[med-svn] [mothur] branch master created (now 46922a5)

[Tomasz Buchert]

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

tomasz pushed a change to branch master
in repository mothur.

        at  46922a5   move packaging from SVN to Git

This branch includes the following new commits:

       new  ec90091   Rudimentary packaging of Mothur.w
       new  9c9a841   More improvements.
       new  2385c2d   Set mergeWIthUpstream flag
       new  d785121   set source format to 3.0 (quilt)
       new  68042f1   The Makefile was helped with an -f option to rm to allow for dpkg-buildpackage's initial clean.
       new  5e71277   Improved description, downloading.
       new  4df7c4a   Adjusting group management.
       new  b6d32d0   Update to latest upstream.
       new  dfd12f4   Added previously forgotten patch to get the makefile to make
       new  edaf9fd   Added "clean" target.
       new  b26398a   New upstream version, "make clean" patch no longer required
       new  7963d98   Provide watch file; rewrite get-orig-source based on the last version obtained by uscan
       new  2055daf   Make latest version build
       new  e089fcd   Added upstream-metadata.yaml
       new  2bb9235   Several polishing, remarks about obtaining source in watch file, NO LICENSE!, manpage
       new  77e8bbc   Do not link against unneeded libncurses
       new  2fa76bb   Minor fixes to clean: target of rules file and copyright, still no license for this package.
       new  29a5ce5   Finally uploaded latest version of mothur to unstable after license was clarified with upstream
       new  ce0650b   Re-added Tim's changelog entry for lucid (even if I do not know, whether this is needed)
       new  2571627   In version 1.17.3, there is a LICENSE file that indicates GPL version 3.
       new  f82b44d   Proofread copyright file, and validated syntax with the following command.
       new  5dc4088   New upstream version with explicite copyright statement uploaded to new
       new  bf599fe   Clarified copyright issues
       new  19b1dfd   Mothur 1.18 changes the layout of the upstream zipfile. Have modified the package to handle this and re-done patches.
       new  5172990   New upstream version
       new  36a6497   preparation of new version
       new  ee6509d   Upload to unstable after readding quilt (did not build in pbuilder otherwise), upstream spelling errors ignored for the moment
       new  5ab7770   New upstream version and fix for FTBFS (-msse)
       new  fcb8aa7   Fixed auto_clean to remove files in uchime_src.
       new  c6de6e4   Patch to build on any UNIX (incl. BSD)
       new  3dd850d   Renamed debian/upstream-metadata.yaml to debian/upstream.
       new  e47dd96   debian/upstream: Moved DOI and PMID to the Reference namespace.
       new  f68fd01   Corrected the files that did not validate with YAML::XS.
       new  d7e9f3e   New upstream version
       new  1f86c2d   fixed typo: s/TITILE/TITLE/; moved DOI+PMID to references
       new  f15b51d   Adapted patches to new upstream version
       new  b0a4e79   get-orig-source more silent; debhelper 9; Build-Depends: gfortran
       new  2a08624   Upload to unstable and DEP5 changes and verified using       cme fix dpkg-copyright
       new  b4e6a98   Upload new upstream version with adapted patches
       new  1027bb7   New upstream version; More complete Authors field in proper BibTeX format
       new  c14bad7   Updated for the latest Mothur (only tested on Ubuntu)
       new  513a856   Use dversionmangle to properly detect upstream version
       new  585ba64   Hopefully BioLinux will use ~repack in the future - enable also this dversionmangle expression
       new  8093106   drop explicite quilt dependency which is just given by source format 3.0 (quilt)
       new  e3ddcbd   Add Files-Excluded to document what was removed from original source
       new  08212f4   Committing various tweaks made for Bio-Linux but relevant for Debian. The most important change is that the makefile definitely shouldn't have "-march=native" as it enables optimisations specific to the build machine and potentially incompatible with other CPUs.
       new  5d5a428   Fit new version of suggested uscan implementation
       new  a3c2803   Use enhanced uscan for new upstream version
       new  848f8c3   cme fix dpkg-control
       new  e4f35ae   Debhelper 9
       new  b00186a   Refresh patches
       new  c4467dd    use anonscm for Vcs fields
       new  daad70f   Hardening for uchime
       new  3acbf8b   Add manpage for uchime
       new  389170b   Fix some spellings
       new  bdfc0bb   Link mothur-mpi manpage to mothur manpage
       new  010f93f   Upload to unstable
       new  82720e1   Start work on mothur 1.31.2+dfsg-2, to fix #721770 (ia64 FTBFS).
       new  204bbcb   debian/patches/makefile.patch: Leave off -m64, which ia64 doesn't support and other 64-bit architectures don't need.  (Closes: #721770.)
       new  22d4846   Finalize mothur 1.31.2+dfsg-2 for unstable (as a team upload).
       new  b0a648a   Move debian/upstream to debian/upstream/metadata
       new  9e77699   New upstream version (adapted patches)
       new  60ff276   Standards-Version: 3.9.5
       new  199f0b2   Upload to unstable
       new  893a088   New upstream version
       new  8f8d9db   Add the important .pat files and tell Mothur how to find them (certainly not in /usr/bin).
       new  97cc00a   Release changes of BioLinux into Debian
       new  251d3eb   Imported Upstream version 1.17.3
       new  5183ca6   Imported Debian patch 1.17.3-1
       new  2ed76c7   Imported Upstream version 1.18.1
       new  d953f18   Imported Debian patch 1.18.1-1
       new  8028b79   Imported Upstream version 1.22.1
       new  4178d8b   Imported Debian patch 1.22.1-1
       new  61a0adb   Imported Upstream version 1.22.2
       new  96b04c6   Imported Debian patch 1.22.2-1
       new  0e2a602   Imported Debian patch 1.22.2-2
       new  6380ddc   Imported Upstream version 1.23.1
       new  2122f6c   Imported Debian patch 1.23.1-1
       new  e7b9af1   Imported Upstream version 1.24.1
       new  4951914   Imported Debian patch 1.24.1-1
       new  8853b1b   Imported Upstream version 1.31.2+dfsg
       new  5161377   Imported Debian patch 1.31.2+dfsg-1
       new  4d0be91   Imported Debian patch 1.31.2+dfsg-2
       new  41448d1   Imported Upstream version 1.33.0+dfsg
       new  c97d160   Imported Debian patch 1.33.0+dfsg-1
       new  86cfdd9   Imported Upstream version 1.33.3+dfsg
       new  66586ff   Imported Debian patch 1.33.3+dfsg-1
       new  012d298   Imported Debian patch 1.33.3+dfsg-2
       new  d0caf4b   Merge branch 'svn'
       new  657199f   watch: switch to github
       new  051476d   d/copyright: no need to exclude files now
       new  787f345   d/*: dont repack upstream tarball
       new  5f9dbcf   watch: remove dfsg suffix
       new  0253eb0   rules: use parallel
       new  65bdac0   rules: make build simpler
       new  99749cf   Imported Upstream version 1.36.1
       new  514a1b6   Merge tag 'upstream/1.36.1'
       new  64d7f0b   patches: refreshed
       new  5af120a   rules: update to new upstream directory structure
       new  e87a711   d/changelog: new entry (+ me in uploaders)
       new  f5f5efa   XXX: skip MPI build (for debug)
       new  06a3716   d/control: build with boost
       new  9a5f732   d/mothur.install: drop pat files
       new  54b6bab   d/patches: more spelling corrections
       new  d5f8389   d/copyright: update
       new  aac6db2   d/patches: fix wrong patch
       new  4c6eb7d   d/patches: pass CXXFLAGS too
       new  d5346aa   d/control: bump std-ver to 3.9.6
       new  90c8595   d/patches: pass CXX properly
       new  80a9d9e   activate MPI build
       new  4293446   Allow to specify MPI compiler
       new  e07edb6   Add note about using ccache (and removed previous note)
       new  1c88661   d/changelog: update
       new  643f541   d/mothur.1: give credit where it is due
       new  46922a5   move packaging from SVN to Git

The 115 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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