seaview (1:5.0.5-2) unstable; urgency=medium [ Charles Plessy ] * Patch for command-line arguments of MUSCLE 5. [ Andreas Tille ] * Standards-Version: 4.6.2 (routine-update) -- Charles Plessy Sun, 18 Dec 2022 08:24:57 +0100 seaview (1:5.0.5-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.6.0 (routine-update) * Avoid explicitly specifying -Wl,--as-needed linker flag. -- Andreas Tille Thu, 03 Feb 2022 16:01:36 +0100 seaview (1:5.0.4-1) unstable; urgency=medium * Team Upload. * New upstream version 5.0.4 -- Nilesh Patra Sat, 19 Sep 2020 15:59:30 +0530 seaview (1:5.0.2-4) unstable; urgency=medium * Team upload. -- Nilesh Patra Sat, 19 Sep 2020 15:52:00 +0530 seaview (1:5.0.2-3) unstable; urgency=medium * Team Upload. * Fix gcc-10 FTBFS (Closes: #957783) * compat version: 13 -- Nilesh Patra Tue, 28 Jul 2020 19:47:08 +0530 seaview (1:5.0.2-2) unstable; urgency=medium * Team upload. [ Andreas Tille ] * Fix autopkgtest Closes: #961399 [ Nilesh Patra ] * Use xvfb to run autopkgtests -- Nilesh Patra Sun, 24 May 2020 21:21:17 +0200 seaview (1:5.0.2-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 12 (routine-update) * Secure URI in copyright format (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * Remove trailing whitespace in debian/control (routine-update) * Remove trailing whitespace in debian/copyright (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. (routine-update) * Wrap long lines in changelog entries: 20060918-1. (routine-update) * Use secure URI in Homepage field. (routine-update) * Remove obsolete fields Contact, Name from debian/upstream/metadata (already present in machine-readable debian/copyright). (routine-update) * Extended description in d/copyright -- Steffen Moeller Fri, 15 May 2020 13:20:44 +0200 seaview (1:4.7-1) unstable; urgency=medium * New upstream version * Drop patch since upstream has fixed Makefile * Re-add example which was lost by accident * Add autopkgtest -- Andreas Tille Wed, 09 May 2018 14:39:32 +0200 seaview (1:4.6.5-1) unstable; urgency=medium * New upstream version * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * Add ldflags used in Makefile of last version to build successfully * Comment installation of example that is missing in upstream source * Remove duplicated reference with non-standard interface -- Andreas Tille Sat, 28 Apr 2018 07:25:07 +0200 seaview (1:4.6.4-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.1.3 * debhelper 11 -- Andreas Tille Sat, 17 Feb 2018 14:31:40 +0100 seaview (1:4.6.1.2-2) unstable; urgency=medium * Enable reading number of bootstraps from phyml runs Closes: #853835 -- Andreas Tille Wed, 01 Feb 2017 12:54:56 +0100 seaview (1:4.6.1.2-1) unstable; urgency=medium * New upstream version * debhelper 10 * d/watch: version=4 * Add Keyword to desktop file -- Andreas Tille Fri, 18 Nov 2016 08:26:19 +0100 seaview (1:4.6.1.1-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control -- Andreas Tille Sat, 10 Sep 2016 07:10:54 +0200 seaview (1:4.6-2) unstable; urgency=medium * Do not require user input at stdin when calling phyml -- Andreas Tille Wed, 20 Apr 2016 13:21:29 +0200 seaview (1:4.6-1) unstable; urgency=medium * New upstream version * Move packaging from SVN to Git * Better hardening -- Andreas Tille Sun, 20 Mar 2016 07:12:09 +0100 seaview (1:4.5.4.8-2) unstable; urgency=medium * Rebuild using -fPIC Closes: #809713 -- Andreas Tille Sun, 03 Jan 2016 14:40:56 +0100 seaview (1:4.5.4.8-1) unstable; urgency=medium [ Charles Plessy ] * Drop menu file as per decision of the Technical Committee. [ Andreas Tille ] * New upstream version -- Andreas Tille Mon, 09 Nov 2015 08:29:12 +0100 seaview (1:4.5.4.7-1) unstable; urgency=medium * New upstream version (remove patch applied upstream) -- Andreas Tille Tue, 22 Sep 2015 21:10:52 +0200 seaview (1:4.5.4.5-1) unstable; urgency=medium * New upstream version (remove patch applied upstream) -- Andreas Tille Tue, 28 Jul 2015 18:24:20 +0200 seaview (1:4.5.4.4-1) unstable; urgency=medium * New upstream version -- Andreas Tille Tue, 07 Jul 2015 16:20:43 +0200 seaview (1:4.5.3.1-2) unstable; urgency=medium * Remove unneeded build-dependance on libjpeg8-dev (Closes: #765824). -- Charles Plessy Sun, 19 Oct 2014 08:15:00 +0900 seaview (1:4.5.3.1-1) unstable; urgency=medium * New upstream bugfix release * Architecture any -- Andreas Tille Sat, 04 Oct 2014 10:27:09 +0200 seaview (1:4.5.3-1) unstable; urgency=medium * New upstream version that can go to main since third party code from PHYLIP is now free * cme fix dpkg-control * debian/copyright: Third party code from PHYLIP is now BSD-2-Clause -- Andreas Tille Mon, 22 Sep 2014 21:59:39 +0200 seaview (1:4.5.2-1) unstable; urgency=medium * New upstream version. * New homepage. -- Charles Plessy Sun, 21 Sep 2014 19:48:42 +0900 seaview (1:4.5.1-1) unstable; urgency=medium * New upstream version [ Andreas Tille ] * debian/upstream -> debian/upstream/metadata * cme fix dpkg-control [ Charles Plessy ] * debian/patches/add-ldl.patch: removed (applied upstream). * Build-depend on libjpeg8-dev instead of libjpeg62-dev. * debian/seaview.mime: removed (redundant with FreeDesktop entry). -- Charles Plessy Sat, 10 May 2014 17:29:33 +0900 seaview (1:4.4.2-1) unstable; urgency=low * New upstream version Closes: #688632 * debian/control: - cme fix dpkg-control - anonscm in Vcs fields * debian/patches/add-ldl.patch: Provide lacking -ldl for successfull linking -- Andreas Tille Mon, 12 Aug 2013 13:03:12 +0200 seaview (1:4.4.0-1) unstable; urgency=low New upstream release using Clustal Omega instead of Clustal W. [ Andreas Tille ] * debian/rules: do not force hardening * debian/upstream: Keep old information from tasks file as additional citation [ Charles Plessy ] * debian/patches/use-dpkg-buildflags.patch: removed parts adopted upstream. * debian/control: recommend Clustal Omega instead of Clustal W. -- Charles Plessy Thu, 20 Sep 2012 13:30:40 +0900 seaview (1:4.3.3-3) unstable; urgency=low * debian/control: drop cdbs Build-Dependency * debian/rules: switch to short dh * debian/patches/use-dpkg-buildflags.patch: Patch for upstream Makefile to ensure hardening flags (Thanks to Simon Ruderich for the patch) Closes: #662818 * mv debian/examples debian/example_files because lintian claimed executable debhelper file (missinterpreting dir as debhelper input file) -- Andreas Tille Tue, 06 Mar 2012 20:38:53 +0100 seaview (1:4.3.3-2) unstable; urgency=low * Build on libpng-dev instead of libpng12-dev (Closes: #662499). * Harden through Debhelper's compatibility level 9. -- Charles Plessy Tue, 06 Mar 2012 13:47:02 +0900 seaview (1:4.3.3-1) unstable; urgency=low * New upstream release. * Include upstream example in Nexus format (debian/seaview.examples). * Complies with Policy 3.9.3 (debian/control, no other changes needed). -- Charles Plessy Fri, 24 Feb 2012 13:36:57 +0900 seaview (1:4.3.2-1) unstable; urgency=low * New upstream release. * Moved help file to /usr/share/seaview and left a symbolic link. -- Charles Plessy Sun, 08 Jan 2012 18:57:12 +0900 seaview (1:4.3.1-1) unstable; urgency=low * New upstream release incorporating debian/patches/format-security.patch. * Build seaview on armel architecture (debian/control). * Build-depend on libjpeg62-dev directly (debian/control), as libjpeg62-dev no more Provides libjpeg-dev since 6b1-2. -- Charles Plessy Sat, 03 Dec 2011 11:17:44 +0900 seaview (1:4.3.0-2) unstable; urgency=low * debian/patches/format-security.patch: Handle format strings properly Closes: #648121 * debian/control: Fix Vcs fields -- Andreas Tille Wed, 09 Nov 2011 08:26:27 +0100 seaview (1:4.3.0-1) unstable; urgency=low * New upstream version with SVG output. * Built on FLTK 1.3 (debian/control). * Corrected location of the help file (debian/rules). -- Charles Plessy Mon, 25 Jul 2011 18:57:42 +0900 seaview (1:4.2.12-1) unstable; urgency=low * New upstream versions. * Using Debhelper compatibility level 8 (debian/control, debian/compat). * Clean extra files through dh_clean (debian/clean, debian/rules). * Simplified build system using CDBS to pass options through CFLAGS, removing need for patching Makefile (debian/rules, debian/patches, debian/control). * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/control, no changes needed). -- Charles Plessy Fri, 10 Jun 2011 15:26:56 +0900 seaview (1:4.2.10-1) unstable; urgency=low * New upstream version * debian/patches/10_makefile.patch: - Linker flag -Wl,--as-needed to avoid useless linking and dependencies - Activate suggested Options in Makefile -- Andreas Tille Thu, 25 Nov 2010 18:30:25 +0100 seaview (1:4.2.9-1) unstable; urgency=low * New upstream version (Closes: #601244). -- Charles Plessy Wed, 27 Oct 2010 16:12:00 +0900 seaview (1:4.2.6-1) unstable; urgency=low * New upstream version. * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). * Refreshed debian/copyright according to latest DEP-5 discussions. * Moved debian/upstream-metadata.yaml's PMID and DOI keys in the Reference namespace. -- Charles Plessy Mon, 23 Aug 2010 14:30:30 +0900 seaview (1:4.2.5-1) unstable; urgency=low * New upstrem version * debian/watch: Force passive mode for ftp, because this works more reliably * Using dpkg source format version ‘3.0 (quilt)’ (debian/source/format) * debian/seaview.doc-base.reference: There is no docbase section Bibliography (even if this would be interesting) and thus it was moved to Science/Biology -- Andreas Tille Fri, 25 Jun 2010 11:56:05 +0200 seaview (1:4.2.4-1) unstable; urgency=low * New upstream release. * debian/control: - Incremented Standards-Version to reflect conformance with Policy 3.8.4 (no changes needed). - Support only i386 and amd64 until non-free autobuilders get more robust. * Updated bibliographic reference in ‘debian/upstream-metadata.yaml’. -- Charles Plessy Thu, 08 Apr 2010 13:07:41 +0900 seaview (1:4.2.1-1) unstable; urgency=low [ Charles Plessy ] * New upstream release that can be compiled with GCC 4.4.2 Closes: #560438, Thanks to Luk Claes for the help. * Updated bibliographic reference and Debian copyright file. [ Andreas Tille ] * s/Debian-Med/Debian Med/ in debian/control. -- Charles Plessy Wed, 06 Jan 2010 21:59:51 +0900 seaview (1:4.2-1) unstable; urgency=low * New upstream release. * debian/control: - Build depend on unversionned libjpeg-dev package. - Added XS-Autobuild: yes to benefit from the non-free autobuilders. - checked package conformance with Policy 3.8.3 (no changes needed). * Documented zlib.conf in debian/copyright. * Added various informations in debian/upstream-metadata.yaml. -- Charles Plessy Sun, 18 Oct 2009 17:10:08 +0900 seaview (1:4.1-1) unstable; urgency=low * New upstream version adding nucleotide ambiguity symbols in consensus DNA sequences. * debian/control: checked package conformance with Policy 3.8.2 and incremented Standards-Version accordingly (no changes needed). * debian/seaview.1*: accepted upstream and therefore deleted. -- Charles Plessy Mon, 13 Jul 2009 18:54:00 +0900 seaview (1:4.0-1) unstable; urgency=low * New upstream version - Computes and draws parsimony, distance and PhyML phylogenetic trees. - This new version unfortunately uses non-free files, and has therefore been removed from Debian, but is distributed in the ‘non-free’ section of its archive as a service its users. * debian/control: - Changed section to non-free/science. - Build-Depends on libxft-dev and libxext-dev. - Recommends phyml, muscle and clustalw. - Dropped dependency on xterm. - checked package conformance with Policy 3.8.1. - Updated description and removed reference from it. - Dropped build dependency on quilt. * debian/patches and debian/README.source removed: - 20-no-PDF-in-help.patch: upstream wording became true for Debian as well. - 21-location-of-seaview.help.patch: passing -DHELPFILENAME through debian/rules instead. - 40-seaview_align.sh-newline.patch, seaview_align-full_path.patch: seaview_align.sh was removed upstream. * debian/README.Debian deleted as well (obsolete). * debian/rules: - Makes `seaview' instead of `seaviewps' as (non-free) PDF support is not default anymore. - Indicate the location of the help file with: -DHELPFILENAME=\\\"/usr/share/doc/seaview/seaview.html\\\" - Uses `dh clean' and $(RM) macro in the clean target. - Uses `dh binary-arch` in the binary-arch target (created debian/docs, debian/seaview.examples, and debian/manpages). - Removed protein.mase from examples (removed upstream). - Removed patching facilities (no patches to apply anymore). * Removed `seaview_align.sh' from debian/install, as it was removed upstream. * debian/copyright: - Incremented year and version. - Link to the precise versions of the GNU GPL and LGPL. - Added the necessary disclaimers because SeaView became non-free. * Updated the manpage (debian/seaview.1*). * Registered the new help file with doc-base (debian/seaview.doc-base.help). -- Charles Plessy Wed, 27 May 2009 08:07:40 +0900 seaview (1:3.2-1) unstable; urgency=low * New upstream version: - Version 3.2: Database import can be done using a keyword. - Version 3.1: now use Fl_Native_File_Chooser. - Version 3.0: sequences can be imported from embl, genbank, swissprot if internet access. * debian/copyright: - Added the FL directory from Upstream sources. - Updated to the latest version of the machine-readable format. * debian/seaview.svg: vector icon made for SeaView and forwarded upstream. * debian/seaview.1*: added year 2008 to copyright statements. * Updated my email address. * debian/control, debian/compat: using Debhelper 7. * debian/control: added build-dependency on libpng12-dev and zlib1g-dev. * Experimental handling of bibliographic references: - debian/references contains a BibTeX-formatted reference. - debian/seaview.doc-base.references registers it for Doc-base in a "Bibliography" section to be proposed later. -- Charles Plessy Sun, 14 Dec 2008 22:58:57 +0900 seaview (1:2.4-1) unstable; urgency=low * New upstream version: - Version 2.3: corrected bug if adding/deleting/moving sequences when in 'view as proteins' mode. - Version 2.4: PHYLIP format: user can customize the max length of names. * debian/control: - Suggests: muscle, clustalw (non-free). Seaview detects if they are not present and grays the corresponding option. - Allows the upload by Debian Maintainers. - Checked that the package conforms to Policy 3.7.3. * debian/copyright: made machine-readable * MIME support: - debian/seaview.sharedmimeinfo associates .aln suffix and text/x-clustalw-alignment, debian/seaview.mime and debian/seaview.desktop associate seaview with this MIME type. - debian/rules executes dh_installmime. * debian/seaview.1.xml: increased version number to 2.4 (no other changes needed) * debian/seaview.1: rebuilt with DocBook XSL Stylesheets v1.73.2. -- Charles Plessy Sat, 12 Jan 2008 15:30:07 +0900 seaview (1:2.2-1) unstable; urgency=low [ Nelson A. de Oliveira ] * Updated watch file. [ Charles Plessy ] * New upstream release: - introduced interface to external alignment programs. - Work with several alignment windows; copy and paste sequence data between them. * Moved the Homepage: field out from the package's description. * Removed the XS- prefix of the Vcs fields in debian/control * Building the manpage offline: added seaview.1 to the package, and removed xsltproc, docbook-xml and docbook-xsl from the build-dependencies. * Patches to Seaview: - Refreshed. - Suppressed xterm_to_x-terminal-emulator.patch : strange communication problems happen between seaview and some terminal emulators, such as gnome-terminal or konsole. - Hardcoded the path to seaview_align.sh. -- Charles Plessy Sun, 18 Nov 2007 23:35:29 +0900 seaview (1:2.0-1) unstable; urgency=low * New upstream release. Use "Props:View as proteins" to align protein-coding DNA sequences. -- Charles Plessy Fri, 24 Aug 2007 00:02:33 +0900 seaview (20070615-1) unstable; urgency=low * New upstream release correcting problems with lowercase characters. * Converted the SVN repository which hosts the Debian source package to use the MergeWithUpstream option. * Moved examples to debian/examples. * Using 'quilt' as a patch management system instead of 'dpatch'. * Managing all the changes to the sources with quilt. * Adding $(misc-Depends) in debian/control. * Debian Menu transition: moving entry to Applications/Science/Biology. * Manpage: automatic date update; upgrading revision number. * Adding bibliographic reference to debian/copyright and debian/control. * Dropping 'config.h' patch from .diff.gz. -- Charles Plessy Sat, 21 Jul 2007 12:43:23 +0900 seaview (20070417-1) unstable; urgency=low * New upstream release adding processing of comments in FASTA format. -- Charles Plessy Sun, 29 Apr 2007 22:51:23 +0900 seaview (20070215-1) unstable; urgency=low * New upstream release, adding a new "Edit sequence" option in the Edit menu. * Updated manpage and converted it to Unicode. * Add Subversion repository URL to debian/control. * Including /usr/share/dpatch/dpatch.make in debian/rules. -- Charles Plessy Thu, 5 Apr 2007 09:38:08 +0900 seaview (20061005-1) unstable; urgency=low * New upstream release. The xpm icon and its sources are now included in. * New maintainer email: the previous one was not the intended mailing list. * Removing options passed to x-terminal-emulator if they are not a MUST in the policy chapter 11.8.3. * Improved manpage. -- Charles Plessy Sat, 28 Oct 2006 17:27:02 +0900 seaview (20060918-1) unstable; urgency=low * New upstream release (Closes: #357585) * Uses muscle instead of clustalw, therefore moving to main (Closes: #357587) * Update debian/copyright: the current licence of seaview is GPL (Closes: #357581) * Conforms to Standards version 3.7.2 and debhelper compatibility level 5. * Collective maintenance: Debian-Med Packaging Team is the new Maintainer. * Outputs PS instead of PDF as Debian can not support the PDFlib. * Uses x-terminal-emulator instead of xterm. * Support for freedesktop menus, and nice new icon. * Updated manpage. -- Charles Plessy Thu, 28 Sep 2006 12:13:53 +0900 seaview (20021127-4.1) unstable; urgency=medium * Non-maintainer upload. * Medium-urgency upload for RC bugfix. * Rebuild for the C++ ABI transition. Closes: #328175. -- Steve Langasek Thu, 22 Sep 2005 02:07:07 -0700 seaview (20021127-4) unstable; urgency=low * Cleaned up debian/rules file. * Conforms to Standards version 3.6.1. -- Brian R Furry Sun, 30 Nov 2003 00:04:02 +0000 seaview (20021127-3) unstable; urgency=low * Adopted by new maintainer; closes: 100261 * Conforms to Standards version 3.6.0. -- Brian R Furry Thu, 11 Sep 2003 21:12:40 -0400 seaview (20021127-2.2) unstable; urgency=low * NMU. * Downgrade dependency on clustalw to a recommendation, since we don't absolutely need it and it doesn't exist on mips(el). -- Aaron M. Ucko Tue, 17 Jun 2003 13:22:55 -0400 seaview (20021127-2.1) unstable; urgency=low * NMU. * Rebuild with Xft2-based FLTK (>= 1.1.3-2.1). -- Aaron M. Ucko Wed, 7 May 2003 20:36:02 -0400 seaview (20021127-2) unstable; urgency=low * QA upload. * Built with g++ 3.2 and libfltk1.1c102 (closes: #176147). -- Colin Watson Sat, 11 Jan 2003 02:50:11 +0000 seaview (20021127-1) unstable; urgency=low * QA upload. * New upstream release. * Conforms to Standards version 3.5.8. -- Matej Vela Sun, 1 Dec 2002 22:14:33 +0100 seaview (20021010-1) unstable; urgency=low * QA upload. * New upstream release. * Provide a config.h for old_file_chooser.cxx. * debian/menu: Use `section=Apps/Science hints=Biology' (see #162812). -- Matej Vela Sat, 19 Oct 2002 21:26:13 +0200 seaview (20020409-1) unstable; urgency=low * QA upload. * New upstream version (there's no version number in the sources). Closes: #128357. * align.cxx: - Handle temporary files securely (seaview 0.0 is not vulnerable). - Use x-terminal-emulator rather than xterm or rxvt. * seaview.1: - List NEXUS among the supported formats. - `-reducefonts' is no longer accepted. * Switched to debhelper 4. * Moved /usr/lib/seaview/seaview.help to /usr/share/seaview as architecture-independent. * Changed section from contrib/misc to contrib/science. * Added menu support. * debian/changelog: Remove obsolete Emacs local variables. * Conforms to Standards version 3.5.7. -- Matej Vela Fri, 20 Sep 2002 18:25:47 +0200 seaview (0.0-6.1) unstable; urgency=low * NMU * Update to build against XForms 0.89. (closes: Bug#118138) -- Doug Porter Mon, 12 Nov 2001 11:43:51 -0500 seaview (0.0-6) unstable; urgency=low * Maintainer set to Debian QA Group . -- Adrian Bunk Fri, 24 Aug 2001 23:58:22 +0200 seaview (0.0-5) unstable; urgency=low * Adopted by new maintainer; closes: #92802 * Moved all doc files to /usr/share/doc; closes: #91647 * Moved manpage to /usr/share/man; closes: #91064 * Updated to latest policy, and added Build-Depends. * Removed some unnecessary files in debian dir. -- Dr. Guenter Bechly Sat, 7 Apr 2001 18:00:30 +0200 seaview (0.0-4) unstable; urgency=low * A few examples added * New bug in seaview_align.sh, this time fixed seriously. -- Stephane Bortzmeyer Thu, 3 Jun 1999 10:07:55 +0200 seaview (0.0-3) unstable; urgency=low * Big bug in seaview_align.sh (not all parameters were passed). -- Stephane Bortzmeyer Wed, 26 May 1999 14:39:26 +0200 seaview (0.0-2) unstable; urgency=low * No longer depends on c-shell or xterm. Closes #34700 * Manual page. Closes #34615 -- Stephane Bortzmeyer Tue, 25 May 1999 14:42:15 +0200 seaview (0.0-1) unstable; urgency=low * Initial Release. -- Stephane Bortzmeyer Mon, 1 Mar 1999 16:41:51 +0100