qiime REMOVED from testing

[Andreas Tille]

Hi Steven,

On Tue, Jan 21, 2014 at 11:35:33PM +0000, Steven Chamberlain wrote:
> >>> https://buildd.debian.org/status/package.php?p=libjogl-java
> > 
> >>>> FastTree.c downloaded successfully.
> >>>> FastTree built.
> >>>> Traceback (most recent call last):
> >>>>   File "setup.py", line 183, in <module>
> >>>>     if download_UCLUST():
> >>>>   File "setup.py", line 140, in download_UCLUST
> >>>>     raise SystemError, ("Platform not supported by UCLUST")
> >>>> SystemError: Platform not supported by UCLUST
> 
> Oddly, I didn't get that error building qiime 1.7.0+dfsg-1 just now, it
> built successfully.

Good.  As I said:  There should be nothing downloaded specifically not
UCLUST which is non-free.

> But the resulting package is going to be uninstallable on kfreebsd
> unless we manage to port packages (gluegen2 first I think, and then)
> libjogl-jni, libjogl-java, king.
> 
> If king is absolutely needed for qiime to be useful, I think the only
> available option currently is to make it Architecture: linux-any and
> request that ftpmaster remove the old packages built for kfreebsd-* from
> sid.

Well, for king we have another problem that it depends from the
deprecated libjogl-java and should be replaced by libjogl2-java.
Unfortunately upstream did not answered my request[1].  I just tried the
"brute force" method to simply replace the JAR filename jogl.jar by
jogl2.jar and see what might happen[2].  It results in 100 errors (most
probably a lot of consequences of some initial errors - I have injected
the relevant build log snippet into the patch file[2] as well in case
this might enlight somebody else than me (since I have no idea about
jogl nor about Java in general).

May be if we could somehow deal with this it could be some option for
the further steps.

Alternatively I inspected the qiime code and it actually provides an
alternative to the default use of king which is called InVUE.  This is
not yet packaged but looks interesting even if there are no proper
upstream releases but just a SVN repository.  May be packaging InVUE
could bring ous out of the trouble with the deprecated libjogl-java.

Kind regards

       Andreas.

[1] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=706922#10
[2] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/king/trunk/debian/patches/use_jogl2.patch?view=markup
[3] http://sourceforge.net/apps/mediawiki/invue

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