Re: proteinortho does not find diamon(-aligner) executable
Hi again,
I wonder whether its so hard so say fill in that form:
[ ] Please provide /usr/bin/diamond in diamond-aligner package
[ ] Please patch proteinortho to find /usr/bin/diamond-aligner
My question boils down to that simple decision and I'm quite astonished
that nobody steps up to draw it.
Kind regards
Andreas.
On Tue, Dec 17, 2019 at 09:26:55PM +0100, Andreas Tille wrote:
> Hi again,
>
> 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
>
> Andreas.
>
> 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
> >
> > Andreas.
> >
> > 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[1] and the name
> > > /usr/bin/diamond was occupied (documented in README.Debian of diamond).
> > > Since this was removed[2] 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.
> > >
> > >
> > > [1] https://tracker.debian.org/pkg/diamond
> > > [2] https://tracker.debian.org/news/1082936/removed-40515-5-from-unstable/
> > >
> > > --
> > > http://fam-tille.de
> > >
> > >
> >
> > --
> > http://fam-tille.de
> >
> >
>
> --
> http://fam-tille.de
>
>
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