[Debian-med-packaging] Bug#731190: qiime REMOVED from testing

[Andreas Tille]

Hi Steven,

thanks for your quick response.

On Tue, Jan 21, 2014 at 08:44:27PM +0000, Steven Chamberlain wrote:
> On 21/01/14 20:32, Andreas Tille wrote:
> > [...] #731190 which boils down to the question why libjogl-java is not
> > available on kfreebsd.
> 
> AFAICT that package has never been available on kfreebsd:
> https://buildd.debian.org/status/logs.php?pkg=libjogl-java&arch=kfreebsd-amd64
> 
> I'm currently not sure of the best action to take:
> 
> If that package is only needed for qiime to work on Linux, the
> dependency could be limited to [linux-any].

I admit I have no idea about the usage of libjogl-java in qiime, but
since it is no direct dependency but it is introduced by a dependency of
king and libjogl-java is deprecated (see #706922) we most probably will
not be very lucky.

> Or if that package crucial for qiime to work at all, you can only
> request its removal from kfreebsd.  (From unstable - by filing a bug
> with ftpmaster).
> 
> Or with luck, someone might be able to get libjogl-java built on
> kfreebsd.  (I think changes to gluegen2 are needed).

I have no idea what gluegen2 might be.
 
> There's a more immediate problem that qiime now FTBFS on kfreebsd-*:
> 
> >    http://buildd.debian-ports.org/status/package.php?p=libjogl-java
> > 
> > shows and kfreebsd is not even on the list of architectures any more.
> 
> That's the wrong page - that's the debian-ports.org infrastructure.
> Architectures for Debian sid are here:
> 
> https://buildd.debian.org/status/package.php?p=libjogl-java
> 
> I'm curious why it talks about 'downloading', it's not really
> downloading source code during the build, I hope?

No, it is not.  At least under amd64 is builds fine in pbuilder.
 
> > 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
> 
> Seems like some porting is needed, maybe not much.  I'm looking into it
> right now...

>From where did you got this line.  I'm aware of it from the test suite
which is known to fail for this reason.  UCLUST is non-free and was
removed from the soures - so this must fail obviously (patching the test
suite is work in progress).
 
Kind regards

    Andreas. 

-- 
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