Re: samtools 1.2 package layout change
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,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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