[Debian-med-packaging] Mothur - Debian patches

[Andreas Tille]

Hi Tomasz,

On Sat, Apr 28, 2018 at 07:12:02AM +0200, Tomasz Buchert wrote:
> On 26/04/18 09:57, Andreas Tille wrote:
> > On Wed, Apr 25, 2018 at 11:26:16PM +0200, Tomasz Buchert wrote:
> > > On 14/09/15 16:14, Tomasz Buchert wrote:
> > > Let me resurrect this old thread: I've just merged the new release of
> > > mothur [1] and had trouble to reapply the old patch [2]. Qustion,
> > > especially directed to Tim, is: how should it be reapplied in 1.40.2?
> >
> > Since you just uploaded mothur I assume you have done a decision about
> > this question.  It seems most parts of the patch you was refering to[2]
> > are void now anyway.  I was stumbling about
> 
> actually, I did not.

OK.
 
> > debian/patches/catchall_fix.patch and have sent a mail to the CatchAll
> > authors.  I'm not sure how successful this will be and whether we will
> > be able to build a mono program - but at least I've tried since it is
> > on the list of our Bio-Linux related targets anyway[3].
> >
> > BTW, since we are talking about mothur packaging.  I'd always recommend
> > to install cme and libconfig-model-dpkg-perl from unstable and run
> >
> >     cme fix dpkg-control
> 
> It's not the first time you mention it.

May be I'll forget in the future and will mention it again. ;-)

> I don't like it very much
> because it messes up with wrap-and-sort that I use. These are cosmetic
> changes and in the case of std-ver I usually just wait till lintian
> complains about it :).

Lintian from unstable (2.5.84) - and I think everybody should use
lintian from unstable no matter what release is installed - is
complaining about it. ;-)

> > You have either old versions of these packages or did not run this -
> > otherwise Standards-Version would have been bumped to 4.1.4.
> >
> > Kind regards
> >
> >         Andreas.
> 
> Ok, then. I guess I will upload the version without this patch and if
> you get some response from the folks you mentioned, we can upload it
> again.

The patch is assembling different things anyway.  For instance it is
refering to CatchAll which we did not packaged yet - but should.  See my
mail to the authors[4] and may be you add some ping since it is
obviously needed also for mothur.

Kind regards

        Andreas.
 
> > > [1] https://salsa.debian.org/med-team/mothur/commit/9be3b4658c1b1b8bddfd66daa8503ae1082a809e
> > > [2] https://salsa.debian.org/med-team/mothur/commit/08212f49803e2f432fbaeef5b60f3255a09e256e
> > [3] https://salsa.debian.org/med-team/community/bio-linux/blob/master/debian-med_missings.txt
[4] https://lists.debian.org/debian-med/2018/04/msg00133.html

-- 
http://fam-tille.de