Wednesday 1 February 2012

Report from Debian Med sprint (Posted by Andreas Tille)

The Debian Med team has organised its second sprint in Southport last weekend. This is a report from my personal perspective. I added a short
version of my agenda
to the Wiki page.

  1. Ensembl packaging specifically working on installation in unstable without any conflicts (=trying to solve libwww issue)
    One main item for this meeting on my agenda was fixing the Ensembl package to finally enable a migration from experimental to unstable. One of the big showstopers is #636923. However, unfortunately the to persons who I urgently needed to discuss this topic did finally not attend and I was only able to determine, that the problem can be stripped down to the problematic package is actually liblwp-parallel-perl. I'll try to keep on working on this.

  2. The Beast-mcmc finishing
    This package is on my agenda since about one year and I was able to iron out nearly all included binary JAR files. However I get struck on the last problematic JAR mtj.jar is a mess of other included JARs based on f2j blas/arbapck JARs. I reached a state where I got a hint from upstream to the sources for the last JAR in this chain and I need to see whether I will be able to compile. I'll give this a try in the next couple of weeks if not I will push the package to non-free first and leave the final freeing to some later point in
    time. As usual, any help is welcome.

  3. Continuing with current MoM; presenting MoM to the audience to gather more potential students
    I kept on mentoring the student and there is further progress with the package we are focussing on. Moreover it might be that some participants from the workshop might step in for later Monthes.

  4. Finishing sofa-framework which needs to be updatet to new version
    Nothing done on this front

  5. Bug squashing of Debian Med team maintained packages
    Two bugs fixed by new upstream version of GinkgoCADx (#657827, #648167)

  6. If time permits work on some Beast related phylogeny packages
    Uploaded phy-spread package

  7. Checking status of Debian Med tasks
    The attempt to check the tasks was completely spoiled when noticing that the tools are broken because of technical changes in Debian infrastructure. Sorting this out and enabling regularly updated tasks pages is now on highest position in my priority list.

  8. Spontaneous mentoring of people
    I gave a spontaneous introductional talk about Debian and Blends structure Moreover I was mentoring Quyen, Laszlo (see list of attendees) and others about gpg keys

  9. Working on Blends sentinel bugs overview
    This was terribly blocked by non-functional fetching translations from which is down. Caring for alternatives to at least get tasks pages updated again but no success so far. (see also item 7) above)

  10. Helping others packaging and sponsoring
    • Sponsored chado (gmod suite) prepared by Olivier Sallou
    • Helped Charles Plessy getting snappy-java using Debian packaged library
    • Worked with Ivo Maintz on copasi
    • Helped Martin Steghöfer with Python packaging
    • Dived a bit into a Ruby package together with Quyen Nguyen with no certain outcome - needs further negotiation with Quyen and other upstream how to proceed
    • Checking the work of Piero Fariselli on three Python packages
    • Had a look with Toni into OpenMicroscopy noticing that it is a beast containing >100 binary JAR files inside the source and will take a talented and very patient Java expert to cope with all this stuff The good news is that upstream was quite supportive to provide a downloadable versioned archive which simplifies obtaining the source Needs (a lot) of further work which I'm unable to do myself

  11. License checking
    I was suggesting an ePetition to free Phylip and wrote a first draft for it.

  12. Mapping Southport :-)
    Added some Hotels and Restaurants to OpenStreetMap
Thanks to al participants who joined the workshop and made it a success (again). Looking foreward to next Debian Med workshop.

Also thanks to EagleGenomics for sponsering my travel expenses.