Re: proteinortho does not find diamon(-aligner) executable
I'd like to stress again that this is a **user** question that should be
answered by **users** of the according programs. Its not really a
packaging question - we can implement into packaging whatever is
decided. But we need a decision.
I also CC Tony in this mail. Tony, you are quite close to users and I
trust your insight a lot but unfortunately you are writing your opinion
very seldomly. Similar with the tophat question and others. I'd like
to repeat: We **really** want to design Debian Med according to users
request. If there is no request we will fail. In the worst case users
will blame Debian to have drawn the wrong decision. So its time to
raise your opinion about what should be inside Debian and how to
sensibly name those tools.
Thanks a lot
On Sat, Dec 14, 2019 at 09:51:32PM +0100, Andreas Tille wrote:
> Hi Steffen,
> in my mail I explained the reasons for the issue you stumbled upon and I
> think from this you can obtain two ways for a solution easily (1. use
> /usr/bin/diamond since its free now in diamond or 2. patch proteinortho
> to use the Debian name). Would you mind acting accordingly - preferably
> after filing a bug where you document the issue?
> Kind regards
> On Fri, Dec 13, 2019 at 06:36:11AM +0100, Andreas Tille wrote:
> > Hi Steffen,
> > On Fri, Dec 13, 2019 at 12:33:26AM +0100, Steffen Möller wrote:
> > > Hello,
> > >
> > > I am just updating proteinortho and found that its tests look for a
> > > series of binaries and executes the tests only if those binaries are in
> > > the PATH. The diamond-aligner is a build package, likely for the reason
> > > to be tested. The diamond-aligner's executable is also named
> > > diamond-aligner - and not found.
> > There was a package diamond inside Debian and the name
> > /usr/bin/diamond was occupied (documented in README.Debian of diamond).
> > Since this was removed the name is free again and we might consider
> > taking over this name again.
> > > Is this a bug of the diamond-aligner package to not offer some
> > > compatibility layer or of proteinortho to use a non-standard executable
> > > name? I'll team-upload proteinortho as it is now but something needs to
> > > be done.
> > If you suspect a bug why not filing one to make sure it will be found
> > later? I do not consider it the best idea to upload a known to be
> > broken package. You can contribute to our Advent bug squashing party
> > by filing a bug find a solution and close it.
> > Kind regards
> > Andreas.
> >  https://tracker.debian.org/pkg/diamond
> >  https://tracker.debian.org/news/1082936/removed-40515-5-from-unstable/
> > --
> > http://fam-tille.de