Re: samtools 1.2 package layout change
Hi Charles,
Thanks for the explanation. I can see why this all makes sense so I'll
use the package as it is, once 1.3 comes out.
Cheers,
TIM
On Fri, 2015-08-14 at 07:55 +0900, Charles Plessy wrote:
> Le Thu, Aug 13, 2015 at 03:03:34PM +0100, Tim Booth a écrit :
> >
> > I was looking to see if it was worth pulling the samtools 1.2 package
> > into Bio-Linux (Ubuntu LTS Backports) and I can see that the package for
> > 1.2 has all the utility scripts going into /usr/bin where before they
> > were in /usr/{lib,share}/samtools. A slew of Lintian warnings results.
> >
> > I wondered if this is a deliberate change or just an artefact of the new
> > build system? I'd be happy to commit a fix that either restores the old
> > layout or else adds Lintian overrides. What do you think?
>
> Hi Tim,
>
> in the current 1.2 package, the scripts are installed in /usr/bin by the
> upstream build system, while before version 1.0 we installed them by hand in
> /usr/share, since they were not installed by the upstream build system.
>
> For the sake of compatibility with other distributions and platforms (that is,
> the rest of the World), I think that we should not remove the file extensions.
> Feel free to add a Lintian overrides. On my side, I am not doing so because
> overrides should be for false positives, while here it is the Policy that is
> plain wrong.
>
> Regarding missing manpages, before writing them I would recommend to contact
> upstream to make sure they would adopt them and maintain them. Otherwise, they
> will bitrot and we will send wrong information to our users, again in a "only
> Debian does it wrong" way. For these Lintian warnings, I also do not write
> overrides because they are true positives. But feel free to override them if
> they annoy you.
>
> For "spelling-error-in-manpage" "allows to allows one to", once one upstream
> developer who was native speaker disagreed; since then I ignore this "spelling
> error".
>
> I think that "spelling-error-in-binary usr/bin/samtools compres compress" is a
> false positive; sorry for not overriding it earlier. "compres" only appears
> in the output of "strings /usr/bin/samtools" in a way that does not seem
> to be related to user output, and not in the source code.
>
> Have a nice day,
>
--
Nothing is inherently mysterious - nothing that actually exists, that
is. If I am ignorant about a phenomenon, that is a fact about my state
of mind, not a fact about the phenomenon; to worship a phenomenon
because it seems so wonderfully mysterious, is to worship your own
ignorance.
- Eliezer Yudkowsky
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