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 ) 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 Tue, 02 Sep 2014 15:15:06 +0200 arb (5.5-5) unstable; urgency=low * build-depend on libtiff-dev instead of libtiff4-dev (thanks for the patch to Logan Rosen ) Closes: #729769 * cme fix dpkg-control * cme fix dpkg-copyright * canonical Vcs fields * debian/patches/hardening.patch: Propagate hardening options -- Andreas Tille Wed, 04 Dec 2013 09:24:14 +0100 arb (5.5-4) unstable; urgency=low * Build-Depends: libglew-dev instead of libglew1.5-dev Closes: #714327 -- Andreas Tille Fri, 28 Jun 2013 09:42:35 +0200 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 Thu, 27 Jun 2013 14:52:57 +0200 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 Mon, 24 Jun 2013 09:42:03 +0200 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 for the translation) Closes: #686275 * debian/rules: Add '-lm' as suggested in patch by Konstantinos Margaritis to fix the build problem on armhf. This together with new upstream closes: #692499 -- Andreas Tille Tue, 11 Dec 2012 09:59:08 +0100 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 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 Thu, 26 Jul 2012 12:15:21 +0200 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 Thu, 09 Feb 2012 13:44:22 +0100 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 ) Closes: #632206 -- Andreas Tille Thu, 15 Dec 2011 17:00:46 +0100 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 Fri, 11 Nov 2011 11:46:22 +0100 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 ) Closes: #576020 - Danish (thanks to Joe Dalton ) Closes: #584283 - Brazilian Portuguese (thanks to Gustavo Jordan ) 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 Wed, 09 Feb 2011 16:56:15 +0100 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 ) Closes: #536516 * Added Galician debconf translation (Thanks to marce ) Closes: #537534 * Added Japanese debconf translation (Thankse to Hideki Yamane ) Closes: #554882 * Added: Spanish debconf translation (Thanks to Francisco Javier Cuadrado ) Closes: #573005 * Switch to source format 3.0 [ David Paleino ] * Removed myself from Uploaders * New watch file -- Andreas Tille Tue, 23 Mar 2010 14:37:30 +0100 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 ) Closes: #516958 * Added Depends: ${misc:Depends} to all packages -- Andreas Tille Fri, 20 Mar 2009 08:14:21 +0100 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 Tue, 10 Feb 2009 23:32:41 +0100 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 ) Closes: #495650 * arb-common.config: Make sure that config file will not fail when NIS is used -- Andreas Tille Tue, 23 Sep 2008 13:32:05 +0200 arb (0.0.20071207.1-4) unstable; urgency=low * debian/arb-common.postrm: Remove stuff arb leaves behind in /var/lib in case the package is purged Closes: #463010 * More precise copyright / license statements in debian/copyright * debian/arb-doc.lintian-overrides: Explain why arb-doc should not be in section doc * Moved debian/*.lintian.overrides to *.lintian-overrides and make use of dh_lintian (includes increasing versioned depends of debhelper to >= 6.0.7) * Strip rpath from ARB.so using chrpath * Better short description which was to generic after [Biology] marker was removed. -- Andreas Tille Wed, 23 Jul 2008 08:10:46 +0200 arb (0.0.20071207.1-3) unstable; urgency=low [ Charles Plessy ] * Changed the doc-base section according to the new policy. [ Andreas Tille ] * Updated dependency from libglew (Build-Depends: libglew-dev -> libglew1.5-dev) Closes: #489330 * Standards-Version: 3.8.0 (no changes needed) * debian/patches/30_Makefile_main: Enable gcc-4.3 * Applied upstream patches to compile with gcc-4.3 (thanks to Ralf Westram ) -- Andreas Tille Mon, 07 Jul 2008 09:11:40 +0200 arb (0.0.20071207.1-2) unstable; urgency=low * Added XS-Autobuild: yes to enable autobuilding * Slightly enhanced description -- Andreas Tille Thu, 06 Mar 2008 23:23:07 +0100 arb (0.0.20071207.1-1) unstable; urgency=low [ David Paleino ] * 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 - removing XS- from DM-Upload-Allowed * debian/watch added * debian/po/it.po added * debian/rules updated [ Andreas Tille ] * New upstream source debian/get-orig-source: Obtain official release. Remark: The originally downloaded source from 2007_12_07 was different from the currently available one. This is expressed in the additional ".1" in the version number. * Removed warning from long description because this is now an official release * debian/rules: - removed get-orig-source.old target - added missing '-' in clean target * Switched to quilt (dpatch was not able to apply patches from previous version) -- Andreas Tille Mon, 25 Feb 2008 09:34:30 +0100 arb (0.0.20071207-1) unstable; urgency=low * New upstream version Closes: #446666 * Added Build-Depends libglew-dev which is needed for 3D version * Added Build-Depends libxpm4-dev according to the advise of Charles Plessy in bug #364908 * Added x11proto-print-dev, libxpm-dev, libxp-dev, libgl1-mesa-swx11-dev (> 6.5.1-0.4) to build dependencies * Added to Build-Depends: libtiff4-dev, libxaw7-dev * Standards-Version: 3.7.2 (no changes necessary) * debhelper 5 * use dpatch * Added license of new component RAxML to debian/copyright * Substituded ${Source-Version} by ${source:Version} resp. ${binary:Version} * debian/arb.menu: Applications/Science/Biology * move files from lib/* directly to /usr/lib/arb/lib instead of /usr/share/arb/lib and a bunch of symlinks * Set maintainer to Maintainer: Debian-Med Packaging Team * Added Portugese debconf translations (thanks to Miguel Figueiredo Closes: #341558 * Updated Czech debconf translations (thanks to Jakub Kasparec ) Closes: #356713, #392683 * Do not build molphy and symlink to molphy executables instead * New configuration file format for arb_tcp.dat * Added Vcs-Browser, Vcs-Svn * Moved Homepage from long description to tags field -- Andreas Tille Mon, 05 Nov 2007 18:17:32 +0100 arb (0.0.20050526-7) unstable; urgency=low * arb-common recommends arb * Added Build-Depends: g++ * Because there is no sign that this version shows the behaviour reported in #325640 against the former version and the bug reporter did not respond to any request I decide to close this bug. Feel free to reopen if it seems necessary. Clsoes: #325640 -- Andreas Tille Mon, 21 Nov 2005 14:09:01 +0100 arb (0.0.20050526-6) unstable; urgency=low * Added transfig to depends * Removed "Depends: arb" from arb-common to avoid circular dependencies Closes: #339861 * Added gcc 4.0.3 to supported compilers in Makefile -- Andreas Tille Wed, 9 Nov 2005 13:17:52 +0100 arb (0.0.20050526-5) unstable; urgency=low * Enable writing of large amounts of sequence files. (Thanks for the patch to Elmar Pruesse ) Closes: #333391 * Updated Swedish debconf template (Thanks to Daniel Nylander ) Closes: #332788 * Updated French debconf template (Thanks to Jean-Luc Coulon ) Closes: #333108 -- Andreas Tille Wed, 12 Oct 2005 09:25:15 +0200 arb (0.0.20050526-4) unstable; urgency=low * Included names.dat.template in arb-common:/var/lib/nas actually not only the file is missing but the directory of the file is also not found because a link to /var/lib/arb/nas is needed To enable a clean installation of the link the old empty directory has to be removed in a preinst script * Fixed location of arb nameserver in debian/conf/{arb_tcp,arb_ntree}.dat Closes: #332436 * Make sure that nameserver directory is accessible by members of group arb in postinst file * Changed debconf template to ask for arb users * Added warning to arb wrapper script if the user who starts arb is not yet member of group arb and thus not allowed to write to /var/lib/arb -- Andreas Tille Thu, 6 Oct 2005 21:38:12 +0200 arb (0.0.20050526-3) unstable; urgency=low * Added Swedish debconf templates translation (thanks to Daniel Nylander Closes: #330428 * Added ssh to dependencies because it is used in some scripts * Dropped last version number in Standards-Version (now: 3.6.2) -- Andreas Tille Wed, 28 Sep 2005 11:18:17 +0200 arb (0.0.20050526-2) unstable; urgency=low * Added explicite permission to distribute with Debian to debian/copyright * Fixed debian/rules + WINDOW/Makefile to ensure that libARB can be found in the build process (Many thanks to Petr Salinger ) * Reduced number of architectures to the set that features xviewg-dev -- Andreas Tille Thu, 8 Sep 2005 14:08:07 +0200 arb (0.0.20050526-1) unstable; urgency=low * New upstream version. * Added disclaimer from FTP-download directory to debian/arb.README.Debian and debian/copyright * Added parts of the disclaimer from FTP-download directory to debian/control * Patch for NAMES/names.cxx (Thanks to Petr Salinger ) -- Andreas Tille Tue, 30 Aug 2005 09:49:01 +0200 arb (0.0.20050506-3) unstable; urgency=low * Recommend: xfig * solved debconf | debconf-2.0 issue by ${misc:Depends} * debian/control: Homepage: http://www.arb-home.de/ * Renamed debian/po/cz.po to cs.po (Thanks to Denis Barbier ) Closes: #325062 * Depends: freeglut3-dev | libglu-dev * Build-Depends: libpng12-dev (Thanks to Petr Salinger ) * Some patches that where necessary for building with gcc 4.0.x (Thanks to Petr Salinger ) * arb-common: Depends: adduser * arb-common.config: Removed bashism -- Andreas Tille Fri, 26 Aug 2005 12:58:01 +0200 arb (0.0.20050506-2) unstable; urgency=low * Enable killing all arb processes in arb-kill * Standards-Version: 3.6.2.1 * menu items moved (no changes in packaging, just use new debhelper) * Czech debconf translation, thanks to Igor Jasa Closes: #318442 -- Andreas Tille Wed, 1 Jun 2005 13:15:04 +0200 arb (0.0.20050506-1) unstable; urgency=low * New upstream version * Adapted get-orig-source target to new directory layout * Added French debconf template Closes: #309222 -- Andreas Tille Mon, 30 May 2005 15:17:44 +0200 arb (0.0.20050318-1) unstable; urgency=low * New upstream snapshot * Added freeglut3-dev and libglew-dev Build-dependency * First official package uploaded to Debian Closes: #282037 -- Andreas Tille Thu, 10 Mar 2005 11:23:28 +0100 arb (0.0.20041206-1) unstable; urgency=low * New upstream snapshot * Reintegrate also arb-nas package because it is the main Arb application according to the author. It makes no sense to separate it in an extra package. -- Andreas Tille Mon, 06 Dec 2004 10:48:01 +0100 arb (0.0.20041112-4) unstable; urgency=low * Group arb which has rw-permissions to arb databases * Split configuration file into several pieces and megre them in postinst. This enables splitting into several independent packages because upstream uses a single config file * Script arb-add-pt-server enables users of group arb to add PT_SERVER entries to configuration files * Manage users of group arb via debconf -- Andreas Tille Tue, 23 Nov 2004 12:50:22 +0100 arb (0.0.20041112-3) unstable; urgency=low * Dropped package arb-extra and abr-server after discussing with the authors because it does not really make sense to split this from main package. * Enhanced package arb-nas * New package libarb with dynamic libraries -- Andreas Tille Fri, 19 Nov 2004 15:56:53 +0100 arb (0.0.20041112-2) unstable; urgency=low * Compile with libmotif-dev because liblesstif has trouble with some controls in the search inteface. * Moved some files to the server package. * Exclude arb/lib/BUGS from package because its irrelevant * Move arb/lib/help_html to doc package * Wrote placeholder manpage * Added lintian.overrides * Moved arb_tcp.dat to /etc/arb and set symlink -- Andreas Tille Tue, 16 Nov 2004 18:23:59 +0100 arb (0.0.20041112-1) unstable; urgency=low * Inoffcial test release. -- Andreas Tille Fri, 12 Nov 2004 13:15:16 +0100