Hi again,
anybody up for contacting upstream as a first step?
Kind regards
Andreas.
On Tue, Jun 09, 2020 at 05:28:28PM +0200, Andreas Tille wrote:
> Hi,
>
> is anybody up for this challenge? This is needed for the minimap2
> Python module which we need for other packages.
>
> Kind regards
>
> Andreas.
>
> On Fri, May 15, 2020 at 02:30:02PM +0200, Andreas Tille wrote:
> > Hi Steffen,
> >
> > On Fri, May 15, 2020 at 02:39:51AM +0200, Steffen Möller wrote:
> > > I am happy that you asked - it is here
> > > https://salsa.debian.org/med-team/ksw2
> > >
> > > Sadly not a problem of that library which features the same files that
> > > are also distributed with minimap2, just as an older version in the
> > > separate ksw2 repository if I am not erroneous.
> >
> > Yes, file ksw2_exts2_sse.c seems to be older than in the code copy in
> > minimap2.
> >
> > > We need to find the
> > > problem within the minimap2 package, I am afraid. Was looking for a
> > > while now - thought multiple times that I had it - but ... sigh.
> > >
> > > That ksw2 library needs some love by upstream and I suggest to avoid
> > > packaging it for now. Also, it does not ship with a license and comes
> > > with the sources of a journal publication - er - have a look.
> >
> > Besides that I agree that it should be sorted out with upstream I
> > think the proper action would be:
>
>
> >
> > 1. Sort out the code update with upstream
> > 2. Ask upstream for a proper release
> > 3. Fix the build system I've invented to get a proper library
> >
> > Regarding the last item: I have added extremely rough automake stuff to
> > the packaging. The idea was that I want a proper library with static and
> > dynamic library. However, my automake skills are limited. Here are the
> > flaws:
> >
> > 1. Proper check for zlib is needed (see the dirty hack in d/rules)
> > 2. There is no propagation of HAVE_KALLOC definition (no idea why)
> > 3. Check and use parasail
> > 4. May be package gaba (whatever this might be and check and link
> > against this)
> >
> > Finally I took over the simde patch from minimap2. Unfortunately I have
> > no idea how to add this to the linker. This has also be done inside
> > my weak attempt of automake. (If you comment the simde patch the package
> > at least builds.)
> >
> > Kind regards
> >
> > Andreas.
> >
> > --
> > http://fam-tille.de
> >
> >
>
> --
> http://fam-tille.de
>
>
--
http://fam-tille.de
