[med-svn] [seqan] annotated tag upstream/1.4.1+dfsg created (now 86cc58f)

[Andreas Tille]

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tille pushed a change to annotated tag upstream/1.4.1+dfsg
in repository seqan.

        at  86cc58f   (tag)
   tagging  d67dea9e18d5eb9f7b657e1d1a152581aafb15df (commit)
 tagged by  Andreas Tille
        on  Thu Jul 9 09:36:22 2015 +0200

- Log -----------------------------------------------------------------
Upstream version 1.4.1+dfsg

Andreas Tille (32):
      Fetch also upstream RC candidates in watch file, update packaging standards (policy,debhelper,source format)
      Upstream has changed method to release archives => Fix watch file; some fixes to orig-tar.sh
      Bumped standards-version
      Rely more on debhelper files to simplify debian/rules; make sure package builds twice in a row; tried to switch from cdbs to dh but failed (left the changes as comments); TODO: Find a way to call cmake with the right options using dh
      Add doc-base control file; shamelessly give up to convince cdbs to do what's claimed in the doc and leave two lintian warnings about useless LICENSE files.  Any volunteer to kick cdbs into ... hmmm, where it needs to be kicked ...
      Normalised citation information
      Fixed watch file
      debian/orig-tar.sh: Removed because the removed file is not part of the source any more
      Mass commit my current changes to seqan; Attention: I can not test the build since it needs more memory than my current Build machine
      Droping -fstack-protector flag helps **drastically** reducing memory consumption when building the package!!!!
      Building docs works now; uncomment parts of dh_install to proceed somehow for the moment
      Fix installation of demos.
      Doing a bit of reorganisation how files are installed; create manpages automatically using help2man
      Close "new upstream" bug, no zero length manpages
      Add python to Build-Depends - seems to be ready for upload
      Need to rename /usr/bin/join to /usr/bin/seqan-join to avoid name clash with coreutils --> this needs to be discussed with upstream!
      Make sure only needed exectuables will be installed as links in /usr/bin and document this in README.Debian; manpages (via help2man) only for binaries in /usr/bin
      UPstream source is not yet uploaded but this watch file seems a bit better in catching it
      Fix common typo: sequan -> seqan
      Add hint to add /usr/lib/seqan/bin to PATH variable
      Upload to unstable
      Rename /usr/bin/mason to /usr/bin/seqan_mason
      Upload to unstable
      Run test suite only on powerfull architectures (amd64) at build time
      Deal with arch-dep builds but mention that the test suite issue is not yet solved
      deacticate test for apps splazers
      Exclude three test that are failing according to a hint of upstream
      Try to build 32bit arches without O2 optimisation
      Exclude unused compressed JS code
      Upload to unstable
      Do proper manipulation of build options
      Imported Upstream version 1.4.1+dfsg

Charles Plessy (22):
      Upstream tarball location changed; here I propose new watch and get-orig-source facilities.
      Added a BibTeX reference, see ‘http://wiki.debian.org/DebianScience/References’.
      Collected various informations in ‘debian/upstream-metadata.yaml’.
      Compress the source with xz (this saves three megabytes).
      Corrected Vcs URLs.
      New upstream release available.
      Build according to upstream's instructions, and avoid programs with generic names in /usr/bin.
      Use Debhelper 8.
      Incremented Standards-Version after reading Policy's upgrade checklist.
      Compress binary packages with xz.
      Build with the cmake class of CDBS.
      Converted debian/copyright to machine-readable format.
      Investigating the diff between 1.2 and 1.3; found a convenience copy of SAMtools.
      Removed convenience code copy of SAMtools to prevent accidental use at build time.
      Patch to correct path to SAMtools headers in Debian.
      Depend on zlib1g-dev, as seqan needs to detect zlib to set SEQAN_HAS_SAMTOOLS to 1.
      Depend on libboost-dev as Cmake was looking for it.
      Finished to check the debdiff, and formatted with config-edit.
      Set Priority to optional and sequan-apps’s Section to science.
      Uploaded.
      Renamed debian/upstream-metadata.yaml to debian/upstream.
      debian/upstream: Moved DOI and PMID to the Reference namespace.

James McCoy (1):
      Move debian/upstream to debian/upstream/metadata

Nelson A. de Oliveira (1):
      s/Debian-Med/Debian Med

Soeren Sonnenburg (6):
      import seqan
      finally a new upstream...
      restructure to svn repo layout
      build apps and add man pages
      polish copyright
      install manpages and fix synopsis

Steffen Moeller (1):
      Improved one-line description of seqan (no leading article,

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