[med-svn] [seqan] branch master created (now 069ce1b)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository seqan.

        at  069ce1b   Moved to Git

This branch includes the following new commits:

       new  4d8a1be   import seqan
       new  34a29df   Upstream tarball location changed; here I propose new watch and get-orig-source facilities.
       new  bfffc6e   Added a BibTeX reference, see ‘http://wiki.debian.org/DebianScience/References’.
       new  5feb04e   finally a new upstream...
       new  17111fd   restructure to svn repo layout
       new  7102bcd   build apps and add man pages
       new  361ef57   polish copyright
       new  27169ee   install manpages and fix synopsis
       new  c642dcb   s/Debian-Med/Debian Med
       new  5721201   Collected various informations in ‘debian/upstream-metadata.yaml’.
       new  3f18b75   Improved one-line description of seqan (no leading article, adding "biological")
       new  639e381   Fetch also upstream RC candidates in watch file, update packaging standards (policy,debhelper,source format)
       new  620545e   Compress the source with xz (this saves three megabytes).
       new  3bff2b3   Corrected Vcs URLs.
       new  2416e34   New upstream release available.
       new  f124b9a   Build according to upstream's instructions, and avoid programs with generic names in /usr/bin.
       new  43b5f74   Use Debhelper 8.
       new  1466eef   Incremented Standards-Version after reading Policy's upgrade checklist.
       new  d035cb2   Compress binary packages with xz.
       new  0dd4547   Build with the cmake class of CDBS.
       new  f9bb2cf   Converted debian/copyright to machine-readable format.
       new  68c484e   Investigating the diff between 1.2 and 1.3; found a convenience copy of SAMtools.
       new  a224bb5   Removed convenience code copy of SAMtools to prevent accidental use at build time.
       new  4aae536   Patch to correct path to SAMtools headers in Debian.
       new  70c386f   Depend on zlib1g-dev, as seqan needs to detect zlib to set SEQAN_HAS_SAMTOOLS to 1.
       new  e99c665   Depend on libboost-dev as Cmake was looking for it.
       new  8a2df4c   Finished to check the debdiff, and formatted with config-edit.
       new  9230b11   Set Priority to optional and sequan-apps’s Section to science.
       new  ff3d556   Uploaded.
       new  23f6897   Renamed debian/upstream-metadata.yaml to debian/upstream.
       new  c147775   debian/upstream: Moved DOI and PMID to the Reference namespace.
       new  99d228e   Upstream has changed method to release archives => Fix watch file; some fixes to orig-tar.sh
       new  e0e995f   Bumped standards-version
       new  b7cd11b   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
       new  a48d869   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 ...
       new  0a5e433   Normalised citation information
       new  dcdfcaa   Fixed watch file
       new  1c290f1   debian/orig-tar.sh: Removed because the removed file is not part of the source any more
       new  0ecbe52   Mass commit my current changes to seqan; Attention: I can not test the build since it needs more memory than my current Build machine
       new  ca75301   Droping -fstack-protector flag helps **drastically** reducing memory consumption when building the package!!!!
       new  442eb24   Building docs works now; uncomment parts of dh_install to proceed somehow for the moment
       new  1a45fdc   Fix installation of demos. Seems we need some additional package seqan-extras and when reading the doc Magnus pointed out   http://trac.seqan.de/wiki/BuildManual/UsingTheSeqAnBuildSystem razers3 might deserve a further additional package ... checking this out now
       new  54d6bd2   Doing a bit of reorganisation how files are installed; create manpages automatically using help2man
       new  cc76f74   Close "new upstream" bug, no zero length manpages
       new  298d4c0   Add python to Build-Depends - seems to be ready for upload
       new  b11cdde   Need to rename /usr/bin/join to /usr/bin/seqan-join to avoid name clash with coreutils --> this needs to be discussed with upstream!
       new  e115412   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
       new  da21bdc   UPstream source is not yet uploaded but this watch file seems a bit better in catching it
       new  e4691c7   Fix common typo: sequan -> seqan
       new  f1d185c   Add hint to add /usr/lib/seqan/bin to PATH variable
       new  d6f5521   Upload to unstable
       new  ac41930   Rename /usr/bin/mason to /usr/bin/seqan_mason
       new  3520a1e   Upload to unstable
       new  023b16a   Run test suite only on powerfull architectures (amd64) at build time
       new  6c9a1f5   Deal with arch-dep builds but mention that the test suite issue is not yet solved
       new  b365959   deacticate test for apps splazers
       new  339f82e   Exclude three test that are failing according to a hint of upstream
       new  a13de08   Try to build 32bit arches without O2 optimisation
       new  5675d10   Move debian/upstream to debian/upstream/metadata
       new  bb7c826   Exclude unused compressed JS code
       new  c2ed79c   Upload to unstable
       new  cca59b9   Do proper manipulation of build options
       new  c0dde10   New upstream version
       new  0eb457f   cme fix dpkg-control
       new  5f7813b   Lets see whether we really need to skip these tests (and than adapt the patch as needed)
       new  d3d78c3   disable doc creation which works differently than in previous versions
       new  fa12582   correct opts in d/watch
       new  17fe800   Upgrade copyright
       new  43a2284   New Build-Depends: python-jinja2 needed in test suite
       new  b8deb19   Further Build-Depends: libbz2-dev, python-sphinx, python-nose, default-jdk
       new  c75926e   Enable parallel builds
       new  5daeb7d   For the moment ignore errors in tests.  The problems need to be investigated separately and we want to see some package to enable deeper inspection
       new  9d13b05   Remove some minimised JS scripts without source which are packaged for Debian
       new  952c3e0   Fix location of include files, docs are somewhere else and should be moved to a separate package
       new  6313230   New package seqan-doc; Attention: the link targets of dh-linktrees are random wild guesses and need to be fixed most probably.  They were just injected as placeholders for the removed JS files and are pointing to the assumed location guessed from the location in the source tarball
       new  2bde027   The dix is now named dox instead of docs - but it is empty anyway.  Just let the package build for the moment.
       new  d67dea9   Imported Upstream version 1.4.1+dfsg
       new  cfaf4bb   Merge tag 'upstream/1.4.1+dfsg'
       new  7330c18   Re-add files present in original svn2git but vanished after gbp import-orig (well known issue)
       new  e8d90b2   Imported Upstream version 2.0.0+dfsg
       new  fdf01f1   Merge tag 'upstream/2.0.0+dfsg'
       new  069ce1b   Moved to Git

The 82 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


-- 
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