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

[Michael Brudno]

Hi Andreas,

Lagan is no longer maintained (has not been for over 10 years). Please
feel free to make any changes necessary. There are a few minor fixes
others have made to make the system more portable: some changes to
make the sort calls more modern, and also renaming one sub-function
that had a name conflict (getline, iirc).

e.g. https://github.com/incertae-sedis/lagan

Best of luck,

Mike
On Tue, Dec 4, 2018 at 2:19 AM Andreas Tille <andreas at an3as.eu> wrote:
>
> 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
>
> --
> http://fam-tille.de