debian/0000755000000000000000000000000012214326216007165 5ustar debian/changelog0000644000000000000000000002236512214326216011047 0ustar njplot (2.4-2build1) saucy; urgency=low * No change rebuild against libvibrant6b (LP: #1222965) -- Stefano Rivera Thu, 12 Sep 2013 13:58:35 +0200 njplot (2.4-2) unstable; urgency=low [ Aaron M. Ucko ] * Team upload. * Eliminate extraneous build dependencies, most critically lesstif2-dev, as Vibrant has switched to Motif now that it's free. (Closes: #710205.) * debian/rules: Contrive to pass hardened CPPFLAGS and LDFLAGS. * Standards-Version: 3.9.4. (Already compliant.) [ Charles Plessy ] * debian/patches/fix-underlinking.patch (new): Explicitly link njplot and unrooted against -lm for compatibility with strict linkers (as on Ubuntu) that default to --no-copy-dt-needed. (Closes: #701756. LP: #1133488.) [ Andreas Tille ] * debian/upstream: Added citation information -- Aaron M. Ucko Wed, 29 May 2013 18:41:31 -0400 njplot (2.4-1) unstable; urgency=low * New upstream release integrating Debian patches. * Removed debian/patches. * Updated debian/copyright to latest format and removed superfluous fields. * Simplified Homepage URL (debian/control). -- Charles Plessy Wed, 04 Jan 2012 19:02:39 +0900 njplot (2.3-4) unstable; urgency=low * Fix FTBFS with -Werror=format-security (Thanks for the patch to Ilya Barygin ) Closes: #653001 * debian/control: - Standards-Version: 3.9.2 (no changes needed) - Fixed Vcs fields - Removed article in short description * Debhelper 8 (control+compat) -- Andreas Tille Fri, 23 Dec 2011 13:58:26 +0100 njplot (2.3-3) unstable; urgency=low * Standards-Version: 3.9.1 (no changes needed) * debian/source/format: 3.0 (quilt) * debian/rules: Do not use deprecated variable DEB_OPT_FLAG any more but use CFLAGS instead Closes: #614432 * debian/patches: Do not link against unused libs (X11, Xmu) -- Andreas Tille Tue, 22 Feb 2011 13:15:08 +0100 njplot (2.3-2) unstable; urgency=low * debian/control: - Mention that the trees are phylogenetic and in Newick format. Closes: #517010 - Added missing comma in the Depends field. * debian/get-orig-source: obsolete, removed. (Also in debian/rules). -- Charles Plessy Wed, 25 Feb 2009 22:35:05 +0900 njplot (2.3-1) unstable; urgency=low * New upstream release: NJplot can draw multibranched trees with or without branch lengths. * debian/rules: uses 'DEB_OPT_FLAG +=' instead of 'DEB_OPT_FLAG =' so that CDBS still manages the optimisation levels and the 'noopt' build option. * debian/control: depend on ${misc:Depends} to better use Debhelper. * debian/dirs: useless therefore deleted. * Using Debhelper 7 (debian/compat, debian/control). * Checked compliance to Policy 3.8.0 (no changes needed). * debian/copyright converted to machine-readable format. * Updated my email address. -- Charles Plessy Sat, 03 Jan 2009 23:10:31 +0100 njplot (2.2-1) unstable; urgency=low [ Andreas Tille ] * Added Vcs-Browser, Vcs-Svn * Added -DHELPFILENAME=\"/usr/share/njplot/njplot.help\" to build options [ Charles Plessy ] * New upstream version: - NJplot can display several tree windows simultaneously. * debian/control: - added myself as Uploader. - allowed the upload by Debian Maintainers. - Removed the [biology] tag and the Homepage pseudo-field from the description. - Checked conformance with Policy 3.7.3. - Dropped build dependency on dpatch * MIME support: - debian/njplot.sharedmimeinfo declares that .phb and .ph files are Clustal W phylogenetic trees. - debian/njplot.mime, debian/njplot.desktop and debian/unrooted.desktop declare that NJplot and Unrooted can open Clustal W phylogenetic trees. * Removed debian/README.Debian, as its contents were obsolete. -- Andreas Tille Tue, 15 Jan 2008 09:39:01 +0100 njplot (2.0-2) unstable; urgency=low [ Nelson A. de Oliveira ] * Fixed watch file Closes: #450104 -- Andreas Tille Wed, 07 Nov 2007 08:04:06 +0100 njplot (2.0-1) unstable; urgency=low * New upstream version that started proper version numbering * debian/menu: Apps/Science -> Applications/Science/Biology * Added debian/watch because upstream started proper version numbering * Upstream included man pages, so remove debian/*.1 -- Andreas Tille Tue, 09 Oct 2007 22:42:13 +0200 njplot (0.20070618-1) unstable; urgency=low * New upstream version * New debian/README.Debian explaining the issue how a rebuilt upstream source is needed. * debian/get-orig-source: Code to obtain the orig.tar.gz * debian/control: Replaced XBCS-URL by Homepage * Switched to cdbs, dpatch * debian/control: team maintenance Maintainer: Debian-Med Packaging Team Uploaders: Andreas Tille -- Andreas Tille Mon, 01 Oct 2007 20:45:37 +0200 njplot (0.20060606-3) unstable; urgency=low * Fixed .desktop file (Thanks to Adri2000 ) Closes: #401231 -- Andreas Tille Tue, 12 Dec 2006 08:08:34 +0100 njplot (0.20060606-2) unstable; urgency=low * Added desktop files (thanks to Charles Plessy) Closes: #380633 -- Andreas Tille Tue, 1 Aug 2006 08:07:30 +0200 njplot (0.20060606-1) unstable; urgency=low * New upstream version * Removed 'binary' from package description because njplot now can draw all types of trees * Replace dependencies "libvibrant6-dev | vibrant-dev, ncbi-tools6-dev" by libncbi6-dev * Replace dependency lesstif-dev by lesstif2-dev Closes: #374230 * Standards-Version: 3.7.2 - no changes needed * debian/compat: 5 -- Andreas Tille Mon, 10 Jul 2006 08:25:26 +0200 njplot (0.20051109-1) unstable; urgency=low * New upstream version * Build-Depends: libxt-dev instead of xlibs-dev Closes: #347123 * Standards-Version: 3.6.2, no changes necessary -- Andreas Tille Mon, 9 Jan 2006 08:21:08 +0100 njplot (0.20041129-2) unstable; urgency=low * According to the ncbi maintainer switched back from priority extra to optional because the package depends now are adjusted * Build-Depends now libvibrant6-dev | vibrant-dev -- Andreas Tille Wed, 1 Dec 2004 22:04:35 +0100 njplot (0.20041129-1) unstable; urgency=low * Fixed upstream version * Standards-Version: 3.6.1.1 * Did not patched upstream makefile that much but moved own patches to debian/rules * Package was optional and has a Depends on vibrant6 (>= 6.1.20020828) which is extra --> moved package to extra * Added quotes to menu items * Added information from the homepage -- Andreas Tille Wed, 1 Dec 2004 14:56:41 +0100 njplot (0.20030331-1) unstable; urgency=low * What difference does it make to the dead, the orphans and the homeless, whether the mad destruction is wrought under the name of totalitarianism or the holy name of liberty or democracy? -- Mahatma Gandhi (1869 - 1948), "Non-Violence in Peace and War" * New upstream version. -- Andreas Tille Wed, 23 Apr 2003 15:19:03 +0200 njplot (0.20021017-1) unstable; urgency=low * The "I'm against war" release Mankind must put an end to war before war puts an end to mankind. -- John F. Kennedy * New upstream release * New maintainer * Build-Depends: debhelper (>= 4.0) * Standards-Version: 3.5.9 * debian/compat now stores debhelper compatibility version * Compliant to developers reference "6.3.2. Upstream home page" and XBCS-URL: http://pbil.univ-lyon1.fr/software/njplot.html * Added README from FTP-Server to docs * Added examples from FTP-Server to examples * use dh_installman instead of dh_installmanpages * moved njplot.help to /usr/share/njplot * added menu -- Andreas Tille Mon, 14 Apr 2003 08:06:48 +0200 njplot (0.0-4) unstable; urgency=low * Added CPPFLAGS=-DWIN_MOTIF in rules file (closes: #134083) -- Francesco Paolo Lovergine Mon, 18 Feb 2002 13:17:50 +0100 njplot (0.0-3) unstable; urgency=low * Maintainer set to Debian QA Group . -- Adrian Bunk Fri, 24 Aug 2001 23:36:54 +0200 njplot (0.0-2) unstable; urgency=low * Package adopted by new maintainer; closes: #92803, #48172 * Removed some unnecessary files in the debian directory. * Updated to latest standards version (changed control and rules). * Added Build-Depends; closes: #84579 * Modified dirs and copyright file. * Wrote manpages for njplot and unrooted; closes: #34614 * Shifted package from section x11 to science. -- Dr. Guenter Bechly Tue, 10 Apr 2001 18:13:39 +0200 njplot (0.0-1.1) unstable; urgency=low * NMU. * Recompile against lesstif1. Closes: #48172 * Updated to standards-version 3.0.1. * FHS compliant. * Lintian 1.9.2 clean. -- Adam Heath Mon, 25 Oct 1999 16:32:42 -0500 njplot (0.0-1) unstable; urgency=low * Initial Release. -- Stephane Bortzmeyer Sat, 6 Mar 1999 20:46:41 +0100 Local variables: mode: debian-changelog End: debian/rules0000755000000000000000000000100112151501202010223 0ustar #!/usr/bin/make -f # debian/rules for njplot using cdbs # Andreas Tille , GPL include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/makefile.mk # despite the fact that cdbs should use distclean as default, the clean target is called # so force distclean DEB_MAKE_CLEAN_TARGET = distclean DEB_MAKE_INVOKE += CC='gcc $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS)' CFLAGS = -c -I/usr/include/ncbi -DNO_PDF -DWIN_MOTIF \ -DHELPFILENAME=\\\"/usr/share/njplot/njplot.help\\\" debian/njplot.mime0000644000000000000000000000026512151261451011346 0ustar text/x-clustalw-tree; njplot '%s'; description=Clustal W Phylogenetic Tree ; nametemplate=%s.phb chemical/njplot; njplot '%s' ; description=Phylogenetic Tree ; nametemplate=%s.phb debian/watch0000644000000000000000000000012012151261451010206 0ustar version=3 ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplot-(.*)\.tar.gz debian/njplot.sharedmimeinfo0000644000000000000000000000107512151261451013411 0ustar Phylogenetic tree in Clustal W format Arbre phylogénétique au format Clustal W Phylogenetischer Baum im Clustal W Format debian/unrooted.desktop0000644000000000000000000000140212151261451012413 0ustar [Desktop Entry] Version=1.0 Terminal=false Icon=unrooted Exec=unrooted %f Name=NJplot (unrooted) Name[en]=NJplot (unrooted) Name[fr]=NJplot (non enraciné) Name[pt_BR]=NJplot (não enraizado) GenericName=Tree Plotter GenericName[en]=Tree Plotter GenericName[fr]=Traceur d'arbres GenericName[pt_BR]=Plotador de árvores Comment=Displays and exports in PostScript format unrooted phylogenetic trees Comment[en]=Displays and exports in PostScript format unrooted phylogenetic trees Comment[fr]=Affiche et exporte au format PostScript des arbres phyolgénétiques non enracinés Comment[pt_BR]=Exibe e exporta em formato PostScript árvores filogenéticas não enraizadas Type=Application Categories=Biology;Science;Education; MimeType=text/x-clustalw-tree;chemical/njplot; debian/install0000644000000000000000000000017612151261451010561 0ustar njplot unrooted newickto* usr/bin njplot.help usr/share/njplot debian/*.desktop usr/share/applications debian/compat0000644000000000000000000000000212151501424010357 0ustar 8 debian/source/0000755000000000000000000000000012151502461010463 5ustar debian/source/format0000644000000000000000000000001412151261451011672 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000151212151261451011116 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplot-2.4.tar.gz Files: * Copyright: © 1996–2009 Manolo Gouy License: Artistic On Debian systems, the complete text of the Artistic Licence can be found in /usr/share/common-licenses/Artistic file. Files: debian/* Copyright: © 2008–2011 Charles Plessy © 2003–2008 Andreas Tille © 2002 Francesco Paolo Lovergine © 2001 Adrian Bunk © 2001 Dr. Guenter Bechly © 1999 Adam Heath © 1999 Stephane Bortzmeyer License: Same See above debian/njplot.desktop0000644000000000000000000000121212151261451012061 0ustar [Desktop Entry] Version=1.0 Terminal=false Icon=njplot Exec=njplot %f Name=NJplot GenericName=Tree Plotter GenericName[en]=Tree Plotter GenericName[fr]=Traceur d'arbres GenericName[pt_BR]=Plotador de árvores Comment=Displays, modifies and exports in PostScript format phylogenetic trees Comment[en]=Displays, modifies and exports in PostScript format phylogenetic trees Comment[fr]=Affiche, modifie et exporte au format PostScript des arbres phyolgénétiques Comment[pt_BR]=Exibe, modifica e exporta em formato PostScript árvores filogenéticas Type=Application Categories=Biology;Science;Education; MimeType=text/x-clustalw-tree;chemical/njplot; debian/control0000644000000000000000000000165212151501640010570 0ustar Source: njplot Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille , Charles Plessy Build-Depends: cdbs, debhelper (>= 8), libvibrant6-dev Standards-Version: 3.9.4 Homepage: http://pbil.univ-lyon1.fr/software/njplot Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/njplot/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/njplot/trunk/ Package: njplot Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: phylogenetic tree drawing program NJplot is able to draw any dendrogram expressed in the Newick standard phylogenetic tree format (e.g., the format used by the Phylip package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. debian/manpages0000644000000000000000000000000412151261451010674 0ustar *.1 debian/upstream0000644000000000000000000000051312151261451010746 0ustar Reference: Author: Perrière, G. and Gouy, M. Title: "WWW-query: An on-line retrieval system for biological sequence banks" Journal: Biochimie Year: 1996 Volume: 78 Number: 5 Pages: 364–369 DOI: 10.1016/0300-9084(96)84768-7 PMID: 8905155 URL: http://www.sciencedirect.com/science/article/pii/0300908496847687 debian/patches/0000755000000000000000000000000012151502461010612 5ustar debian/patches/series0000644000000000000000000000002712151477051012034 0ustar fix-underlinking.patch debian/patches/fix-underlinking.patch0000644000000000000000000000063012151476062015116 0ustar --- a/makefile +++ b/makefile @@ -23,11 +23,11 @@ njplot : $(OBJECTS) $(CC) -o njplot $(OBJECTS) \ - -lvibrant -lncbi -lXm -lXt + -lvibrant -lncbi -lXm -lXt -lm unrooted : $(OBJUNROOTED) $(CC) -o unrooted $(OBJUNROOTED) \ - -lvibrant -lncbi -lXm -lXt + -lvibrant -lncbi -lXm -lXt -lm newicktops: njplot-vib.c $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm debian/menu0000644000000000000000000000050512151261451010053 0ustar ?package(njplot):needs="X11" section="Applications/Science/Biology"\ title="NJPlot" command="/usr/bin/njplot"\ hints="Phylogenetic tree drawing program" ?package(njplot):needs="X11" section="Applications/Science/Biology"\ title="NJPlot unrooted" command="/usr/bin/unrooted"\ hints="Phylogenetic tree drawing program" debian/examples0000644000000000000000000000004212151261451010721 0ustar bigtree.phb example.phb multi.phb debian/docs0000644000000000000000000000002412151261451010033 0ustar README *.html *.gif debian/links0000644000000000000000000000020512151261451010224 0ustar usr/share/man/man1/njplot.1.gz usr/share/man/man1/newicktops.1.gz usr/share/man/man1/njplot.1.gz usr/share/man/man1/newicktotxt.1.gz