[Debian-med-packaging] Bug#914687: lagan: /usr/bin/chaos is already provided by emboss

[Andreas Tille]

Control: forwarded -1 Michael Brudno <brudno at cs.toronto.edu>

Hi Michael,

recently the Debian Med team has packaged lagan for official Debian.
This has uncovered the fact that there is a name space conflict with
EMBOSS.  This is specifically unfortunate since both packages are
from the field of bioinformatics and it should be avoided.  (Remark:
I even think that the choice of /usr/bin/chaos is a bit unfortunate
in general since it is quite a generic name.)

In Debian the package that has occupied a name first usually wins and
the other package has to rename.  In this case I also think that EMBOSS
is quite famous and has lots of users (according to Debian popularity
contest which is measuring the number of users of a package).  Thus we
need to choose a different name for chaos provided by lagan.

For the moment I would solve this bug in Debian by moving /usr/bin/chaos
to /usr/lib/lagan/bin/chaos and provide a symlink /usr/bin/lagan_chaos.
I will document this in /usr/share/doc/lagan/README.Debian.

I would consider it a good idea if you would remove chaos in your
distribution as well since this name space conflict might happen also
for other users and it might create some confusion you probably want
to avoid.

Kind regards and thanks for providing lagan as Free Software

       Andreas.

On Mon, Nov 26, 2018 at 11:03:47AM +0100, Andreas Beckmann wrote:
> Package: lagan
> Version: 2.0-2
> Severity: serious
> User: debian-qa at lists.debian.org
> Usertags: piuparts
> 
> Hi,
> 
> during a test with piuparts I noticed your package fails to upgrade from
> 'sid' to 'experimental'.
> It installed fine in 'sid', then the upgrade to 'experimental' fails
> because it tries to overwrite other packages files without declaring a
> Breaks+Replaces relation.
> 
> See policy 7.6 at
> https://www.debian.org/doc/debian-policy/ch-relationships.html#overwriting-files-and-replacing-packages-replaces
> 
> >From the attached log (scroll to the bottom...):
> 
>   Preparing to unpack .../archives/lagan_2.0-2_amd64.deb ...
>   Unpacking lagan (2.0-2) ...
>   dpkg: error processing archive /var/cache/apt/archives/lagan_2.0-2_amd64.deb (--unpack):
>    trying to overwrite '/usr/bin/chaos', which is also in package emboss 6.6.0+dfsg-7
>   dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)
>   Errors were encountered while processing:
>    /var/cache/apt/archives/lagan_2.0-2_amd64.deb

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