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Re: problem with Abyss

Just a short note:  I installed the latest abyss and I get:

$ cat /usr/lib/abyss/ABYSS-P

echo >&2 "error: ABySS was not configured with support for MPI. For details"
echo >&2 "       on compiling ABySS with MPI suppor see:"
echo >&2 "       https://github.com/bcgsc/abyss#compiling-abyss-from-source";
exit 1

That's probably worth a but report as well, which I'm going to file now.

Kind regards


On Thu, Feb 14, 2019 at 10:07:07PM +0100, Andreas Tille wrote:
> Hi Tony,
> On Thu, Feb 14, 2019 at 07:27:16PM +0000, Tony Travis wrote:
> > On 14/02/2019 17:14, Andreas Tille wrote:
> > > I have no idea about the Ubuntu version but the stretch version is
> > > 2.0.2-2 which sounds pretty close.  My guess is that the build system
> > > has some tweaks we missed to call to create ABYSS-P.  Since I'm
> > > currently swamped with other stuff:  Would you mind filing a bug report
> > > via
> > >       reportbug abyss
> > 
> > Well, "reportbug" notified me that a newer version of abyss 2.1.5-4 is
> > available in Debian testing (mine is abyss 2.0.2-3) so I decided not to file
> > a bug report, because "ABYSS-P" is present in that version:
> Ahhh, yes, your are right.  I was a bit in a hurry.  What I can do at
> least is providing a backport for Stretch.
> > > Definitely not.  But I'm very sorry, I have no idea how packages are
> > > propagating to Ubuntu and why this is missing. :-(
> > 
> > Actually, I think it probably is a manifestation of the same problem: Some
> > packages are not imported automatically into Ubuntu from Debian testing. I
> > can make a 'sync' request but, this is not a Debian issue!
> Seems so and it seems you are right that abyss and metaphlan2 are really
> the same issue in this respect.
> > Maybe we can have a chat about the sync failure in Vilnius?
> Hmmmm, I can only repeat what I said:  I simply have no idea about the
> Ubuntu sync mechanism and the best thing we could do is to invite some
> Ubuntu people to our sprint.  My knowledge is that they are forking
> unstable at some point in time but I neither know when this point in
> time is nor why packages are excluded.  If someone might be able to find
> out that point in time for the fork we could try to check before whether
> our packages are in a good shape - but that's all hidden knowledge to
> me and I have no spare cycles to care in addition for Ubuntu (but would
> love if somebody else take over this job).
> Kind regards
>      Andreas.
> -- 
> http://fam-tille.de


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