Author: plessy Date: 2014-09-21 11:02:50 +0000 (Sun, 21 Sep 2014) New Revision: 18082
Added: trunk/packages/seaview/tags/1:4.5.2-1/ trunk/packages/seaview/tags/1:4.5.2-1/debian/changelog trunk/packages/seaview/tags/1:4.5.2-1/debian/control trunk/packages/seaview/tags/1:4.5.2-1/debian/copyright trunk/packages/seaview/tags/1:4.5.2-1/debian/upstream/metadata Removed: trunk/packages/seaview/tags/1:4.5.2-1/debian/changelog trunk/packages/seaview/tags/1:4.5.2-1/debian/control trunk/packages/seaview/tags/1:4.5.2-1/debian/copyright trunk/packages/seaview/tags/1:4.5.2-1/debian/dirs trunk/packages/seaview/tags/1:4.5.2-1/debian/upstream/metadata Log: [svn-buildpackage] Tagging seaview 1:4.5.2-1 Deleted: trunk/packages/seaview/tags/1:4.5.2-1/debian/changelog =================================================================== --- trunk/packages/seaview/trunk/debian/changelog 2014-09-20 03:39:49 UTC (rev 18077) +++ trunk/packages/seaview/tags/1:4.5.2-1/debian/changelog 2014-09-21 11:02:50 UTC (rev 18082) @@ -1,499 +0,0 @@ -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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> - 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Thu, 25 Nov 2010 18:30:25 +0100 - -seaview (1:4.2.9-1) unstable; urgency=low - - * New upstream version (Closes: #601244). - - -- Charles Plessy <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 12 Nov 2001 11:43:51 -0500 - -seaview (0.0-6) unstable; urgency=low - - * Maintainer set to Debian QA Group <[email protected]>. - - -- Adrian Bunk <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Tue, 25 May 1999 14:42:15 +0200 - -seaview (0.0-1) unstable; urgency=low - - * Initial Release. - - -- Stephane Bortzmeyer <[email protected]> Mon, 1 Mar 1999 16:41:51 +0100 Copied: trunk/packages/seaview/tags/1:4.5.2-1/debian/changelog (from rev 18081, trunk/packages/seaview/trunk/debian/changelog) =================================================================== --- trunk/packages/seaview/tags/1:4.5.2-1/debian/changelog (rev 0) +++ trunk/packages/seaview/tags/1:4.5.2-1/debian/changelog 2014-09-21 11:02:50 UTC (rev 18082) @@ -0,0 +1,506 @@ +seaview (1:4.5.2-1) unstable; urgency=medium + + * New upstream version. + * New homepage. + + -- Charles Plessy <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> + 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Thu, 25 Nov 2010 18:30:25 +0100 + +seaview (1:4.2.9-1) unstable; urgency=low + + * New upstream version (Closes: #601244). + + -- Charles Plessy <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 12 Nov 2001 11:43:51 -0500 + +seaview (0.0-6) unstable; urgency=low + + * Maintainer set to Debian QA Group <[email protected]>. + + -- Adrian Bunk <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Tue, 25 May 1999 14:42:15 +0200 + +seaview (0.0-1) unstable; urgency=low + + * Initial Release. + + -- Stephane Bortzmeyer <[email protected]> Mon, 1 Mar 1999 16:41:51 +0100 Deleted: trunk/packages/seaview/tags/1:4.5.2-1/debian/control =================================================================== --- trunk/packages/seaview/trunk/debian/control 2014-09-20 03:39:49 UTC (rev 18077) +++ trunk/packages/seaview/tags/1:4.5.2-1/debian/control 2014-09-21 11:02:50 UTC (rev 18082) @@ -1,38 +0,0 @@ -Source: seaview -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Charles Plessy <[email protected]>, - Andreas Tille <[email protected]> -Section: non-free/science -XS-Autobuild: yes -Priority: optional -Build-Depends: debhelper (>= 9), - libfltk1.3-dev, - libjpeg8-dev, - libpng-dev, - libxft-dev, - libxext-dev, - libxinerama-dev, - zlib1g-dev -Standards-Version: 3.9.5 -Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/seaview/trunk/ -Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/seaview/trunk/ -Homepage: http://pbil.univ-lyon1.fr/software/seaview.html - -Package: seaview -Architecture: i386 amd64 armel -Depends: ${shlibs:Depends}, - ${misc:Depends} -Recommends: clustalo, - muscle, - phyml -Description: Multiplatform interface for sequence alignment and phylogeny - SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, - PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. - Alignments can be manually edited. It drives the programs Muscle or Clustal - Omega for multiple sequence alignment, and also allows one to use any external - alignment algorithm able to read and write FASTA-formatted files. It computes - phylogenetic trees by parsimony using PHYLIP's dnapars/protpars algorithm, by - distance with NJ or BioNJ algorithms on a variety of evolutionary distances, or - by maximum likelihood using the program PhyML 3.0. SeaView draws phylogenetic - trees on screen or PostScript files, and allows one to download sequences from - EMBL/GenBank/UniProt using the Internet. Copied: trunk/packages/seaview/tags/1:4.5.2-1/debian/control (from rev 18079, trunk/packages/seaview/trunk/debian/control) =================================================================== --- trunk/packages/seaview/tags/1:4.5.2-1/debian/control (rev 0) +++ trunk/packages/seaview/tags/1:4.5.2-1/debian/control 2014-09-21 11:02:50 UTC (rev 18082) @@ -0,0 +1,38 @@ +Source: seaview +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Charles Plessy <[email protected]>, + Andreas Tille <[email protected]> +Section: non-free/science +XS-Autobuild: yes +Priority: optional +Build-Depends: debhelper (>= 9), + libfltk1.3-dev, + libjpeg8-dev, + libpng-dev, + libxft-dev, + libxext-dev, + libxinerama-dev, + zlib1g-dev +Standards-Version: 3.9.5 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/seaview/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/seaview/trunk/ +Homepage: http://doua.prabi.fr/software/seaview + +Package: seaview +Architecture: i386 amd64 armel +Depends: ${shlibs:Depends}, + ${misc:Depends} +Recommends: clustalo, + muscle, + phyml +Description: Multiplatform interface for sequence alignment and phylogeny + SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, + PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. + Alignments can be manually edited. It drives the programs Muscle or Clustal + Omega for multiple sequence alignment, and also allows one to use any external + alignment algorithm able to read and write FASTA-formatted files. It computes + phylogenetic trees by parsimony using PHYLIP's dnapars/protpars algorithm, by + distance with NJ or BioNJ algorithms on a variety of evolutionary distances, or + by maximum likelihood using the program PhyML 3.0. SeaView draws phylogenetic + trees on screen or PostScript files, and allows one to download sequences from + EMBL/GenBank/UniProt using the Internet. Deleted: trunk/packages/seaview/tags/1:4.5.2-1/debian/copyright =================================================================== --- trunk/packages/seaview/trunk/debian/copyright 2014-09-20 03:39:49 UTC (rev 18077) +++ trunk/packages/seaview/tags/1:4.5.2-1/debian/copyright 2014-09-21 11:02:50 UTC (rev 18082) @@ -1,126 +0,0 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.5.1.tar.gz -Disclamer: This package is not part of the Debian operating system. - The seaview source and binary Debian packages are part of the “non-free” area - in our archive. The packages in this area are not part of the Debian system, - although they have been configured for use with Debian. We nevertheless support - the use of the seaview source and binary Debian packages and provide - infrastructure for non-free packages (such as our bug tracking system and - mailing lists). The licences of SeaView do not forbid Debian from using - autobuilders to create binary packages. - -Files: * -Copyright: 1996-2014 Manolo Gouy <[email protected]> -License: GPL-3+ with PHYLIP exception - This program, except where indicated, is free software; you can redistribute it and/or - modify it under the terms of the GNU General Public - License as published by the Free Software Foundation; - either version 3 of the License, or (at your option) any later version.. - . - Two files (dnapars.c and protpars.c) have a distinct license - which authorizes distribution that does not generate revenue. - . - Three files (bionj.c, phyml_util.c and phyml_util.h) are also covered by the - GNU General Public License but are copyright Stephane Guindon. - . - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - General Public License for more details. - . - Additional permission under GNU GPL version 3 section 7 - . - If you modify this Program, or any covered work, by linking or combining it with PHYLIP - (or a modified version of that library), containing parts covered by the terms of - the University of Washington license, the licensor of this Program grants you additional - permission to convey the resulting work. - . - A copy of the GNU General Public License is available - from http://www.gnu.org/licenses/gpl.txt . -Comment: - On Debian systems, the complete text of the GNU General Public License version - 3 can be found in ‘/usr/share/common-licenses/GPL-3’. - -Files: csrc/bionj.c csrc/phyml_util.h -Copyright: © Stephane Guindon. Oct 2003 onward -License: GPL-2+ with PHYLIP exception - This program is free software; you can redistribute it and/or modify it under the terms of the - GNU General Public License as published by the Free Software Foundation; either version 2 of - the License, or (at your option) any later version. - . - This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without - even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - General Public License for more details. - . - You should have received a copy of the GNU General Public License along with this program; if not, - see <http://www.gnu.org/licenses>. - . - Linking PHYML statically or dynamically with other modules is making a combined work based on PHYML. - Thus, the terms and conditions of the GNU General Public License cover the whole combination. - . - In addition, as a special exception, the copyright holders of PHYML give you permission to combine - PHYML with free software programs or libraries that are released under the GNU LGPL and with code - included in the standard release of PHYLIP under the University of Washington license (or modified - versions of such code, with unchanged license). You may copy and distribute such a system following - the terms of the GNU GPL for PHYML and the licenses of the other code concerned. - . - Note that people who make modified versions of PHYML are not obligated to grant this special exception - for their modified versions; it is their choice whether to do so. The GNU General Public License gives - permission to release a modified version without this exception; this exception also makes it possible - to release a modified version which carries forward this exception. - -Files: csrc/dnapars.c csrc/protpars.c -Copyright: © 1980-2008. University of Washington -License: PHYLIP - (c) Copyright 1980-2008. University of Washington. All rights reserved. Permission is - granted to reproduce, perform, and modify these programs and documentation files. - Permission is granted to distribute or provide access to these programs provided - that this copyright notice is not removed, the programs are not integrated with or - called by any product or service that generates revenue, and that your distribution - of these documentation files and programs are free. Any modified versions of these - materials that are distributed or accessible shall indicate that they are based on - these programs. Institutions of higher education are granted permission to - distribute this material to their students and staff for a fee to recover - distribution costs. Permission requests for any other distribution of these - program should be directed to license (at) u.washington.edu . - -Files: zconf.h -Copyright: © 1995-1998 Jean-loup Gailly and Mark Adler -License: zlib - This software is provided 'as-is', without any express or implied - warranty. In no event will the authors be held liable for any damages - arising from the use of this software. - . - Permission is granted to anyone to use this software for any purpose, - including commercial applications, and to alter it and redistribute it - freely, subject to the following restrictions: - . - 1. The origin of this software must not be misrepresented; you must not - claim that you wrote the original software. If you use this software - in a product, an acknowledgment in the product documentation would be - appreciated but is not required. - 2. Altered source versions must be plainly marked as such, and must not be - misrepresented as being the original software. - 3. This notice may not be removed or altered from any source distribution. - . - Jean-loup Gailly Mark Adler - [email protected] [email protected] - -Files: debian/* -Copyright: © 1999 Stephane Bortzmeyer <[email protected]> - © 2001 Dr. Guenter Bechly <[email protected]> - © 2001 Adrian Bunk <[email protected]> - © 2001 Doug Porter <[email protected]> - © 2002 Matej Vela <[email protected]> - © 2003 Colin Watson <[email protected]> - © 2003 Aaron M. Ucko <[email protected]> - © 2003 Brian R Furry <[email protected]> - © 2005 Steve Langasek <[email protected]> - © 2007 Nelson A. de Oliveira <[email protected]> -License: unknown - The Copyright field above lists the developers who uploaded the package before - this machine-readable file was assembled. - . - Please treat the contributions of Charles Plessy as if they were in the public - domain. - Copied: trunk/packages/seaview/tags/1:4.5.2-1/debian/copyright (from rev 18078, trunk/packages/seaview/trunk/debian/copyright) =================================================================== --- trunk/packages/seaview/tags/1:4.5.2-1/debian/copyright (rev 0) +++ trunk/packages/seaview/tags/1:4.5.2-1/debian/copyright 2014-09-21 11:02:50 UTC (rev 18082) @@ -0,0 +1,97 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.5.1.tar.gz +Disclamer: This package is not part of the Debian operating system. + The seaview source and binary Debian packages are part of the “non-free” area + in our archive. The packages in this area are not part of the Debian system, + although they have been configured for use with Debian. We nevertheless support + the use of the seaview source and binary Debian packages and provide + infrastructure for non-free packages (such as our bug tracking system and + mailing lists). The licences of SeaView do not forbid Debian from using + autobuilders to create binary packages. + +Files: * +Copyright: 1996-2014 Manolo Gouy <[email protected]> +License: GPL-3+ with PHYLIP exception + This program, except where indicated, is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public + License as published by the Free Software Foundation; + either version 3 of the License, or (at your option) any later version.. + . + Two files (dnapars.c and protpars.c) have a distinct license + which authorizes distribution that does not generate revenue. + . + Three files (bionj.c, phyml_util.c and phyml_util.h) are also covered by the + GNU General Public License but are copyright Stephane Guindon. + . + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + General Public License for more details. + . + Additional permission under GNU GPL version 3 section 7 + . + If you modify this Program, or any covered work, by linking or combining it with PHYLIP + (or a modified version of that library), containing parts covered by the terms of + the University of Washington license, the licensor of this Program grants you additional + permission to convey the resulting work. + . + A copy of the GNU General Public License is available + from http://www.gnu.org/licenses/gpl.txt . +Comment: + On Debian systems, the complete text of the GNU General Public License version + 3 can be found in ‘/usr/share/common-licenses/GPL-3’. + +Files: csrc/bionj.c csrc/phyml_util.h +Copyright: © Stephane Guindon. Oct 2003 onward +License: GPL-2+ with PHYLIP exception + This program is free software; you can redistribute it and/or modify it under the terms of the + GNU General Public License as published by the Free Software Foundation; either version 2 of + the License, or (at your option) any later version. + . + This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + General Public License for more details. + . + You should have received a copy of the GNU General Public License along with this program; if not, + see <http://www.gnu.org/licenses>. + . + Linking PHYML statically or dynamically with other modules is making a combined work based on PHYML. + Thus, the terms and conditions of the GNU General Public License cover the whole combination. + . + In addition, as a special exception, the copyright holders of PHYML give you permission to combine + PHYML with free software programs or libraries that are released under the GNU LGPL and with code + included in the standard release of PHYLIP under the University of Washington license (or modified + versions of such code, with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for PHYML and the licenses of the other code concerned. + . + Note that people who make modified versions of PHYML are not obligated to grant this special exception + for their modified versions; it is their choice whether to do so. The GNU General Public License gives + permission to release a modified version without this exception; this exception also makes it possible + to release a modified version which carries forward this exception. + +Files: csrc/dnapars.c csrc/protpars.c +Copyright: © 1993–2004 University of Washington +License: PHYLIP + version 3.6 (c) Copyright 1993-2004 by the University of Washington. + Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. + Permission is granted to copy and use this program provided no fee is + charged for it and provided that this copyright notice is not removed. + +Files: debian/* +Copyright: © 1999 Stephane Bortzmeyer <[email protected]> + © 2001 Dr. Guenter Bechly <[email protected]> + © 2001 Adrian Bunk <[email protected]> + © 2001 Doug Porter <[email protected]> + © 2002 Matej Vela <[email protected]> + © 2003 Colin Watson <[email protected]> + © 2003 Aaron M. Ucko <[email protected]> + © 2003 Brian R Furry <[email protected]> + © 2005 Steve Langasek <[email protected]> + © 2007 Nelson A. de Oliveira <[email protected]> +License: unknown + The Copyright field above lists the developers who uploaded the package before + this machine-readable file was assembled. + . + Please treat the contributions of Charles Plessy as if they were in the public + domain. + Deleted: trunk/packages/seaview/tags/1:4.5.2-1/debian/dirs =================================================================== --- trunk/packages/seaview/trunk/debian/dirs 2014-09-20 03:39:49 UTC (rev 18077) +++ trunk/packages/seaview/tags/1:4.5.2-1/debian/dirs 2014-09-21 11:02:50 UTC (rev 18082) @@ -1,2 +0,0 @@ -/usr/share/pixmaps -/usr/share/applications Deleted: trunk/packages/seaview/tags/1:4.5.2-1/debian/upstream/metadata =================================================================== --- trunk/packages/seaview/trunk/debian/upstream/metadata 2014-09-20 03:39:49 UTC (rev 18077) +++ trunk/packages/seaview/tags/1:4.5.2-1/debian/upstream/metadata 2014-09-21 11:02:50 UTC (rev 18082) @@ -1,32 +0,0 @@ -Contact: Manolo Gouy <[email protected]> -Documentation: http://pbil.univ-lyon1.fr/software/seaview_data/seaview -Downloads: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/ -Homepage: http://pbil.univ-lyon1.fr/software/seaview -Name: SeaView -Reference: - - author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier - title: > - SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building - journal: Mol Biol Evol - volume: 27 - number: 2 - pages: 221-224 - year: 2010 - PMID: 19854763 - DOI: 10.1093/molbev/msp259 - URL: http://mbe.oxfordjournals.org/cgi/content/abstract/27/2/221 - eprint: http://mbe.oxfordjournals.org/cgi/reprint/27/2/221.pdf - - Author: N. Galtier and M. Gouy and C. Gautier - Title: SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny - Journal: Comput. Applic. Biosci - Volume: 12 - Number: 6 - Pages: 543-548 - Year: 1996 - PMID: 9021275 - DOI: 10.1093/bioinformatics/12.6.543 - URL: http://bioinformatics.oxfordjournals.org/content/12/6/543.abstract - eprint: http://bioinformatics.oxfordjournals.org/content/12/6/543.full.pdf+html -Screenshots: - - http://pbil.univ-lyon1.fr/binaries/seaview4.png - - http://pbil.univ-lyon1.fr/binaries/seaview-tree.png Copied: trunk/packages/seaview/tags/1:4.5.2-1/debian/upstream/metadata (from rev 18079, trunk/packages/seaview/trunk/debian/upstream/metadata) =================================================================== --- trunk/packages/seaview/tags/1:4.5.2-1/debian/upstream/metadata (rev 0) +++ trunk/packages/seaview/tags/1:4.5.2-1/debian/upstream/metadata 2014-09-21 11:02:50 UTC (rev 18082) @@ -0,0 +1,30 @@ +Contact: Manolo Gouy <[email protected]> +Documentation: http://doua.prabi.fr/software/seaview_data/seaview +Name: SeaView +Reference: + - author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier + title: > + SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building + journal: Mol Biol Evol + volume: 27 + number: 2 + pages: 221-224 + year: 2010 + PMID: 19854763 + DOI: 10.1093/molbev/msp259 + URL: http://mbe.oxfordjournals.org/cgi/content/abstract/27/2/221 + eprint: http://mbe.oxfordjournals.org/cgi/reprint/27/2/221.pdf + - Author: N. Galtier and M. Gouy and C. Gautier + Title: SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny + Journal: Comput. Applic. Biosci + Volume: 12 + Number: 6 + Pages: 543-548 + Year: 1996 + PMID: 9021275 + DOI: 10.1093/bioinformatics/12.6.543 + URL: http://bioinformatics.oxfordjournals.org/content/12/6/543.abstract + eprint: http://bioinformatics.oxfordjournals.org/content/12/6/543.full.pdf+html +Screenshots: + - http://doua.prabi.fr/binaries/seaview4 + - http://doua.prabi.fr/binaries/seaview-tree _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
