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

[Sebastiaan Couwenberg]

Hi Andreas,

Thansk for the feedback.

On 07/04/2015 02:44 PM, Andreas Tille wrote:
> 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.

Yes, please.

Based on the popcon scores my preference is also to rename the binary in
libgnome-perl. The GMT upstream authors also argue that since they've
been using the name since the 1980s they use has set precedence.

> BTW, has Debian
> Perl team set ACLs to enable me commiting the changes in Git?

I'm not sure. But I'm a member of the Perl team too, so if you can't
commit yourself I'm willing to do that too.

> Kind regards
> 
>      Andreas.

Kind Regards,

Bas

> 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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>>
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>>
> 


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