com.sun.medialib.codec.jiio does not exist
    [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/clib/CLibImageReader.java:115:
package com.sun.medialib.codec.jiio does not exist
    [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/clib/CLibImageWriter.java:108:
package com.sun.medialib.codec.jiio does not exist
    [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/clib/CLibImageWriter.java:109:
package com.sun.medialib.codec.jiio does not exist
    [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageReader.java:110:
package com.sun.medialib.codec.jpeg does not exist
    [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageReader.java:111:
package com.sun.medialib.codec.jiio does not exist
    [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageWriter.java:105:
package com.sun.medialib.codec.jpeg does not exist
    [javac] /tmp/openmicroscopy-bioformats-68cf74c/components/forks/jai/build/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageWriter.java:106:
package com.sun.medialib.codec.jiio does not exist


Could you please let me (again?) how am I supposed to compile
bioformats when I decided NOT to use 'clibwrapper_jiio.jar'.

Thanks much,
-- 
Mathieu