[med-svn] [arb] branch master created (now 44460aa)

[Fabian Klötzl]

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kloetzl-guest pushed a change to branch master
in repository arb.

        at  44460aa   document recent changes

This branch includes the following new commits:

       new  863f209   Added arb
       new  b92998a   Several changes that finally build base for a prerelease.
       new  afb2a38   Added vcs tag
       new  ce4dac0   New upstream version
       new  7e94069   Tagged 0.0.20071207-1
       new  de31ce3   +XS-DM-Upload-Allowed: Yes
       new  8304bc7   * debian/control:   - Standards-Version 3.7.3   - long lines wrapped   - architecture set to "any" for architecture-dependent packages   - fixed some typos in long descriptions   - removed [Biology] pseudo-tag from short descriptions -- why not     using DebTags?   - updated Vcs-* fields   - added myself to Uploaders * debian/watch added * debian/po/it.po added * debian/rules updated
       new  74a5945   setting UNRELEASED
       new  2c7dae8   Fixing case mistake
       new  ff833e1     - removing XS- from DM-Upload-Allowed
       new  e5bd4c2   * Using DM-Upload-Allowed instead of XS-DM-Upload-Allowed * Added ?rev=0&sc=0 to Vcs-Browser fields * Sanitized Vcs-* fields
       new  75710e0   Moved from dpathc to quilt because of some problems with new release and dpatch
       new  987dac5   XS-Autobuild: yes to enable auto building
       new  680e884   Enhanced description
       new  5d3f65e   Update to the latest doc-base policy.
       new  d5e888a   Fixes #489330, but reviealed a lot of gcc-4.3 issues - I'm working on these ...
       new  bfc6402   Some gcc-4.3 patches, more will be needed.
       new  c150e49   More gcc-4.3 patches, not finished yet
       new  6130e56   Further gcc-4.3 issues, not finished yet
       new  7159b25   Further include patches.  Hit a larger problem with name clash and need to ask for some hehelp of more skilled C++ person ...
       new  7977c93   After having sended incomplete gcc-4.3 patchset to upstream I've got back a complete patch to work with gcc-4.3.  Just took over the original file name.
       new  f21c2c4   Machine readable copyright file
       new  dbb1846   Fix some lintian warnings
       new  d8468e5   Remove all files on purge - piuparts detected remaining files in /var/lib
       new  80caad1   More detailed copyright statements to enable nonfree at release.debian.net to put arb on their list.
       new  5771200   More work on copyright statements
       new  1ac4289   Make use of dh_lintian and add lintian override that arb-doc is actually in the right section.
       new  83625f7   Strip rpath from ARB.so using chrpath (fixes last remaining lintian problem)
       new  1d81b96   Better short description which was to generic after [Biology] was removed
       new  be12f06   Fix tempfile issue and location of arb name server issue.
       new  8481360   Make sure config script works when using NIS
       new  064d910   Patches for CVE-2008-5378
       new  cd74d39   Fix in Debian own code CVE-2008-5378
       new  25a1250   Enhanced patch for CVE-2008-5378
       new  c8d66b4   Set svn:mergeWithUpstream
       new  e92e927   Avoid rxp dependency
       new  15a0677   Use xmllint instead of rxp
       new  df182f0   Security issues should be solved now
       new  b8234c8   Russian debconf translation and -Wl,--as-needed to avoid dpkg-shlibdeps warnings
       new  cffe153   Revert the latest change in Makefile because it prevents package from beeing built - live with the warnings as before.
       new  0becf8d   Mention CVE-2008-5378 explicitely in changelog
       new  aaea744   Fix description and translation related bugs
       new  fc16906   Fixed some lintian problems
       new  dcf87f6   s/dh_clean -k/dh_clean; dh_prep/ as requested by linitan for using debhelper version 7
       new  4fbee5b   Move package arb-doc to section non-free/doc
       new  507ca8a   Removed myself from Uploaders
       new  b834318   Commit latest changes (perhaps this might become unneeded now since arb released a new version which provides 64 bit support)
       new  2adbb7e   arb now covers version number in download directory.  Thanks for the watchfile to David Paleino
       new  f618c43   New upstream version, bumped standards-version
       new  5e98d19   This file became superflous with the new upstream version
       new  aac9cae   Enable compilation on 32 and 64 bit machines
       new  9983bd8   Updated patches to new version
       new  ab9a436   This version of arb works with gcc 4.3 natively so we can drop our patches
       new  fdabb69   Upstream is now using xmllint instead of rxp
       new  d5750ca   Overworked old patches to make sure all apply correctly
       new  dacdd0d   Build-Depends: xutils-dev, Enable building with gcc 4.3.4
       new  596705e   Adjusted patches to sucessfully compile upstream code
       new  a591003   Recommends bioperl; cleanup regarding several changes in new upstream version
       new  117bf70   CLeanup some leftovers, deal with lintian problems, updated docs
       new  9d4c762   Lintian clean
       new  ed4437d   Some patches to enable compilation using gcc-4.4.3 (does not finally build but I'm working on this)
       new  a5beff1   More gcc-4.4.3 patches
       new  8504896   New upstream version does now compile using latest gcc, debconf translations, source format 3.0
       new  06e4b7a   Make sure scripts will be installed correctly
       new  02c01fb   Start working on new upstream release of arb, however, it does not build
       new  6f726a1   Added debconf translations for three languages, updated debconf translations
       new  8ecb01b   Remove xclient dependency
       new  3bc8967   Really regard DEB_BUILD_ARCH_BITS (patch was wrong); Fix errors in clean targets of upstream Makefiles; use override_dh_* in debian/rules
       new  1898e2b   Get some valid packages at least, needs to verify content and whether program is really working
       new  58c493a   Really remove xview-client dependency.
       new  4df01b0   In arb_CHANGES.txt we have:
       new  74ab9e9   We need only the ssh client (that is provided by openssh-client) and not a full client + server setup. We don't force users to install a SSH server this way.
       new  95b97ee   set mergeWithUpstream 1 for svn-buildpackage
       new  b97a2fe   Several adpatations to new upstrem version; needs further testing
       new  67b96fd   More DEP5 fixes.  Package builds but arb-doc package broken - needs checking how the docs are builded in new version.
       new  5474c4e   Some minor changes in clean target and permission changes; upload to unstable
       new  d045dc6   Some molphy related remarks remained in previous upload and are removed now in SVN
       new  bb33847   Remove explicite dependencies of printing libraries, ad catalan debconf template, upload to unstable
       new  5f529a8   Make sure arb can be properly purged; make sure will be able to "dh build-arch" which seems to be default sbuild behaviour.
       new  5426394   Citation of the day
       new  0497299   Mass changes to fix all open bugs and hopefully finally also build properly with gcc-4.7
       new  c854e81   Enable hardening
       new  23622ed   Upload to unstable
       new  21fba72   New upstream version + adapted patches
       new  2d4d67f   Slovak debconf translation
       new  9ddeec2   Fix remaining part of the patch for armhf to fix #692499
       new  2d0e034   Upload to unstable (arb is not in testing)
       new  b3ddc39   I found an issue building for Ubuntu where the arb_edit4 binary failed to link and was therefore missing from the final arb binary package.  This doesn't affect the current Debian package but it might in the future, and obviously any linking error should cause the build to fail, so the fact that this error was quietly swallowed is a bug in the package.  This small change therefore checks that the binary was created and if not the build will abort.  I've not committed [...]
       new  ef40d10   Mention Tim's change in changelog (thanks to Tim)
       new  f459fa5   DEP3 descriptions for patches
       new  56cc5bf   After Tim's change to ensure arb_edit4 will be created a missing linked library became critical
       new  bfa654a   Some polishing of d/control; enable build with higher versions of gcc
       new  54970b6   Fix build issue that was caused by some brocken $(CFLAGS)
       new  bf0595d   Some issues that occured when building with gcc-4.8 (more to come)
       new  0feb7b4   Avoid trouble with third party raxml by using Debian packaged one
       new  ed58789   use xz compression; upload to unstable
       new  9fc9900   Restrict arb to architectures amd64 i386 kfreebsd-i386 kfreebsd-amd64
       new  ccfe837   Due to upstream openjdk Build-Depends can be removed; upload to unstable
       new  580dcb9   Commit currently uncommited changes for 5.5-4 upload
       new  899f9bb   build-depend on libtiff-dev instead of libtiff4-dev
       new  9705de9   cme fix dpkg-control
       new  ff19f0a   cme fix dpkg-copyright
       new  4d038a7   Canonical Vcs URLs; do not build-depend from dpkg-dev
       new  32b20ec   Upload with not all hardening cases solved, but at least some of them for the moment ...
       new  b5b2e9c   Move debian/upstream to debian/upstream/metadata
       new  e97b9e5   TODO: Run test suite
       new  f85a29b   Adapt d/watch to new upstream version
       new  2c2bda0   Adapted patches to new upstream version (does not build yet!)
       new  66a5469   fix hardeining patch
       new  e2415a6   Switch of GL for the moment since it generates build errors. Hopefully this patch can be deactivated by fixing the GL build problems; consistent naming of patches
       new  b1caf2c   Exclude fasttree, mafft, mrbayes, muscle, phyml and probcons from building in GDE and rather use the according Debian packages by adding these to the list of dependencies
       new  e28ae52   remove build target "arbxtras" (no longer exists upstream)
       new  309dc42   fix patch 72 just re-added "-lm" removed in patch 50
       new  0a3efde   fix build problems
       new  22e1c0d   remove outdated comment
       new  b090d96   update wrapper script for arb 6.0  - pass arguments to arb  - do not link import/export format definitions (ARB 6 scans both global    and user directories now)  - only but demo.arb into $ARBUSERDATA directory if it has just been    created
       new  20cae7f   update default config to the variables understood by ARB 6 --Thisline, and those below, will be ignored--
       new  cae4b51   users adding PT server should not be necessary any longer in ARB 6
       new  0e573e6   remove script that would create arb_tcp.dat from several partial files (it's doing nothing at the moment anyway, exit 0 in second line)
       new  90f80e1   wrote a new manfile for arb
       new  8d4b5b1   fix spelling error
       new  9bff67e   Reworked package for ARB 6.0  - added icons and descriptions for desktop integration  - removed globbing from .install files  - using ARB "install" equivalent now instead of picking from build dir  - removed arb-add-pt server in favor of preconfigured per-user slots  - added libarb-dev with include files and static libs  - replaced "config.makefile" patch with sed script as configure target  - removed patches merged upstream
       new  f19e299   Add Elmar Pruesse <epruesse at mpi-bremen.de> as Uploader
       new  181c525   Remove some cruft
       new  f74824e   remove files that aren't needed for package in install target
       new  7c092af   remove manpage entry for removed script
       new  258ac3c   use upstream's arb_tcp.dat
       new  35f16a3   backport "show progress while opening database" patch from upstream
       new  1c4e9b1   put arb file icon into the right directory
       new  48c6665   fix perms for arb_launcher socket (security issue)
       new  171fab9   fix patch (upstream r12795)
       new  58b3c3a   remove old pt servers when upgrading from 5.5
       new  ed70866   Add explicite --remove-section=.comment option to manual strip call
       new  10ba7e5   cme fix dpkg-control
       new  730c2dd   remove set -x
       new  f4bc1da   update changelog
       new  1310f53   Separated changelog entries between the editors of the changes
       new  b4ee11a   Closes #741890
       new  4e02e0b   Do not create unneeded lintian dir
       new  310c7c5   Add turkish debconf translation
       new  eb394e8   DEP3 headers for patches
       new  e88b50c   fix email (permanent rather than employer)
       new  afae9ee   update short package descriptions (fixes lintian duplicate-short-description)
       new  83f2b70   fix hyphens in man pages
       new  e6b374c   linitian override for ARB.so rpath no longer necessary
       new  701a649   fix duplicate-short-description for libarb
       new  38648d4   KeyWords -> Keywords
       new  8204d4f   add patches to fix lintian warnings
       new  9e0de95   add documentation for r17921
       new  337a897   fix addlibs path
       new  6140fe9   - add upstream keyword and URL to patches cherry picked from upstream - add patch to move nameservers into user HOMEs (avoid user writable dir) - templates: change arb/group description -- only for shared pt servers now - postinst: set setgid on /var/lib/arb/pts directory
       new  3895268   comment previous checkin in changelog
       new  dbed149   use the phyml packaged in debian for all interfaces in ARB
       new  56d6d6c   forgot to quilt refresh...
       new  971e16b   remove question from template
       new  f579076   add override for phyml config.guess (not used in build)
       new  9c54ea0   reworded template to not use imperative and ran debconf-updatepo
       new  7265aaf   Upload to unstable
       new  38eefc9   add Portugese and Russian debconf translations (closes: #761616 and #761503)
       new  ae2db67   Please add new changelog entries after a package was released.  You can use `dch -i` to do so.
       new  e56dbe2   fix broken debian/changelog move arb_CHANGELOG.txt to doc/arb/changelog (fixes lintian complaint)
       new  56c2a7b   Skip compiler version check at all
       new  46068a9   Upload to unstable
       new  0d0995c   Applied all l10n patches - thanks a lot for the great l10n team for pushing this
       new  b150c77   New upstream version with adapted patches, extra linker flag proposed by Tim Booth
       new  2800554   Several lintian issues and upload to unstable
       new  0483ae5   fix building with GCC 6
       new  3d1d0cf   use secure Vcs-Browser
       new  9dad7dc   do not depend on perl-modules
       new  5b51fd8   add patch header
       new  3a813f1   bump Standards-Version
       new  56f032b   fix typo
       new  b7cf97f     * New upstream version   * Update Swedish debconf translation (Thanks to Martin Bagge     <brother at bsnet.se>)     Closes: #769879   * Add Catalan debconf templates translation (Thanks to Innocent De Marchi     <tangram.peces at gmail.com>)     Closes: #788004   * debhelper 10   * d/watch: version=4   * d/rules: hardening=+all (but no effect :-()   * Delete menu file   * Install arb_CHANGES.txt as upstream changelog
       new  45b4b34   Initial upstream branch
       new  7545b16   Imported Upstream version 6.0.6
       new  9227267   Merge tag 'upstream/6.0.6'
       new  79ca829   d/control: transfig → fig2dev
       new  d90cb7a   do not create MAFFT symlinks
       new  093a003   bump standards version
       new  44460aa   document recent changes

The 180 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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