[med-svn] r16905 - in trunk/packages/seaview/tags: . 1:4.5.1-1/debian 1:4.5.1-1/debian/patches
Charles Plessy
plessy at moszumanska.debian.org
Sat May 10 08:40:54 UTC 2014
Author: plessy
Date: 2014-05-10 08:40:54 +0000 (Sat, 10 May 2014)
New Revision: 16905
Added:
trunk/packages/seaview/tags/1:4.5.1-1/
trunk/packages/seaview/tags/1:4.5.1-1/debian/changelog
trunk/packages/seaview/tags/1:4.5.1-1/debian/control
trunk/packages/seaview/tags/1:4.5.1-1/debian/copyright
trunk/packages/seaview/tags/1:4.5.1-1/debian/patches/series
Removed:
trunk/packages/seaview/tags/1:4.5.1-1/debian/changelog
trunk/packages/seaview/tags/1:4.5.1-1/debian/control
trunk/packages/seaview/tags/1:4.5.1-1/debian/copyright
trunk/packages/seaview/tags/1:4.5.1-1/debian/patches/add-ldl.patch
trunk/packages/seaview/tags/1:4.5.1-1/debian/patches/series
trunk/packages/seaview/tags/1:4.5.1-1/debian/seaview.mime
Log:
[svn-buildpackage] Tagging seaview 1:4.5.1-1
Deleted: trunk/packages/seaview/tags/1:4.5.1-1/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog 2014-05-09 13:35:48 UTC (rev 16899)
+++ trunk/packages/seaview/tags/1:4.5.1-1/debian/changelog 2014-05-10 08:40:54 UTC (rev 16905)
@@ -1,492 +0,0 @@
-seaview (1:4.4.3-1) UNRELEASED; urgency=medium
-
- * New upstream version
- * debian/upstream -> debian/upstream/metadata
- * cme fix dpkg-control
-
- -- Andreas Tille <tille at debian.org> Tue, 25 Feb 2014 13:12:19 +0100
-
-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 <tille at debian.org> 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 <plessy at debian.org> 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 <simon at ruderich.org>
- 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 <tille at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> Thu, 25 Nov 2010 18:30:25 +0100
-
-seaview (1:4.2.9-1) unstable; urgency=low
-
- * New upstream version (Closes: #601244).
-
- -- Charles Plessy <plessy at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <vorlon at debian.org> 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 <bfurry at nac.net> 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 <bfurry at nac.net> 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 <ucko at debian.org> 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 <ucko at debian.org> 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 <cjwatson at debian.org> 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 <vela at debian.org> 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 <vela at debian.org> 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 <vela at debian.org> 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 <dsp at debian.org> Mon, 12 Nov 2001 11:43:51 -0500
-
-seaview (0.0-6) unstable; urgency=low
-
- * Maintainer set to Debian QA Group <packages at qa.debian.org>.
-
- -- Adrian Bunk <bunk at fs.tum.de> 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 <gbechly at debian.org> 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 <bortzmeyer at debian.org> 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 <bortzmeyer at debian.org> 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 <bortzmeyer at debian.org> Tue, 25 May 1999 14:42:15 +0200
-
-seaview (0.0-1) unstable; urgency=low
-
- * Initial Release.
-
- -- Stephane Bortzmeyer <bortzmeyer at debian.org> Mon, 1 Mar 1999 16:41:51 +0100
Copied: trunk/packages/seaview/tags/1:4.5.1-1/debian/changelog (from rev 16904, trunk/packages/seaview/trunk/debian/changelog)
===================================================================
--- trunk/packages/seaview/tags/1:4.5.1-1/debian/changelog (rev 0)
+++ trunk/packages/seaview/tags/1:4.5.1-1/debian/changelog 2014-05-10 08:40:54 UTC (rev 16905)
@@ -0,0 +1,499 @@
+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 <plessy at debian.org> 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 <tille at debian.org> 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 <plessy at debian.org> 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 <simon at ruderich.org>
+ 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 <tille at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> Thu, 25 Nov 2010 18:30:25 +0100
+
+seaview (1:4.2.9-1) unstable; urgency=low
+
+ * New upstream version (Closes: #601244).
+
+ -- Charles Plessy <plessy at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <charles-debian-nospam at plessy.org> 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 <vorlon at debian.org> 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 <bfurry at nac.net> 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 <bfurry at nac.net> 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 <ucko at debian.org> 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 <ucko at debian.org> 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 <cjwatson at debian.org> 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 <vela at debian.org> 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 <vela at debian.org> 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 <vela at debian.org> 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 <dsp at debian.org> Mon, 12 Nov 2001 11:43:51 -0500
+
+seaview (0.0-6) unstable; urgency=low
+
+ * Maintainer set to Debian QA Group <packages at qa.debian.org>.
+
+ -- Adrian Bunk <bunk at fs.tum.de> 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 <gbechly at debian.org> 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 <bortzmeyer at debian.org> 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 <bortzmeyer at debian.org> 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 <bortzmeyer at debian.org> Tue, 25 May 1999 14:42:15 +0200
+
+seaview (0.0-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Mon, 1 Mar 1999 16:41:51 +0100
Deleted: trunk/packages/seaview/tags/1:4.5.1-1/debian/control
===================================================================
--- trunk/packages/seaview/trunk/debian/control 2014-05-09 13:35:48 UTC (rev 16899)
+++ trunk/packages/seaview/tags/1:4.5.1-1/debian/control 2014-05-10 08:40:54 UTC (rev 16905)
@@ -1,38 +0,0 @@
-Source: seaview
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
-Section: non-free/science
-XS-Autobuild: yes
-Priority: optional
-Build-Depends: debhelper (>= 9),
- libfltk1.3-dev,
- libjpeg62-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/1:4.5.1-1/debian/control (from rev 16902, trunk/packages/seaview/trunk/debian/control)
===================================================================
--- trunk/packages/seaview/tags/1:4.5.1-1/debian/control (rev 0)
+++ trunk/packages/seaview/tags/1:4.5.1-1/debian/control 2014-05-10 08:40:54 UTC (rev 16905)
@@ -0,0 +1,38 @@
+Source: seaview
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+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.
Deleted: trunk/packages/seaview/tags/1:4.5.1-1/debian/copyright
===================================================================
--- trunk/packages/seaview/trunk/debian/copyright 2014-05-09 13:35:48 UTC (rev 16899)
+++ trunk/packages/seaview/tags/1:4.5.1-1/debian/copyright 2014-05-10 08:40:54 UTC (rev 16905)
@@ -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_4.4.0.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: 1996-2010 Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
-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
- jloup at gzip.org madler at alumni.caltech.edu
-
-Files: debian/*
-Copyright: © 1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
- © 2001 Dr. Guenter Bechly <gbechly at debian.org>
- © 2001 Adrian Bunk <bunk at fs.tum.de>
- © 2001 Doug Porter <dsp at debian.org>
- © 2002 Matej Vela <vela at debian.org>
- © 2003 Colin Watson <cjwatson at debian.org>
- © 2003 Aaron M. Ucko <ucko at debian.org>
- © 2003 Brian R Furry <bfurry at nac.net>
- © 2005 Steve Langasek <vorlon at debian.org>
- © 2007 Nelson A. de Oliveira <naoliv at debian.org>
-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/1:4.5.1-1/debian/copyright (from rev 16900, trunk/packages/seaview/trunk/debian/copyright)
===================================================================
--- trunk/packages/seaview/tags/1:4.5.1-1/debian/copyright (rev 0)
+++ trunk/packages/seaview/tags/1:4.5.1-1/debian/copyright 2014-05-10 08:40:54 UTC (rev 16905)
@@ -0,0 +1,126 @@
+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 <mgouy at biomserv.univ-lyon1.fr>
+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
+ jloup at gzip.org madler at alumni.caltech.edu
+
+Files: debian/*
+Copyright: © 1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
+ © 2001 Dr. Guenter Bechly <gbechly at debian.org>
+ © 2001 Adrian Bunk <bunk at fs.tum.de>
+ © 2001 Doug Porter <dsp at debian.org>
+ © 2002 Matej Vela <vela at debian.org>
+ © 2003 Colin Watson <cjwatson at debian.org>
+ © 2003 Aaron M. Ucko <ucko at debian.org>
+ © 2003 Brian R Furry <bfurry at nac.net>
+ © 2005 Steve Langasek <vorlon at debian.org>
+ © 2007 Nelson A. de Oliveira <naoliv at debian.org>
+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/1:4.5.1-1/debian/patches/add-ldl.patch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/add-ldl.patch 2014-05-09 13:35:48 UTC (rev 16899)
+++ trunk/packages/seaview/tags/1:4.5.1-1/debian/patches/add-ldl.patch 2014-05-10 08:40:54 UTC (rev 16905)
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-LastChanged: Mon, 12 Aug 2013 13:03:12 +0200
-Description: The build was lacking -ldl for successfull linking
-
---- a/Makefile
-+++ b/Makefile
-@@ -17,7 +17,7 @@ FLTK = /usr/include
- #IFLTK = -I$(FLTK)
- #LFLTK = -L$(FLTK)/lib
-
--EXTRALIBS = -lXft -lXext -lfontconfig -ljpeg -lpng -lXinerama $(LPDF)
-+EXTRALIBS = -lXft -lXext -lfontconfig -ljpeg -lpng -lXinerama $(LPDF) -ldl
-
- CC = gcc
- CXX = g++
Deleted: trunk/packages/seaview/tags/1:4.5.1-1/debian/patches/series
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/series 2014-05-09 13:35:48 UTC (rev 16899)
+++ trunk/packages/seaview/tags/1:4.5.1-1/debian/patches/series 2014-05-10 08:40:54 UTC (rev 16905)
@@ -1,2 +0,0 @@
-#use-dpkg-buildflags.patch
-add-ldl.patch
Copied: trunk/packages/seaview/tags/1:4.5.1-1/debian/patches/series (from rev 16901, trunk/packages/seaview/trunk/debian/patches/series)
===================================================================
--- trunk/packages/seaview/tags/1:4.5.1-1/debian/patches/series (rev 0)
+++ trunk/packages/seaview/tags/1:4.5.1-1/debian/patches/series 2014-05-10 08:40:54 UTC (rev 16905)
@@ -0,0 +1 @@
+#use-dpkg-buildflags.patch
Deleted: trunk/packages/seaview/tags/1:4.5.1-1/debian/seaview.mime
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.mime 2014-05-09 13:35:48 UTC (rev 16899)
+++ trunk/packages/seaview/tags/1:4.5.1-1/debian/seaview.mime 2014-05-10 08:40:54 UTC (rev 16905)
@@ -1 +0,0 @@
-text/x-clustalw-alignment; seaview -save clustal '%s'; description=Clustal W multiple sequence alignment; nametemplate=%s.aln
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