Change log : arb package : Debian

6.0.6-7

Published in sid-release on 2023-08-18

arb (6.0.6-7) unstable; urgency=medium

  * Team upload.
  * d/control: revert to Debhelper compat 11
  * Updated source lintian-overrides
  * d/upstream/metadata: add bug and source respository information.
  * d/copyright: be explicit that this package is not part of Debian

 -- Michael R. Crusoe <email address hidden>  Fri, 18 Aug 2023 13:17:20 +0200

Available diffs

diff from 6.0.6-5 to 6.0.6-7 (5.5 KiB)

6.0.6-6

Superseded in sid-release on 2023-08-18

arb (6.0.6-6) unstable; urgency=medium

  * Team upload.
  * d/po/sv: update Swedish debconf translations from Martin Bagge.
    Closes: #918015
  * d/po/pt_BR: update Brazilian Portuguese debconf templates translation from
    Paulo Henrique de Lima Santana. Closes: #1026401
  * d/po/tr: update turkish translation of debconf messages from
    Atila KOÇ. Closes: #1038922
  * d/control: switch Architecture to "any" as raxml is available
    everywhere
  * d/patches/110_narrowing.patch: Fix types for arm64, others
  * d/rules: allow for parallel builds.
  * Standards-Version: 4.6.2 (routine-update)
  * debhelper-compat 13 (routine-update)
  * Remove trailing whitespace in debian/changelog (routine-update)
  * Add salsa-ci file (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * Trim trailing whitespace.

 -- Michael R. Crusoe <email address hidden>  Thu, 17 Aug 2023 19:59:54 +0200

6.0.6-5

Published in bookworm-release on 2023-06-01

Superseded in sid-release on 2023-08-18

arb (6.0.6-5) unstable; urgency=medium

  * Team Upload.
  [ Jelmer Vernooĳ ]
  * Trim trailing whitespace.
  * Use secure copyright file specification URI.

  [ Andreas Tille ]
  * Standards-Version: 4.2.1
  * Remove trailing whitespace in debian/rules
  * Do not parse d/changelog
  * Fix description
    Closes: #926017
  * d/watch: (FIXME) Add location of new upstream releases as comment
  
  [ Elmar Pruesse ]
  * Fix stripping of static libs

  [ Steffen Möller ]
  * Update metadata with ref to conda
  * Update metadata - updated bio.tools ref to lowercase

  [ Nilesh Patra ]
  * Add patch to fix FTBFS with new glibc, add flags to
    use libtirpc-dev (Closes: #998237)
  * Add B-D on libtirpc-dev

 -- Nilesh Patra <email address hidden>  Sat, 06 Nov 2021 02:25:36 +0530

Available diffs

diff from 6.0.6-4ubuntu1 (in Ubuntu) to 6.0.6-5 (5.3 KiB)

6.0.6-4

Published in bullseye-release on 2021-07-22

Published in buster-release on 2018-07-23

Superseded in sid-release on 2021-11-06

arb (6.0.6-4) unstable; urgency=medium

  * Fix symlink
    Closes: #903921
  * debhelper 11
  * Point Vcs fields to salsa.debian.org
  * Standards-Version: 4.1.5

 -- Andreas Tille <email address hidden>  Tue, 17 Jul 2018 15:47:02 +0200

Available diffs

diff from 6.0.6-3 to 6.0.6-4 (1.1 KiB)

6.0.6-3

Superseded in buster-release on 2018-07-23

Superseded in sid-release on 2018-07-19

arb (6.0.6-3) unstable; urgency=medium

  * Add Indonesian debconf translation
    Closes: #862913
  * Standards-Version: 4.1.2

 -- Andreas Tille <email address hidden>  Tue, 19 Dec 2017 11:38:55 +0100

Available diffs

diff from 6.0.6-2 to 6.0.6-3 (1.3 KiB)

6.0.6-2

Superseded in buster-release on 2017-12-24

Superseded in sid-release on 2018-01-04

arb (6.0.6-2) unstable; urgency=medium

  * Team upload
  * Moved packaging to git
  * d/control: transfig → fig2dev (Closes: #866151)
  * do not create MAFFT symlinks (Closes: #857283)
  * bump standards version

 -- Fabian Klötzl <email address hidden>  Tue, 12 Sep 2017 17:32:11 +0200

Available diffs

diff from 6.0.6-1 to 6.0.6-2 (1.2 KiB)

6.0.6-1

Superseded in buster-release on 2017-09-18

Published in stretch-release on 2016-12-18

Superseded in sid-release on 2017-09-13

arb (6.0.6-1) unstable; urgency=medium

  * New upstream version
  * Update Swedish debconf translation (Thanks to Martin Bagge
    <email address hidden>)
    Closes: #769879
  * Add Catalan debconf templates translation (Thanks to Innocent De Marchi
    <email address hidden>)
    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

 -- Andreas Tille <email address hidden>  Wed, 07 Dec 2016 10:34:07 +0100

Available diffs

diff from 6.0.3-2 to 6.0.6-1 (20.9 KiB)

6.0.3-2

Superseded in stretch-release on 2016-12-18

Superseded in sid-release on 2016-12-07

arb (6.0.3-2) unstable; urgency=medium

  * Team upload.
  * Fix building with GCC 6.
    - Use correct return type in method definition.
    - Allow for newer __cplusplus versions.
    Closes: #834170
  * Use secure Vcs-Browser. 
  * Do not depend on perl-modules.
  * Bump Standards-Version.

 -- Sascha Steinbiss <email address hidden>  Sat, 17 Sep 2016 10:34:18 +0000

Available diffs

diff from 6.0.3-1 to 6.0.3-2 (1.5 KiB)

6.0.2-1+deb8u1

Published in jessie-release on 2016-01-23

arb (6.0.2-1+deb8u1) jessie; urgency=medium

  * Skip compiler version check at all
    Closes: #793187

 -- Andreas Tille <email address hidden>  Thu, 10 Dec 2015 10:55:21 +0100

6.0.3-1

Superseded in stretch-release on 2016-09-23

Superseded in sid-release on 2016-10-14

arb (6.0.3-1) unstable; urgency=medium

  * New upstream version
  * Applied all l10n patches - thanks a lot for the great l10n team
    for pushing this
  * Debconf templates and debian/control reviewed by the debian-l10n-
    english team as part of the Smith review project. Closes: #761942
  * [Debconf translation updates]
  * Danish (Joe Hansen).  Closes: #764869
  * Dutch; (Frans Spiesschaert).  Closes: #765088
  * Russian (Yuri Kozlov).  Closes: #765096
  * Portuguese (Américo Monteiro).  Closes: #761503
  * Danish (Joe Hansen).  Closes: #765865
  * Czech (Michal Simunek).  Closes: #766600
  * Italian (Daniele Forsi).  Closes: #766684
  * German (Chris Leick).  Closes: #766689
  * French (Steve Petruzzello).  Closes: #766728
  * Catalan; (Innocent De Marchi).  Closes: #766855
  * Japanese (Hideki Yamane (Debian-JP)).  Closes: #767247
  * extra linker flag proposed by Tim Booth
  * Lintian override to avoid false positives
  * cme fix dpkg-control
  * spelling+lintian fixes in d/copyright

 -- Andreas Tille <email address hidden>  Thu, 10 Dec 2015 12:26:14 +0100

Available diffs

diff from 6.0.2-2 to 6.0.3-1 (18.9 KiB)

6.0.2-2

Superseded in stretch-release on 2015-12-16

Superseded in sid-release on 2015-12-10

arb (6.0.2-2) unstable; urgency=medium

  [ Elmar Pruesse ]
   * Add Portugese debconf translation (thanks to Américo Monteiro 
     <email address hidden> for the patch)
     Closes: #761503
   * Add Russian debconf translation (thanks to Yuri Kozlov 
     <email address hidden> for the patch)
     Closes: #761616
   * debian/arb_CHANGELOG.txt -> debian/changelog (fix lintian complaint)

  [ Andreas Tille ]
  * Skip compiler version check at all
    Closes: #793187

 -- Andreas Tille <email address hidden>  Wed, 22 Jul 2015 22:49:16 +0200

Available diffs

diff from 6.0.2-1 to 6.0.2-2 (3.1 KiB)

6.0.2-1

Superseded in stretch-release on 2015-07-28

Superseded in jessie-release on 2016-01-23

Superseded in sid-release on 2015-07-23

arb (6.0.2-1) unstable; urgency=medium


  [ Andreas Tille ]
  * New upstream version
    Closes: #741890
  * debian/upstream -> debian/upstream/metadata
  * debian/control:
     - Build-Depends: added libglib2.0-dev
     - Depends: added mafft, mrbayes
  * debian/rules
     - Add explicite --remove-section=.comment option to manual strip call
  * cme fix dpkg-control
  * arb-common.dirs: Do not create unneeded lintian dir
  * Add turkish debconf translation (thanks for the patch to Mert Dirik
    <email address hidden>)
    Closes: #757497

  [ Elmar Pruesse ]
  * patches removed:
     - 10_config.makefiles.patch,
       80_no_GL.patch
         removed in favor of creating file from config.makefile.template via 
         sed in debian/control
     - 20_Makefile_main.patch
         merged upstream
     - 21_Makefiles.patch
         no longer needed
     - 30_tmpfile_CVE-2008-5378.patch: 
         merged upstream
     - 50_fix_gcc-4.8.patch:
         merged upstream
     - 40_add_libGLU.patch:
         libGLU not needed for arb_ntree)
     - 60_use_debian_packaged_raxml.patch:
         merged upstream
     - 70_hardening.patch
         merged upstream
     - 72_add_math_lib_to_linker.patch
         does not appear to be needed
  * patches added:
     - 10_upstream_r12793__show_db_load_progress:
         backported patch showing progress while ARB is loading a database
         (needed as indicator/splash screen while ARB is launching)
     - 20_upstream_r12794__socket_permissions:
         backported security fix
     - 30_upstream_r12814__desktop_keywords:
         backported add keywords to desktop (fixes lintian warning)
     - 40_upstream_r12815__lintian_spelling:
         backported fix for lintian reported spelling errors
     - 50_private_nameservers
         change configuration to put nameservers into users home dirs
         (avoids need for shared writeable directory)
     - 60_use_debian_phyml
         use phyml from debian package for both interfaces in ARB
  * debian/rules:
     - create config.makefile from override_dh_configure target
     - use "make tarfile" in override_dh_install
     - remove extra cleaning not needed for ARB 6
     - use "dh_install --list-missing" to avoid missing files
     - added override_dh_fixperms target
  * debian/control:
     - added libarb-dev package
     - Depends: added phyml, xdg-utils
     - Suggests: removed phyml
     - fix lintian duplicate-short-description (new descriptions)
  * debian/*.install:
     - "unrolled" confusing globbing to select files
     - pick files from debian/tmp
     - moved all config files to /etc/arb
  * debian/arb-common.templates: updated
  * scripts:
     - removed arb-add-pt-server
     - launch-wrapper: 
       - only add demo.arb to newly created $ARBUSERDATA
       - pass commandline arguments through bin/arb wrapper
     - preinst: removing old PT server index files on upgrade from 5.5*
     - postinst: set setgid on shared PT dir
  * rewrote arb.1 manfile
  * added file icon for ARB databases
  * using upstream arb_tcp.dat

 -- Elmar Pruesse <email address hidden>  Tue, 02 Sep 2014 15:15:06 +0200

Available diffs

diff from 5.5-5ubuntu1 (in Ubuntu) to 6.0.2-1 (6.9 MiB)

5.5-5

Superseded in jessie-release on 2014-10-02

Superseded in sid-release on 2014-09-27

arb (5.5-5) unstable; urgency=low


  * build-depend on libtiff-dev instead of libtiff4-dev (thanks for the
    patch to Logan Rosen <email address hidden>)
    Closes: #729769
  * cme fix dpkg-control
  * cme fix dpkg-copyright
  * canonical Vcs fields
  * debian/patches/hardening.patch: Propagate hardening options

 -- Andreas Tille <email address hidden>  Wed, 04 Dec 2013 09:24:14 +0100

Available diffs

diff from 5.5-4ubuntu1 (in Ubuntu) to 5.5-5 (3.7 KiB)

5.5-4

Superseded in jessie-release on 2013-12-22

Superseded in sid-release on 2013-12-05

arb (5.5-4) unstable; urgency=low


  * Build-Depends: libglew-dev instead of libglew1.5-dev
    Closes: #714327

 -- Andreas Tille <email address hidden>  Fri, 28 Jun 2013 09:42:35 +0200

Available diffs

diff from 5.5-3ubuntu1 (in Ubuntu) to 5.5-4 (634 bytes)

5.5-3

Superseded in sid-release on 2013-06-28

arb (5.5-3) unstable; urgency=low


  * debian/control:
     - Restrict arb to architectures
         amd64 i386 kfreebsd-i386 kfreebsd-amd64
       because only there raxml is fullfilled.  This makes sense because
       arb will most probably used only on these architectures anyway.
       Closes: #714268
     - Remove Dependency from openjdk which is not needed any more
       according to upstream
  * debian/arb-common.README.debian: Explain restriction to certain
    architectures
  * debian/arb.README.debian: Updated about architecture restriction
    and other things

 -- Andreas Tille <email address hidden>  Thu, 27 Jun 2013 14:52:57 +0200

5.5-2

Superseded in sid-release on 2013-07-18

arb (5.5-2) unstable; urgency=low


  [ Tim Booth ]
  * debian/rules: Make sure arb_edit4 will be really built and abort package
    building process if not

  [ Andreas Tille ]
  * Rebuild against libmotiv-dev in main
    Closes: #713061
  * Add 4.6.3, 4.7.3 and 4.8.[0-3] to ALLOWED_GCC_VERSIONS
    Closes: #713219
  * debian/control:
     - remove DM-Upload-Allowed
     - Build-Depends: libglu1-mesa-dev
     - add raxml to Depends and do not build third party copy any more
       (debian/patches/60_use_debian_packaged_raxml.patch)
  * debian/patches/*: DEP3 comments
  * debian/patches/50_build_naligner.patch: Fix build issue that was
    caused by some brocken $(CFLAGS)
  * debian/rules: use xz compression

 -- Andreas Tille <email address hidden>  Mon, 24 Jun 2013 09:42:03 +0200

5.5-1

Superseded in jessie-release on 2013-07-19

Superseded in sid-release on 2013-06-25

arb (5.5-1) unstable; urgency=low


  * New upstream version (+adapted patches)
  * Standards-Version: 3.9.4 (no changes needed)
  * debian/po: Add Slovak po-debconf translation (Thanks to
    Slavko <email address hidden> for the translation)
    Closes: #686275
  * debian/rules: Add '-lm' as suggested in patch by Konstantinos Margaritis
    <email address hidden> to fix the build problem on armhf.
    This together with new upstream closes: #692499

 -- Andreas Tille <email address hidden>  Tue, 11 Dec 2012 09:59:08 +0100

5.3-4

Superseded in sid-release on 2012-12-25

arb (5.3-4) unstable; urgency=low


  * debian/upstream: Add citations
  * debian/control:
     - Build-Depends: libpng-dev instead of libpng12-dev
       Closes: #662270
     - Standards-Version: 3.9.3 (no changes needed)
  * debian/po/nl.po: Add Dutch translation of debconf templates
    Thanks for the translation to Jeroen Schot <email address hidden>
    Closes: #654763
  * debian/patches/30_Makefile_main:
     - Enable gcc-4.7 as well
       Closes: #682404
     - Enable using hardening flags
  * debian/patches/gcc-4.7.patch: Fix gcc-4.7 build issue
  * debhelper 9 (control+compat)
  * debian/rules:
     - Fixed clean target
     - propagate hardening flags

 -- Andreas Tille <email address hidden>  Thu, 26 Jul 2012 12:15:21 +0200

5.3-3

Deleted in wheezy-release (Reason: None provided.)

Superseded in sid-release on 2012-07-31

arb (5.3-3) unstable; urgency=low


  * debian/control:
     - Build-Depends: time 
       Strangely enough this is not needed in local pbnuilder/sbuild
       environments but on autobuilders this seems to be a problem
       according to comparing the build logs
     - Build-Depends: libbio-perl-perl
       Otherwise some not-critical checks will fail
  * debian/arb.prerm: Care for removal of conffile link created in postinst
    Closes: #656035
  * debian/rules:
     - clean up some manual handling of files and dirs which is not
       needed any more with recent versions
     - insert check which verifies that binary-indep target is really
       builded and changed files and dirs are previousely created
       Closes: #658691

 -- Andreas Tille <email address hidden>  Thu, 09 Feb 2012 13:44:22 +0100

5.3-2

Superseded in sid-release on 2012-02-09

arb (5.3-2) unstable; urgency=low


  * debian/arb.README.Debian: Dropped molphy related notice
  * debian/control:
    - Remove Build-Depends: x11proto-print-dev
    - Remove at least explicite Build-Depends: libxp-dev
      Closes: #623638
  * debian/{control,rules}: Remove quilt which is unneeded when
    using source format 3.0 (quilt)
  * debian/po/ca.po: Catalan translation (thanks to Innocent De Marchi
    <email address hidden>)
    Closes: #632206

 -- Andreas Tille <email address hidden>  Thu, 15 Dec 2011 17:00:46 +0100

5.3-1

Superseded in sid-release on 2011-12-16

arb (5.3-1) unstable; urgency=low


  [ Nelson A. de Oliveira ]
  * Fix FTBFS: replaced sablotron by xsltproc in debian/control
    (Closes: #634999)
  * Replaced arb dependency on the ssh metapackage by openssh-client only

  [ Andreas Tille ]
  * New upstream version (including updateing debian/patches/*)
    This version doese not depend from molphy any more
  * debian/control
    - Do not depend from molphy which is removed from Debian any more
    - Standards-Version: 3.9.2 (no changes needed)
    - Fixed Vcs fields
  * Debhelper 8 (control+compat)
  * debian/copyright: several DEP5 fixes

 -- Andreas Tille <email address hidden>  Fri, 11 Nov 2011 11:46:22 +0100

5.2-1

Superseded in sid-release on 2011-11-14

arb (5.2-1) unstable; urgency=low
  * New upstream version  * Standards-Version: 3.9.1 (no changes needed)  * New debconf translations    - Vietnamese (thanks to Clytie Siddall <email address hidden>)      Closes: #576020    - Danish (thanks to Joe Dalton <email address hidden>)      Closes: #584283    - Brazilian Portuguese (thanks to Gustavo Jordan      <email address hidden>)      Closes: #596647  * Drop xview-clients Suggests in debian/control and replace any occurence    of textedit (which is part of xview-clients) by editor via    debian/patches/no_xview_dependency.patch    Closes: 612534  * debian/patches/20_Makefiles: clean up some errors in clean target  * debian/patches/20_config.makefiles: Really get the DEB_BUILD_ARCH_BITS    applied  * Build-Depends: time -- Andreas Tille <email address hidden>  Wed, 09 Feb 2011 16:56:15 +0100

5.1-1

Superseded in sid-release on 2011-09-20

arb (5.1-1) unstable; urgency=low


  [ Andreas Tille ]
  * New upstream version
    Closes: #522021
  * debian/control:
    - Package arb-doc in non-free/doc
    - Standards-Version: 3.8.4 (Added README.source)
    - Build-Depends: dpkg-dev (>= 1.15.4) to make use of
      `dpkg-architecture -qDEB_BUILD_ARCH_BITS` in Makefile
    - Build-Depends: xutils-dev
    - arb Recommends: bioperl
    - arb Suggests: phyml
    - Build-Depends: openjdk-6-jdk instead of kaffe which might be subject
      of removal from Debian in the near future
  * Removed / changed patches which were applied upstream
    - debian/patches/ARB_release200712_gcc4.3.1.patch removed
    - debian/patches/20_replace_rxp_by_xmllint.patch removed
    - debian/patches/tmpfile_CVE-2008-5378.patch removed applied part
  * debian/{rules,*.install}: Cleanup regarding changes in new upstream version
  * debian/arb.README.debian:
    - Removed useless warning about prereleases
    - Added hint about different phyml versions
  * debian/patches/10_gcc_4.4.3.patch: compile with gcc-4.4.3
  * debian/rules: Add ARBHOME variable explicitly to clean target
  * Added Finish debconf translation (Thanks to Esko Arajärvi <email address hidden>)
    Closes: #536516
  * Added Galician debconf translation (Thanks to marce
    <email address hidden>)
    Closes: #537534
  * Added Japanese debconf translation (Thankse to Hideki Yamane
    <email address hidden>)
    Closes: #554882
  * Added: Spanish debconf translation (Thanks to Francisco Javier Cuadrado
    <email address hidden>)
    Closes: #573005
  * Switch to source format 3.0

  [ David Paleino ]
  * Removed myself from Uploaders
  * New watch file

 -- Andreas Tille <email address hidden>  Tue, 23 Mar 2010 14:37:30 +0100

0.0.20071207.1-7

Superseded in sid-release on 2012-02-25

arb (0.0.20071207.1-7) unstable; urgency=low


  * Bumped debhelper to version 7
     -> dh_clean -k -> dh_clean; dh_prep
  * Standards-Version: 3.8.1 (no changes needed)
  * Enhanced package description of arb-common and arb-doc
    Closes: #517710
  * Added Portuguese translation for debconf messages (thanks to
    Traduz <email address hidden>)
    Closes: #516958
  * Added Depends: ${misc:Depends} to all packages

 -- Andreas Tille <email address hidden>  Fri, 20 Mar 2009 08:14:21 +0100

0.0.20071207.1-6

Deleted in squeeze-release (Reason: None provided.)

Superseded in sid-release on 2012-02-21

arb (0.0.20071207.1-6) unstable; urgency=low


  * Save use of /tmp in arb-kill and addressing the other
    potential tempfile symlink attacks reported in
    CVE-2008-5378: possible symlink attacks
    Closes: #508942
  * Use xmllint instead of rxp to verify helpfile XML because
    rxp is outdate, unmaintained and should be removed.
  * Do not use command-with-path-in-maintainer-script in
    postinst and config
  * Added Russian debconf translation (Thanks to Yuri Kozlov)
    Closes: #511376

 -- Andreas Tille <email address hidden>  Tue, 10 Feb 2009 23:32:41 +0100

0.0.20071207.1-5

Superseded in sid-release on 2011-09-20

arb (0.0.20071207.1-5) unstable; urgency=low


  * Fix tempfile issues in upstream scripts
    Closes: #496396
  * Fix arb name server location in config file (Thanks to
    Felipe Figueiredo <email address hidden>)
    Closes: #495650
  * arb-common.config: Make sure that config file will not fail
    when NIS is used

 -- Andreas Tille <email address hidden>  Tue, 23 Sep 2008 13:32:05 +0200

Debian
arb package

Change log for arb package in Debian

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Debianarb package

Change log for arb package in Debian

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Debian
arb package