[med-svn] [velvet] branch master created (now 4bfc0b2)

[Andreas Tille]

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

tille pushed a change to branch master
in repository velvet.

        at  4bfc0b2   Moved from SVN to Git

This branch includes the following new commits:

       new  156531c   Creating trunk directory
       new  392b5cb   [svn-inject] Applying Debian modifications to trunk
       new  fe9fc4e   Preliminary package
       new  73d52b7   The patches were not necessary in the end.
       new  6c34344   We also have interest in velvet - tried to fix the watch file but failed.  I guess we have to ask upstream for help ....
       new  77bc74c   Do not touch third-party/zlib-1.2.3 at all.  The patch for src/readSet.c might be a little bit rude and perhaps we should suggest a better #ifdef EXTERNAL_ZLIB magic to upstream instead of this.
       new  314bd1b   It is "Uploader_s_" and bumped policy version.
       new  a0f3be1   Reverted Andreases patch, and added a velvet-example package.
       new  3630921   -O2 is the default in Debian, and often -O3 does not make the program faster.
       new  0e5ee7e   Unset OPT as DEB_BUILD_OPTIONS does the job (thanks to D. Leidert).
       new  33ee9e9   Do not use third-party/zlib stuff.  Patch should be suggested upstream.  Remark: The #ifdef (Windows) condition does not work because the inclulde path mentioned there does not exist.
       new  bee6fb6   Machine readable copyrigh
       new  8307172   Polished copyright file, fixed minor errors; ready for upload.
       new  6fbfea1   Forgot to add README.source for Policy 3.8.0.
       new  d65768b   New upstream version.  Hopefully ftpmaster will be able to work down NEW queue soon ...
       new  1d593d2   New version, use help2man to create man pages, moved third party contrib stuff to /usr/share/doc/velvet/examples to make it more visible for users.
       new  8974d3d   Added missing quilt entry in debian/rules
       new  4066842   New upstream release; minor trouble to autogenerate the manpages.
       new  44fe147   New upstream release.
       new  936442e   New upstream release and packaging polishing.
       new  21b5677   New upstream release correcting bugs and enhancing documentation.
       new  786bf90   New upstream release.
       new  f29fc0d   New upstream release available. Will upload soon.
       new  a21d722   Uploaded.
       new  5044128   Corrected broken changelog.
       new  fe5c463   New upstream release.
       new  7f89f88   New upstream release.
       new  a545ffb   New upstream version; ignore two minor lintian warnings for this upload but asked author about fixing the issues upstream; seems to be actively maintained so we might expext an update soon.
       new  8b086e6   New upstream release. Zlib convenience copy removed from Debian source package.
       new  dce88cc   Fixed watch file to reflect ~nozlibcopy extension
       new  e953c85   New upstream release.
       new  c2fc67d   New upstream version, get-orig-source target to strip zlib copy
       new  96565bf   New upstream version, source format 3.0 (quilt), switched from simple-patchsys to quilt
       new  1aa3533   New upstream source
       new  1402132   FIx ld -as-needed FTBFS issue (thanks for the patch to Matthias Klose)
       new  eb05232   New upstream version
       new  feb76ac   Typo
       new  5460e3e   New upstream version, adapted patches to this new version; debhlper 8; prepare building of meta-velvet (whatever this is - needs to be clarified); TODO: exclude contrib/MetaVelvet-v0.3.1 directory from binary package ... and clarify the sense of meta-velvet (separate binary package????)
       new  76ad775   Once we are rebuilding the original tarball anyway, it seems simpler to remove the outdated MetaVelvet code rather than adapting the build system.  If MetaVelvet is needed it should be packaged separately.  The issue is documented in README.source.
       new  fa5b1ba   Bumped STandards-Version and upload to unstable
       new  b389b4b   New upstream, now uses system Zlib by default, so removed one unneedded patch.
       new  7f5f4cb   Shifted from CDBS to DH.  Confirmed that the resulting DEB is identical to the one produced before, apart from some file size difference due to switch from '-O2' to '-O3' compiler flag.  I'm not sure why the two build systems have different defaults?
       new  d2c678a   Revised velvet copyright, remove entries for zlib again because it turns out to be too complicated to mention all those different copyrights :-(
       new  27223f8   Do not remove MetaVelvet any more, do not leave dangling symlink behind
       new  1457265   Build-Depends: texlive-latex-base
       new  bb8fc71   Validated and reformatted with ‘config-edit -application dpkg-copyright’.
       new  fde70f3   Corrected VCS URLs.
       new  87709b1   New upstream release changing only contrib/VelvetOptimiser.
       new  07f94e6   Compress binary packages with xz.
       new  89bb5a8   Compress source package with xz.
       new  195c517   Turn on multithreading with OpenMP.
       new  eb88270   Remove empty directory contrib/MetaVelvet-v0.3.1/obj
       new  c5965e0   Pre-Depends on dpkg (>= 1.15.6) for Ubuntu LTS.
       new  a315c22   Uploaded new upstream release after removing Multi-Arch: foreign.
       new  b406686   Renamed debian/upstream-metadata.yaml to debian/upstream.
       new  6268544   New upstream release, with one more copyright holder.
       new  75a29bf   Using 1.0 URL for the machine-readable Debian copyright format.
       new  9dc0199   Updated debian/patches/include_debians_zlib.patch.
       new  6a755b0   velvet (1.2.03~nozlibcopy-1) unstable; urgency=low
       new  c0452bd   debian/upstream: Moved DOI and PMID to the Reference namespace.
       new  0c1cf9c   Corrected the files that did not validate with YAML::XS.
       new  760a693   New upstream version; debian/watch now copes with +dfsg suffix (in addition to old ~nozlibcopy)
       new  b07e61f   Enable simple changing of suffix for repackaged source
       new  cbf762e   Standards-Version: 3.9.3
       new  f5f53be   Add Files-Excluded to document what was removed from original source
       new  46ee7be   Adapt patch to new upstream version
       new  fbce215   When using source format 3.0 (quilt) there is no need for quilt dependency
       new  3ec98fc     * rename debian/{docs,install} to debian/velvet.{docs,install} which     is more safe in the case of multibinary package   * debian/velvet.install: shuffle* files are in contrib directory now
       new  0c00c61   Exclude useles arch dependant library
       new  9ebc377   Hardening options
       new  d4d58f0   For those who are not using uscan from VCS enable creating proper upstream tarball
       new  b14051b   bumped python from Recommends to Depends because there are Python scripts installed in velvet/contrib
       new  f545c0a   Take over mass changes from preliminary Git repository
       new  fb627de   cme fix dpkg-control
       new  acf5f44   Updated explanation for repackaging, droped some outdated information
       new  112abb6   Do not try to rmdir nonexisting directory
       new  f5569d8   use anonscm in Vcs fields
       new  d3d4387   use install instead of examples to move the examples into /usr/share/doc/velvet directly.  Also all contrib stuff was moved here to not bloat main velvet binary package with potentially unused stuff in /usr/share
       new  49661f3   Upload to unstable
       new  d3dd74b   Move debian/upstream to debian/upstream/metadata
       new  80d600c   Sync package with Bio-Linux version.  If the changes are accepted as-is, then VelvetOptimiser should be added to Debian.
       new  4afe047   Base get-orig-source target on recent uscan that understands Files-Excluded
       new  28be328   debian/rules: no need to explicitly force xz compression any more
       new  01e20a4   Include test_data.tar.xz instead of the data directory.
       new  d55b466   Remove MeteVelvet and VelvetOptimiser in dh_clean, not dh_install.
       new  26ee408   -2biolinux1
       new  c4a497f   Please do not force us to skip a version number in Debian but bump only the biolinux version
       new  197e5b0   Drop more stuff from upstream source via Files-Excluded
       new  c4d0343   cme fix dpkg-control
       new  d31be73   Add autopkgtest
       new  2581bbd   Document the way you can test the package manually
       new  1140dc0   After realising that the manpages created at package build time have duplicated content I switched the manpage generation to a script which should be run before the final install.  Manpages are created that way for all binaries.
       new  6900f98   Fix gcc-5 build issue
       new  80d94f0   cme fix dpkg-control
       new  dbd723a   Imported Upstream version 1.2.10+dfsg1
       new  30f0ff0   Merge tag 'upstream/1.2.10+dfsg1'
       new  79c9340   Readd debian/ dir
       new  4bfc0b2   Moved from SVN to Git

The 98 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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