[med-svn] r1161 - in trunk/packages/njplot/tags: . 2.2-1

tille at alioth.debian.org tille at alioth.debian.org
Fri Jan 18 16:20:53 UTC 2008


Author: tille
Date: 2008-01-18 16:20:52 +0000 (Fri, 18 Jan 2008)
New Revision: 1161

Added:
   trunk/packages/njplot/tags/2.2-1/
   trunk/packages/njplot/tags/2.2-1/changelog
   trunk/packages/njplot/tags/2.2-1/compat
   trunk/packages/njplot/tags/2.2-1/control
   trunk/packages/njplot/tags/2.2-1/copyright
   trunk/packages/njplot/tags/2.2-1/dirs
   trunk/packages/njplot/tags/2.2-1/docs
   trunk/packages/njplot/tags/2.2-1/examples
   trunk/packages/njplot/tags/2.2-1/get-orig-source
   trunk/packages/njplot/tags/2.2-1/install
   trunk/packages/njplot/tags/2.2-1/links
   trunk/packages/njplot/tags/2.2-1/manpages
   trunk/packages/njplot/tags/2.2-1/menu
   trunk/packages/njplot/tags/2.2-1/njplot.desktop
   trunk/packages/njplot/tags/2.2-1/njplot.mime
   trunk/packages/njplot/tags/2.2-1/njplot.sharedmimeinfo
   trunk/packages/njplot/tags/2.2-1/rules
   trunk/packages/njplot/tags/2.2-1/unrooted.desktop
   trunk/packages/njplot/tags/2.2-1/watch
Log:
Tagged 2.2-1


Added: trunk/packages/njplot/tags/2.2-1/changelog
===================================================================
--- trunk/packages/njplot/tags/2.2-1/changelog	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/changelog	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,191 @@
+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 myseld 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 <tille at debian.org>  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 <tille at debian.org>  Wed, 07 Nov 2007 08:04:06 +0100
+
+njplot (2.0-1) unstable; urgency=low
+
+  * New upstream version that startet proper version numbering
+  * debian/menu: Apps/Science -> Applications/Science/Biology
+  * Added debian/watch because upstream startet proper version numbering
+  * Upstream included man pages, so remove debian/*.1
+
+ -- Andreas Tille <tille at debian.org>  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 rebuilded
+    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 maintainance
+    Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+    Uploaders: Andreas Tille <tille at debian.org>
+
+ -- Andreas Tille <tille at debian.org>  Mon, 01 Oct 2007 20:45:37 +0200
+
+njplot (0.20060606-3) unstable; urgency=low
+
+  * Fixed .desktop file (Thanks to Adri2000 <adri2000 at gmail.com>)
+    Closes: #401231
+
+ -- Andreas Tille <tille at debian.org>  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 <tille at debian.org>  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 <tille at debian.org>  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 <tille at debian.org>  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 <tille at debian.org>  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 <tille at debian.org>  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 <tille at debian.org>  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 <tille at debian.org>  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 <frankie at debian.org>  Mon, 18 Feb 2002 13:17:50 +0100
+
+njplot (0.0-3) 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 23:36:54 +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 <gbechly at debian.org>  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 <doogie at debian.org>  Mon, 25 Oct 1999 16:32:42 -0500
+
+njplot (0.0-1) unstable; urgency=low
+
+  * Initial Release.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org>  Sat,  6 Mar 1999 20:46:41 +0100
+
+Local variables:
+mode: debian-changelog
+End:

Added: trunk/packages/njplot/tags/2.2-1/compat
===================================================================
--- trunk/packages/njplot/tags/2.2-1/compat	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/compat	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1 @@
+5

Added: trunk/packages/njplot/tags/2.2-1/control
===================================================================
--- trunk/packages/njplot/tags/2.2-1/control	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/control	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,21 @@
+Source: njplot
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+XS-DM-Upload-Allowed: Yes
+Uploaders: Andreas Tille <tille at debian.org>, Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: cdbs, debhelper (>= 5), libncbi6-dev, libvibrant6-dev, lesstif2-dev, libxt-dev
+Standards-Version: 3.7.3
+Homepage: http://pbil.univ-lyon1.fr/software/njplot.html
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/njplot/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/njplot/
+
+Package: njplot
+Architecture: any
+Depends: ${shlibs:Depends}
+Description: A tree drawing program
+ NJplot is able to draw any tree expressed  in the 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. 

Added: trunk/packages/njplot/tags/2.2-1/copyright
===================================================================
--- trunk/packages/njplot/tags/2.2-1/copyright	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/copyright	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,19 @@
+This package was debianized by Stephane Bortzmeyer bortzmeyer at debian.org on
+Sat,  6 Mar 1999 20:46:41 +0100.
+
+The original tar archive is at
+   ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplot-unrooted.tar
+
+Reference server: http://pbil.univ-lyon1.fr/software/njplot.html
+
+Upstream Author: 
+Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
+
+Copyright: Artistic
+
+This software is copyright (c) by Manolo Gouy
+
+You are free to distribute this software under the terms of
+the Artistic Licence.
+On Debian systems, the complete text of the Artistic
+Licence can be found in /usr/share/common-licenses/Artistic file.

Added: trunk/packages/njplot/tags/2.2-1/dirs
===================================================================
--- trunk/packages/njplot/tags/2.2-1/dirs	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/dirs	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,4 @@
+usr/bin
+usr/share/doc/njplot
+usr/share/njplot
+usr/share/man/man1

Added: trunk/packages/njplot/tags/2.2-1/docs
===================================================================
--- trunk/packages/njplot/tags/2.2-1/docs	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/docs	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,3 @@
+README
+*.html
+*.gif

Added: trunk/packages/njplot/tags/2.2-1/examples
===================================================================
--- trunk/packages/njplot/tags/2.2-1/examples	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/examples	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,3 @@
+bigtree.phb
+example.phb
+multi.phb

Added: trunk/packages/njplot/tags/2.2-1/get-orig-source
===================================================================
--- trunk/packages/njplot/tags/2.2-1/get-orig-source	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/get-orig-source	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,42 @@
+#!/bin/sh -e
+echo This is outdated, because upstream switched to proper version numbering
+exit
+
+NAME=njplot
+UTARBALL="$NAME"-unrooted.tar
+rm -rf tmp
+mkdir -p tmp
+cd tmp
+wget --quiet ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/"$NAME"/"$UTARBALL"
+tar -xf "$UTARBALL"
+rm -f  "$UTARBALL"
+VERSION=`ls -lt | grep '^.rw.r' | sed -e '2,$d' -e 's/^.[-rwxr]\{9\} [0-9] \w\+ \w\+[[:space:]]\+[0-9]\+ \([0-9]\{4\}\)-\([0-9]\{2\}\)-\([0-9]\{2\}\).*/0.\1\2\3/'`
+mkdir "$NAME"-"$VERSION"
+mv *.c makefile "$NAME"-"$VERSION"
+cd "$NAME"-"$VERSION"
+
+MOREFILES="$NAME.help README bigtest.phb multi.phb test.ph"
+for mf in $MOREFILES ; do
+    wget --quiet ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/"$NAME"/$mf
+done
+
+wget --quiet http://pbil.univ-lyon1.fr/software/njplot.html
+wget --quiet http://pbil.univ-lyon1.fr/binaries/njplot.gif
+wget --quiet http://pbil.univ-lyon1.fr/help/helpers.html
+sed -e '/<TABLE BORDER=4 CELLPADDING=8>/,/<\/TABLE>/d' njplot.html \
+    -e 's/"\/binaries\/\(njplot.gif"\)/"\1/' \
+    -e 's/"\/help\/\(helpers.html"\)/"\1/' \
+    -e 's/"\(\/comments.html"\)/"http:\/\/pbil.univ-lyon1.fr\1/' \
+    -e 's/"\(\/pbil.html">\)<IMG SRC="\/binaries\/home.gif">/"http:\/\/pbil.univ-lyon1.fr\1PBIL home page/' \
+    -e '/<I>Back to PBIL home page<\/I>/d' \
+ > njplot_.html
+touch -r njplot.html njplot_.html
+mv njplot_.html njplot.html
+
+cd ..
+
+GZIP=-9 tar -czf "$NAME"_"$VERSION".orig.tar.gz "$NAME"-"$VERSION"
+
+mv "$NAME"_"$VERSION".orig.tar.gz ..
+cd ..
+rm -rf tmp

Added: trunk/packages/njplot/tags/2.2-1/install
===================================================================
--- trunk/packages/njplot/tags/2.2-1/install	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/install	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,3 @@
+njplot unrooted newickto* usr/bin
+njplot.help               usr/share/njplot
+debian/*.desktop          usr/share/applications

Added: trunk/packages/njplot/tags/2.2-1/links
===================================================================
--- trunk/packages/njplot/tags/2.2-1/links	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/links	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,2 @@
+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

Added: trunk/packages/njplot/tags/2.2-1/manpages
===================================================================
--- trunk/packages/njplot/tags/2.2-1/manpages	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/manpages	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1 @@
+*.1

Added: trunk/packages/njplot/tags/2.2-1/menu
===================================================================
--- trunk/packages/njplot/tags/2.2-1/menu	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/menu	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,6 @@
+?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"

Added: trunk/packages/njplot/tags/2.2-1/njplot.desktop
===================================================================
--- trunk/packages/njplot/tags/2.2-1/njplot.desktop	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/njplot.desktop	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,17 @@
+[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;

Added: trunk/packages/njplot/tags/2.2-1/njplot.mime
===================================================================
--- trunk/packages/njplot/tags/2.2-1/njplot.mime	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/njplot.mime	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,2 @@
+text/x-clustalw-tree; njplot '%s'; description=Clustal W Phylogenetic Tree ; nametemplate=%s.phb
+chemical/njplot; njplot '%s' ; description=Phylogenetic Tree ; nametemplate=%s.phb

Added: trunk/packages/njplot/tags/2.2-1/njplot.sharedmimeinfo
===================================================================
--- trunk/packages/njplot/tags/2.2-1/njplot.sharedmimeinfo	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/njplot.sharedmimeinfo	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
+  <mime-type type="text/x-clustalw-tree">
+    <comment>Phylogenetic tree in Clustal W format</comment>
+    <comment xml:lang="fr">Arbre phylogénétique au format Clustal W</comment>
+    <comment xml:lang="de">Phylogenetischer Baum im Clustal W Format</comment>
+    <magic priority="50">
+      <match type="string" offset="0" value="(\n"/>
+    </magic>
+    <glob pattern="*.phb"/>
+    <glob pattern="*.ph"/>
+    <sub-class-of type="text/plain"/>
+  </mime-type>
+</mime-info>

Added: trunk/packages/njplot/tags/2.2-1/rules
===================================================================
--- trunk/packages/njplot/tags/2.2-1/rules	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/rules	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,20 @@
+#!/usr/bin/make -f
+# debian/rules for njplot using cdbs
+# Andreas Tille <tille at debian.org>, GPL
+
+# include /usr/share/cdbs/1/rules/dpatch.mk
+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_OPT_FLAG=-c -I/usr/include/ncbi -DNO_PDF -DWIN_MOTIF -DHELPFILENAME=\\\"/usr/share/njplot/njplot.help\\\"
+
+get-orig-source:
+	. debian/get-orig-source
+
+# in case the original makefile is in place which has no clean target
+#clean::
+#	rm -f *.o njplot unrooted newicktops newicktotxt add_root


Property changes on: trunk/packages/njplot/tags/2.2-1/rules
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/njplot/tags/2.2-1/unrooted.desktop
===================================================================
--- trunk/packages/njplot/tags/2.2-1/unrooted.desktop	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/unrooted.desktop	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,20 @@
+[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;

Added: trunk/packages/njplot/tags/2.2-1/watch
===================================================================
--- trunk/packages/njplot/tags/2.2-1/watch	                        (rev 0)
+++ trunk/packages/njplot/tags/2.2-1/watch	2008-01-18 16:20:52 UTC (rev 1161)
@@ -0,0 +1,2 @@
+version=3
+ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/njplot-(.*)\.tar.gz




More information about the debian-med-commit mailing list