Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

[Andreas Tille]

Hi Bas,

while I have not dealt with the libgenome-perl package before I think
your suggestion to hand over /usr/bin/gmt to the gmt package sounds
reaosnable.  The package has a quite low popcon value and in my naive
view the main focus is the Perl module and the accompanying scripts
might (or might not - please correct me if I'm wrong) have a minor
importance.

So I propose the following solution:

   1. install the gmt script to
        /usr/lib/debian-med/bin/gmt
   2. ln -s /usr/lib/debian-med/bin/gmt /usr/bin/genome-module-tools
   3. suggest users of Debian Med to add in front of PATH

The last is provided by med-config (>= 2.1).  This is the same solution
as it is done in plink 1.07-6 which was just uploaded to unstable
(formerly tested in experimental).  Users are informed about this in
NEWS.Debian.

If you agree to this solution I'll upload it that way.  BTW, has Debian
Perl team set ACLs to enable me commiting the changes in Git?

Kind regards

     Andreas.

On Fri, Jul 03, 2015 at 10:11:49PM +0200, Sebastiaan Couwenberg wrote:
> Control: forwarded -1 https://gmt.soest.hawaii.edu/issues/723
> 
> Hi Andreas,
> 
> Thanks for the comprehensive followup.
> 
> I've uploaded a new revision of gmt to experimental that addresses some
> of the issues.
> 
> On 06/30/2015 02:16 AM, Andreas Beckmann wrote:
> > * libgenome-perl
> > 
> >   Filelist libgenome-perl vs. gmt:
> > 
> >   usr/bin/gmt
> > 
> >   Filelist libgenome-perl vs. gmt-common:
> > 
> >   usr/share/man/man1/gmt.1.gz
> 
> This is the most serious conflict to resolve. I've contacted the
> libgenome-perl maintainers [1], but I've not received a reply yet.
> 
> I've put debian-med@ in the CC as they seem the most interested in the
> libgenome-perl package. Please share your opinion on this conflict.
> 
> I've also contacted the GMT upstream developers to raise the issue of
> these conflicts between GMT 5 and other projects. [2]
> 
> [1] https://lists.debian.org/debian-gis/2015/06/msg00119.html
> [2] https://gmt.soest.hawaii.edu/issues/723
> 
> > * libpsl-dev
> >
> >   [...]
> >
> >   Filelist libpsl-dev vs. libgmt-dev:
> >
> >   usr/lib/x86_64-linux-gnu/libpsl.so
> 
> The libpsl & gmt packages use different a SONAME. To ensure dependencies
> on the GMT libpsl it's bundled with libgmt in the libgmt5 package.
> 
> To resolve the conflict I'm considering renaming the GMT libpsl to
> libgmt-psl.
> 
> I've CC'ed the libpsl maintainers, and I would like to ask your opinion
> on this conflict too.
> 
> > * turnin-ng
> > 
> >   [...]
> > 
> >   Filelist turnin-ng vs. gmt-common:
> > 
> >   usr/share/man/man1/project.1.g
> > 
> > * pslib-dev
> > 
> >   [...]
> > 
> >   Filelist pslib-dev vs. gmt-common:
> > 
> >   usr/share/man/man3/pslib.3.gz
> 
> These man page issues should be resolved with the Conflicts that were
> added in gmt (5.1.2+dfsg1-1~exp5).
> 
> Kind Regards,
> 
> Bas
> 
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