Hi Andreas, Lagan is no longer maintained (has not been for over 10 years).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 <andr...@an3as.eu> wrote: > > Control: forwarded -1 Michael Brudno <bru...@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...@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
