My report from Debian Med sprint

[Andreas Tille <andreas@an3as.eu>]

Hi,

as usual the Debian Med sprint was happening at beginning of the year.
Thanks to Michael R. Crusoe it was organised in Bucharest.  We had a
quite productive time which was dominated by bug fixing and upgrading
packages for the stretch release as well as writing or fixing
autopkgtests for Debian Med packages.

My personal report can be found as usual in the Wiki[1] - here is a
copy of my activities:


Packaging

    sra-toolkit update: done
    freebayes: uploaded to new 

Bugs fixed

    libgraphics-colornames-perl: libgraphics-colornames-perl: Build-Depends on perl-modules-5.22
    libgraphics-colorobject-perl: Build-Depends on perl-modules-5.22
    libbio-perl-run-perl: fails to upgrade from 'jessie'
    primer3 FTCBFS: uses build architecture c++ compiler via unconventional variable CPP
    sra-toolkit: /usr/bin/kget is already shipped by the package kget
    snap: Update autokpgtest for name change
    mricron FTBFS because fpc check got more strict 

Updated

    r-cran-shiny to 1.0.0
    snakemake to 3.9.1
    bamtools to 2.4.1
    sniffles to 1.0.2
    r-bioc-annotationdbi to 1.36.1
    r-cran-spdep to 0.6-9
    r-cran-maptools to 0.8-41
    r-cran-maldiquant to 1.16.1-1
    r-cran-googlevis to 0.6.2-1
    qtltools to 1.1
    yaggo to 1.5.9 

Fix autopkgtests

    njplot
    pirs
    art-nextgen-simulation-tools
    artfastqgenerator
    htslib
    bioperl
    pbbarcode
    r-bioc-annotationdbi
    r-bioc-limma
    Test for r-bioc-geneplotter removed since not packaged databases would be needed
    python-biopython
    r-bioc-metagenomeseq
    r-bioc-s4vectors
    r-bioc-rsamtools
    r-bioc-summarizedexperiment
    r-cran-adephylo
    r-cran-bbmle
    r-cran-googlevis 

Mentoring

    Anton by packaging gxargparse and galaxyxml 

Sponsoing

    python-pybedtools (Michael Crusoe)
    python-gffutils (Michael Crusoe) 

New packages

    r-cran-triebeard
    r-cran-httpcode
    r-cran-urltools
    r-cran-crul 


Thanks to Debian for supporting the Debian Med sprint.

Kind regards

      Andreas.


[1] https://wiki.debian.org/Sprints/2017/DebianMed2017#line-142

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