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

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

On Wed, Aug 1, 2012 at 8:36 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:
>
> No worries, I think I misunderstood what you were asking as well.
>
>>   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:
> *snip*
>> Could you please let me (again?) how am I supposed to compile
>> bioformats when I decided NOT to use 'clibwrapper_jiio.jar'.
>
> You do need clibwrapper_jiio.jar in order to compile the JAI JAR.  What
> you do not need is the corresponding libclib_jiio.so library, which is what
> I assumed you were referring to originally.
>
> If clibwrapper_jiio.jar is a problem, we might be able to eliminate the
> dependency on it by removing the classes the require it (basically,
> eliminating anything that would require libclib_jiio.so to function correctly).
> Bio-Formats already does not rely on or benefit from libclib_jiio.so being
> installed, so this shouldn't cause any loss of functionality.
>
> If eliminating the need for clibwrapper_jiio.jar would help, let me know and
> I will investigate further in the next few days.

That would be just awesome. From a debian point of view I cannot touch
this clibwrapper_jiio.jar at any point in time (build time / run-time)
since no source is available.
If you make the compilation conditional, just let me know the name of
the switch.

Thanks *much* again for your help !
-- 
Mathieu