[med-svn] r1544 - in trunk/packages: . treetool treetool/trunk treetool/trunk/debian treetool/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Sun Mar 9 20:46:35 UTC 2008
Author: tille
Date: 2008-03-09 20:46:35 +0000 (Sun, 09 Mar 2008)
New Revision: 1544
Added:
trunk/packages/treetool/
trunk/packages/treetool/trunk/
trunk/packages/treetool/trunk/debian/
trunk/packages/treetool/trunk/debian/README.debian
trunk/packages/treetool/trunk/debian/changelog
trunk/packages/treetool/trunk/debian/compat
trunk/packages/treetool/trunk/debian/control
trunk/packages/treetool/trunk/debian/copyright
trunk/packages/treetool/trunk/debian/debug.debian.patch.alpha
trunk/packages/treetool/trunk/debian/debug.orig.patch.alpha
trunk/packages/treetool/trunk/debian/dirs
trunk/packages/treetool/trunk/debian/docs
trunk/packages/treetool/trunk/debian/examples
trunk/packages/treetool/trunk/debian/get-orig-source
trunk/packages/treetool/trunk/debian/install
trunk/packages/treetool/trunk/debian/manpages
trunk/packages/treetool/trunk/debian/menu
trunk/packages/treetool/trunk/debian/more-than-8bpp.patch
trunk/packages/treetool/trunk/debian/patches/
trunk/packages/treetool/trunk/debian/patches/Makefile.diff
trunk/packages/treetool/trunk/debian/patches/graphics.diff
trunk/packages/treetool/trunk/debian/patches/tree.diff
trunk/packages/treetool/trunk/debian/patches/treetool.diff
trunk/packages/treetool/trunk/debian/rules
trunk/packages/treetool/trunk/debian/sample.tree
trunk/packages/treetool/trunk/debian/treetool.1
Log:
Group maintenance for treetool
Added: trunk/packages/treetool/trunk/debian/README.debian
===================================================================
--- trunk/packages/treetool/trunk/debian/README.debian (rev 0)
+++ trunk/packages/treetool/trunk/debian/README.debian 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,13 @@
+treetool for DEBIAN
+----------------------
+
+Treetool has been patched to accept non-8bpp displays. The
+original patch is in the "more-than-8bpp.patch" file.
+(Flag NOSTORECOLOR in the Makefile.)
+
+The source version number 2.0.2a is in fact no new version but just
+a cleaned source tarball. I just removed all binaries (objects and
+executable files). I was not able to find newer upstream versions
+and the project might be dead.
+
+Stephane Bortzmeyer <bortzmeyer at debian.org>, Wed, 13 Jan 1999 11:02:30 +0100
Added: trunk/packages/treetool/trunk/debian/changelog
===================================================================
--- trunk/packages/treetool/trunk/debian/changelog (rev 0)
+++ trunk/packages/treetool/trunk/debian/changelog 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,96 @@
+treetool (2.0.2a-5) unstable; urgency=low
+
+ * Standards-Version: 3.7.3 (no changes necessary)
+ * Switched to cdbs
+ * Moved font_map file from /usr/lib/treetool to /usr/share/treetool
+ * Group maintenance according to Debian-Med policy
+ * Added Homepage tag (with download page of latest upstream source,
+ uostream seems to be dead since 1995)
+ * Enhanced short description (removed [Biology], added phylogenetic)
+ * XS-Autobuild: yes to enable auto building
+ * debian/compat: 5
+
+ -- Andreas Tille <tille at debian.org> Mon, 03 Mar 2008 14:11:03 +0100
+
+treetool (2.0.2a-4) unstable; urgency=low
+
+ * Build-Depends: libx11-dev, x-dev instead of xlibs-dev
+ Closes: #346939
+ * Standards-Version: 3.6.2, no changes necessary
+ * debian/compat: 4
+ * de_installmanpages -> dh_installman
+
+ -- Andreas Tille <tille at debian.org> Mon, 9 Jan 2006 07:18:01 +0100
+
+treetool (2.0.2a-3) unstable; urgency=low
+
+ * Fixed a FTBFS bug on amd64. Thanks to Andreas Jochens <aj at andaco.de>
+ for the patch.
+ Closes: #297273
+ * Standards-Version: 3.6.1.1
+ No changes needed.
+ * Fixed quotes in menu entries.
+
+ -- Andreas Tille <tille at debian.org> Mon, 28 Feb 2005 16:44:29 +0100
+
+treetool (2.0.2a-2) unstable; urgency=low
+
+ * Really changed the Maintainer address in control field
+ * Some additions to README.Debian
+ * added new source location to copyright file because the original
+ was unavailable
+ * Compile on alpha with -mieee to avoid arithmetic exceptions
+ Many thanks to Helge Kreutzmann <kreutzm at itp.uni-hannover.de>.
+ closes: #66190
+ General remark: The fix from Helge just fixes a symptom, not the reason
+ of the problem. The system is that there is a "Divide by zero" error
+ which is now handled as suggested by IEEE which is not the default on
+ Alpha architecture.
+ On the other hand the value which becomes zero should definitely not be
+ zero. The problem could be verified using the patch
+ debug.debian.patch.alpha (for the Debian-Version of treetool/size.c) or
+ debug.debian.orig.alpha for the original treetool/size.c). This simple
+ patch uses two printf statements to show the problem for further debugging.
+ The value of nd->x just becomes 0 even if it is not touched. The reason
+ may be some strange handling of pointers and doubly linked lists.
+ The code produces lot of warnings and should definitely use a more
+ robust implementation of doubly linked lists (for instance from glib).
+ The problem is that this program has simply no license thus further
+ development is quite hard.
+
+ -- Andreas Tille <tille at debian.org> Sun, 23 Jun 2002 14:54:19 +0200
+
+treetool (2.0.2a-1) unstable; urgency=low
+
+ * New Maintainer
+ * removed binaries (*.o and treetool executable) from upstream source
+ and renamed it to 2.0.2a
+
+ -- Andreas Tille <tille at debian.org> Fri, 11 Jan 2002 12:28:51 +0100
+
+treetool (2.0.2-3) unstable; urgency=low
+
+ * Maintainer set to Debian QA Group <packages at qa.debian.org>.
+
+ -- Adrian Bunk <bunk at fs.tum.de> Sat, 25 Aug 2001 00:06:06 +0200
+
+treetool (2.0.2-2) unstable; urgency=low
+
+ * Adopted by new maintainer; #92800
+ * Updated to latest standards version and added Build-Depends;
+ closes: #59490, #91688
+ * Modified Makefile.
+ * Wrote a manpage; closes: #36465
+ * Removed some unnecessary example files in debian directory.
+ * Added a Debian menu entry.
+ * Moved package to section non-free/science, because it is a tool that
+ is exclusively useful for biologists that reconstruct phylogenetic trees.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> Mon, 16 Apr 2001 18:08:15 +0200
+
+treetool (2.0.2-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Wed, 13 Jan 1999 11:02:30 +0100
+
Added: trunk/packages/treetool/trunk/debian/compat
===================================================================
--- trunk/packages/treetool/trunk/debian/compat (rev 0)
+++ trunk/packages/treetool/trunk/debian/compat 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1 @@
+5
Added: trunk/packages/treetool/trunk/debian/control
===================================================================
--- trunk/packages/treetool/trunk/debian/control (rev 0)
+++ trunk/packages/treetool/trunk/debian/control 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,25 @@
+Source: treetool
+Section: non-free/science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25), debhelper (>= 5),
+ xviewg-dev, libx11-dev, x-dev
+Standards-Version: 3.7.3
+Homepage: http://iubio.bio.indiana.edu/soft/molbio/unix/treetool/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/treetool/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/treetool/trunk/
+XS-Autobuild: yes
+
+Package: treetool
+Architecture: any
+Depends: ${shlibs:Depends}
+Description: interactive tool for displaying phylogenetic trees
+ Treetool is an interactive tool for displaying, editing, and printing
+ phylogenetic trees. The tree is displayed visually on screen, in
+ various formats, and the user is able to modify the format, structure,
+ and characteristics of the tree. Trees may be viewed, compared,
+ formatted for printing, constructed from smaller trees, etc.
+ .
+ The development of this software has stopped in 1995.
Added: trunk/packages/treetool/trunk/debian/copyright
===================================================================
--- trunk/packages/treetool/trunk/debian/copyright (rev 0)
+++ trunk/packages/treetool/trunk/debian/copyright 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,48 @@
+This package was debianized by Stephane Bortzmeyer bortzmeyer at debian.org on
+Wed, 13 Jan 1999 11:02:30 +0100.
+
+It was originally downloaded from
+ <ftp://rdp.life.uiuc.edu/pub/RDP/programs/TreeTool>
+Unfortunately this page is not reachable any more but the source could
+be also found at
+ http://www.rpi.edu/dept/bio/gdenew/treetool2.0.2
+
+Upstream Author: Mike McCaughey <mrmike at clickbang.com>
+
+Copyright (c) 1992, 1993, 1994 University of Illinois board of trustees.
+All rights reserved. Written by Michael Maciukenas for the Ribosomal
+Database Project.
+
+License:
+ No licence yet (still discussing) but I have an authorization:
+
+Date: Sun, 21 Feb 1999 14:50:05 -0500 (20:50 CET)
+To: Stephane Bortzmeyer <bortzmeyer at pasteur.fr>
+From: mrmike <mrmike at clickbang.com>
+Subject: Re: Intent to make a Debian Linux package of treetool
+
+>Hello,
+>
+>I write to you as the author of the TreeTool package. I plan to make
+>a Linux Debian package of TreeTool and I would like your authorization
+>and some information about the TreeTool licence.
+>
+{SNIP}
+>Yours,
+>
+>Stéphane Bortzmeyer
+>Pasteur Institute
+
+Thanks for your interest in treetool. While treetool is "free"; some
+portions are copyright the University of Illlinois. I am currently working
+on getting permission from them to obtain clear rights to the package; in
+the meantime, I cannot place the program under the GNU license (which is my
+desire). I do have permission to distribute the program, so you are
+welcome to include it under the "non-free" area of Debian Linux.
+
+When these issues are cleared up, I will place the package under the GNU
+license and let you know.
+
+Regards,
+Mike McCaughey
+Click! Computer Services, Inc.
Added: trunk/packages/treetool/trunk/debian/debug.debian.patch.alpha
===================================================================
--- trunk/packages/treetool/trunk/debian/debug.debian.patch.alpha (rev 0)
+++ trunk/packages/treetool/trunk/debian/debug.debian.patch.alpha 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,18 @@
+--- size.c.debian Fri Jan 11 12:26:43 2002
++++ size.c Sun Jun 23 15:37:52 2002
+@@ -194,6 +194,7 @@
+ nd->y=(topy+boty)/2.0;
+
+ /* calculate bounds */
++printf("%s(%i): *scalex=%g, nd->x=%g\n", __FILE__, __LINE__, *scalex, w, nd->x); fflush(stdout);
+ if(showlabel(n, Boxed))
+ {
+ if(*scalex==-1.0 || (w-textw-nd->lx)/nd->x<*scalex)
+@@ -205,6 +206,7 @@
+ }
+ else
+ {
++printf("%s(%i): *scalex=%g, nd->x=%g\n", __FILE__, __LINE__, *scalex, w, nd->x); fflush(stdout);
+ if(*scalex==-1.0 || w/nd->x<*scalex)
+ *scalex=w/nd->x;
+ if(nd->y<*y1)
Added: trunk/packages/treetool/trunk/debian/debug.orig.patch.alpha
===================================================================
--- trunk/packages/treetool/trunk/debian/debug.orig.patch.alpha (rev 0)
+++ trunk/packages/treetool/trunk/debian/debug.orig.patch.alpha 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,29 @@
+--- size.c.orig Mon May 2 22:35:24 1994
++++ size.c Sun Jun 23 15:37:52 2002
+@@ -194,6 +194,7 @@
+ nd->y=(topy+boty)/2.0;
+
+ /* calculate bounds */
++printf("%s(%i): *scalex=%g, nd->x=%g\n", __FILE__, __LINE__, *scalex, w, nd->x); fflush(stdout);
+ if(showlabel(n, Boxed))
+ {
+ if(*scalex==-1.0 || (w-textw-nd->lx)/nd->x<*scalex)
+@@ -205,6 +206,7 @@
+ }
+ else
+ {
++printf("%s(%i): *scalex=%g, nd->x=%g\n", __FILE__, __LINE__, *scalex, w, nd->x); fflush(stdout);
+ if(*scalex==-1.0 || w/nd->x<*scalex)
+ *scalex=w/nd->x;
+ if(nd->y<*y1)
+@@ -419,7 +421,9 @@
+ a=0.0;
+ else
+ a=atan2(dy,dx);
+- sincos(a,&s,&c); /* s=sin, c=cos */
++ /* sincos(a,&s,&c); */ /* s=sin, c=cos */
++ s = sin(a);
++ c = cos(a);
+
+ /* find vector from center of text to an edge, in the same direction
+ as the branch vector */
Added: trunk/packages/treetool/trunk/debian/dirs
===================================================================
--- trunk/packages/treetool/trunk/debian/dirs (rev 0)
+++ trunk/packages/treetool/trunk/debian/dirs 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,3 @@
+usr/bin
+usr/share/doc/treetool
+usr/share/man/man1
Added: trunk/packages/treetool/trunk/debian/docs
===================================================================
--- trunk/packages/treetool/trunk/debian/docs (rev 0)
+++ trunk/packages/treetool/trunk/debian/docs 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,3 @@
+debian/more-than-8bpp.patch
+treetool/user.manual
+treetool/README
Added: trunk/packages/treetool/trunk/debian/examples
===================================================================
--- trunk/packages/treetool/trunk/debian/examples (rev 0)
+++ trunk/packages/treetool/trunk/debian/examples 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1 @@
+debian/sample.tree
Added: trunk/packages/treetool/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/treetool/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/treetool/trunk/debian/get-orig-source 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,29 @@
+#!/bin/sh -e
+set -x
+NAME=treetool
+UVERSION=2.0.2
+DVERSION="$UVERSION"a
+UPSTREAMTAR="$NAME""$UVERSION".tar.gz
+UPSTREAMDIR="$NAME""$UVERSION"
+
+# URL="http://rdp8.cme.msu.edu/download/programs/TreeTool"
+URL="http://iubio.bio.indiana.edu/soft/molbio/unix/treetool/"
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+if [ ! -f "$UPSTREAMTAR" ] ; then
+ wget "$URL"/"$UPSTREAMTAR"
+fi
+tar -xzf "$UPSTREAMTAR"
+
+cd "$UPSTREAMDIR"
+
+# remove binary and backup files
+rm -rf obj treetool_release/treetool `find . -name \*~` `find . -name \*.o`
+
+cd ..
+
+GZIP=-9 tar -czf "$NAME"_"$DVERSION".orig.tar.gz "$NAME""$UVERSION"
+
+rm -rf "$UPSTREAMDIR"
Property changes on: trunk/packages/treetool/trunk/debian/get-orig-source
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/treetool/trunk/debian/install
===================================================================
--- trunk/packages/treetool/trunk/debian/install (rev 0)
+++ trunk/packages/treetool/trunk/debian/install 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1 @@
+graphics/font_map usr/share/treetool
Added: trunk/packages/treetool/trunk/debian/manpages
===================================================================
--- trunk/packages/treetool/trunk/debian/manpages (rev 0)
+++ trunk/packages/treetool/trunk/debian/manpages 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1 @@
+debian/treetool.1
Added: trunk/packages/treetool/trunk/debian/menu
===================================================================
--- trunk/packages/treetool/trunk/debian/menu (rev 0)
+++ trunk/packages/treetool/trunk/debian/menu 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,2 @@
+?package(treetool):needs="X11" section="Applications/Science/Biology"\
+ title="treetool" command="/usr/bin/treetool"
Added: trunk/packages/treetool/trunk/debian/more-than-8bpp.patch
===================================================================
--- trunk/packages/treetool/trunk/debian/more-than-8bpp.patch (rev 0)
+++ trunk/packages/treetool/trunk/debian/more-than-8bpp.patch 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,28 @@
+Pierre Rioux <riouxp at megasun.BCH.UMontreal.CA> :
+
+ This message might help people having the same problem
+under Solaris:
+
+ I succeeded in "patching" treetool 2.0.1 such that it works
+on displays with more than just 8 bitplanes. I simply commented
+out in the file graphics/color.c the lines that called
+XStoreColor(). There are exactly 6 such lines in the file,
+one of them is
+
+ /* result=XStoreColor(ch->xdpy, ch->cmap, &ch->cl->c); */
+
+(shown here after I commented it out!) Just look for the string
+"XStoreColor"; BTW sometimes the function's return value is
+ignored.
+
+ Now it runs on 24 bit displays; however the "color editor"
+panels won't work at all (you're stuck with the default colors,
+but here at the OGMP we don't mind that since we never change
+the colors anyway). It's up to you to decide if this is good
+enough or not. I agree this "patch" is not the most amazing
+invention since sliced bread. :-)
+
+ Pierre
+--
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+:: riouxp at iro.umontreal.ca :: A millihelen is the amount of beauty ::
Added: trunk/packages/treetool/trunk/debian/patches/Makefile.diff
===================================================================
--- trunk/packages/treetool/trunk/debian/patches/Makefile.diff (rev 0)
+++ trunk/packages/treetool/trunk/debian/patches/Makefile.diff 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,57 @@
+--- Makefile.orig 2006-09-10 20:55:37.000000000 +0200
++++ Makefile 2006-09-10 21:07:52.000000000 +0200
+@@ -3,26 +3,32 @@
+ # Works with gcc -traditional if you ignore the typcast warnings
+ # Seems to work with acc, but lots of warnings
+
++ARCH=$(shell arch)
++
+ CC= gcc
+-OBJDIR=${PWD}/obj
+-BINDIR=${PWD}/bin
+-INCDIR=${PWD}/include
++ifeq ($(ARCH),alpha)
++CFLAGS=-g -O2 -mieee
++else
++CFLAGS=-g -O2
++endif
++ROOT=${DESTDIR}
++PWD := $(shell pwd)
++OBJDIR := $(PWD)/obj
++BINDIR := $(PWD)/bin
++INCDIR := $(PWD)/include
+ # Change this to reflect path of openwin/include in Solaris
+ XVDIR=/usr/openwin/include
+-INC=-I${PWD}/include -I${XVDIR}
+-THISDIR=${PWD}
++INC=-I$(INCDIR) -I${XVDIR}
++#THISDIR=
+
+ all:
+- (cd tree;make "CC=${CC}" "INC=${INC}" "INCDIR=${INCDIR}" \
++ mkdir -p $(OBJDIR)
++ (cd tree;make "CC=${CC}" "CFLAGS=${CFLAGS}" "INC=${INC}" "INCDIR=${INCDIR}" \
+ "OBJDIR=${OBJDIR}" "BINDIR=${BINDIR}")
+- (cd graphics;make "CC=${CC}" "INC=${INC}" "INCDIR=${INCDIR}" \
++ (cd graphics;make "CC=${CC}" "CFLAGS=${CFLAGS} -DNOSTORECOLOR" "INC=${INC}" "INCDIR=${INCDIR}" \
+ "OBJDIR=${OBJDIR}" "BINDIR=${BINDIR}")
+- (cd treetool;make "CC=${CC}" "INC=${INC}" "INCDIR=${INCDIR}" \
++ (cd treetool;make "CC=${CC}" "CFLAGS=${CFLAGS}" "INC=${INC}" "INCDIR=${INCDIR}" \
+ "OBJDIR=${OBJDIR}" "BINDIR=${BINDIR}")
+- mv treetool/t treetool_release/treetool
+- cp graphics/font_map treetool_release
+- cp treetool/user.manual treetool_release
+- cp treetool/README treetool_release
+
+ clean:
+ (cd graphics;make clean)
+@@ -30,7 +36,8 @@
+ (cd treetool;make clean)
+ ## Do not remove parts of your own upstream source! (Andreas Tille)
+ # rm -f treetool_release/*
+- rm treetool.tar.Z
++ rm -f treetool.tar.Z
++ rm -rf $(OBJDIR)
+
+ tarfile:
+ tar -cvf treetool2.0.1.tar treetool2.0.1
Added: trunk/packages/treetool/trunk/debian/patches/graphics.diff
===================================================================
--- trunk/packages/treetool/trunk/debian/patches/graphics.diff (rev 0)
+++ trunk/packages/treetool/trunk/debian/patches/graphics.diff 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,124 @@
+diff -ubrN graphics.orig/canvas.c graphics/canvas.c
+--- graphics.orig/canvas.c 1994-05-02 22:34:56.000000000 +0200
++++ graphics/canvas.c 2006-09-10 18:59:24.000000000 +0200
+@@ -1330,7 +1330,7 @@
+ tmp->fg=colors[fg];
+ tmp->bg=colors[bg];
+ sa.background_pixel=tmp->bg;
+- XChangeWindowAttributes(tmp->xdpy, tmp->win, CWBackPixel, sa);
++ /* XChangeWindowAttributes(tmp->xdpy, tmp->win, CWBackPixel, sa); */
+ tmp->magx=1;
+ tmp->magy=1;
+ tmp->xpos=0;
+diff -ubrN graphics.orig/color.c graphics/color.c
+--- graphics.orig/color.c 1994-05-02 22:34:56.000000000 +0200
++++ graphics/color.c 2006-09-10 18:59:24.000000000 +0200
+@@ -177,7 +177,9 @@
+ ch=(tcolor)titem_get_intdata(s);
+ new=65535*v/100;
+ ch->cl->c.red=new;
++#ifndef NOSTORECOLOR
+ result=XStoreColor(ch->xdpy, ch->cmap, &ch->cl->c);
++#endif
+ tptext_set_val(ch->t, "");
+ }
+
+@@ -193,7 +195,9 @@
+ ch=(tcolor)titem_get_intdata(s);
+ new=65535*v/100;
+ ch->cl->c.green=new;
++#ifndef NOSTORECOLOR
+ result=XStoreColor(ch->xdpy, ch->cmap, &ch->cl->c);
++#endif
+ tptext_set_val(ch->t, "");
+ }
+
+@@ -209,7 +213,9 @@
+ ch=(tcolor)titem_get_intdata(s);
+ new=65535*v/100;
+ ch->cl->c.blue=new;
++#ifndef NOSTORECOLOR
+ result=XStoreColor(ch->xdpy, ch->cmap, &ch->cl->c);
++#endif
+ tptext_set_val(ch->t, "");
+ }
+
+@@ -282,7 +288,9 @@
+ tpslider_set_val(ch->rs, rn);
+ tpslider_set_val(ch->bs, bn);
+ tpslider_set_val(ch->gs, gn);
++#ifndef NOSTORECOLOR
+ result=XStoreColor(ch->xdpy, ch->cmap, &ch->cl->c);
++#endif
+ }
+ }
+ return(tptext_insert);
+@@ -310,7 +318,9 @@
+ tpslider_set_val(ch->rs, rn);
+ tpslider_set_val(ch->bs, bn);
+ tpslider_set_val(ch->gs, gn);
++#ifndef NOSTORECOLOR
+ result=XStoreColor(ch->xdpy, ch->cmap, &ch->cl->c);
++#endif
+ tptext_set_val(ch->t, "");
+ }
+
+@@ -344,7 +354,9 @@
+ ch->cl->c.green=1000;
+ ch->cl->c.blue=0;
+ ch->cl->c.flags=DoRed|DoGreen|DoBlue;
++#ifndef NOSTORECOLOR
+ XStoreColor(ch->xdpy, ch->cmap, &ch->cl->c);
++#endif
+ ch->f=tframe_new(where, 0, 0, 500, 500, 0, 1, 0, s, args);
+ ch->p=(tpanel)tframe_dialog_panel(ch->f);
+ ch->do_events=do_events;
+diff -ubrN graphics.orig/font.c graphics/font.c
+--- graphics.orig/font.c 1994-05-02 22:34:56.000000000 +0200
++++ graphics/font.c 2006-09-10 18:59:24.000000000 +0200
+@@ -373,7 +373,7 @@
+ }
+ }
+ if(font_map==NULL)
+- font_map=fopen("/usr/lib/font_map", "r");
++ font_map=fopen("/usr/share/treetool/font_map", "r");
+ }
+ if(font_map==NULL)
+ {
+diff -ubrN graphics.orig/Makefile graphics/Makefile
+--- graphics.orig/Makefile 1994-05-02 22:53:49.000000000 +0200
++++ graphics/Makefile 2006-09-10 18:59:24.000000000 +0200
+@@ -11,16 +11,16 @@
+ cp interface.h ${INCDIR}
+
+ canvas.o: canvas.c generic.h interface.h itemtypes.h canvas.h
+- ${CC} -c canvas.c ${INC} ${DBG}
++ ${CC} ${CFLAGS} -c canvas.c ${INC} ${DBG}
+ context.o: context.c generic.h interface.h itemtypes.h context.h
+- ${CC} -c context.c ${INC} ${DBG}
++ ${CC} ${CFLAGS} -c context.c ${INC} ${DBG}
+ draw.o: draw.c generic.h interface.h itemtypes.h canvas.h context.h
+- ${CC} -c draw.c ${INC} ${DBG}
++ ${CC} ${CFLAGS} -c draw.c ${INC} ${DBG}
+ notice.o: notice.c interface.h itemtypes.h
+- ${CC} -c notice.c ${INC} ${DBG}
++ ${CC} ${CFLAGS} -c notice.c ${INC} ${DBG}
+
+ %.o: %.c generic.h interface.h itemtypes.h
+- ${CC} -c $*.c ${INC} ${DBG}
++ ${CC} ${CFLAGS} -c $*.c ${INC} ${DBG}
+
+ build:
+ cp *.c ${BLD}
+diff -ubrN graphics.orig/pchoice.c graphics/pchoice.c
+--- graphics.orig/pchoice.c 1994-05-02 22:34:56.000000000 +0200
++++ graphics/pchoice.c 2006-09-10 18:59:24.000000000 +0200
+@@ -283,7 +283,7 @@
+ NULL);
+ m->sel=i;
+ }
+- (void *)(m->do_events)=tpitem_get_event_procedure(i);
++ m->do_events=tpitem_get_event_procedure(i);
+ tpitem_set_event_procedure(i, tpchoice_notify);
+ return(1);
+ }
Added: trunk/packages/treetool/trunk/debian/patches/tree.diff
===================================================================
--- trunk/packages/treetool/trunk/debian/patches/tree.diff (rev 0)
+++ trunk/packages/treetool/trunk/debian/patches/tree.diff 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,46 @@
+diff -ubrN tree.orig/findnode.c tree/findnode.c
+--- tree.orig/findnode.c 1994-05-02 21:36:26.000000000 +0200
++++ tree/findnode.c 2006-09-10 18:59:24.000000000 +0200
+@@ -11,7 +11,7 @@
+ #define PEEKC() (*sp)
+ #define UNGETC(c) (--sp)
+ #define RETURN(c) return(c)
+-#define ERROR(c) {regerr(c);return(ep);}
++#define ERROR(c) {regerr(c);return(c);}
+ #include <regexp.h>
+
+ int reg_error;
+@@ -38,7 +38,7 @@
+ return(3);
+
+ compile(str, expbuf, &expbuf[1000+1], '\0');
+- circf=1;
++ /* circf=1; */
+
+ if(reg_error!=0)
+ return(2);
+diff -ubrN tree.orig/include tree/include
+--- tree.orig/include 1970-01-01 01:00:00.000000000 +0100
++++ tree/include 2006-09-10 18:59:24.000000000 +0200
+@@ -0,0 +1,9 @@
++typedef struct DYNAMIC {
++ unsigned length; /* length of string */
++ unsigned alloc; /* memory allocated for string */
++ char *data; /* string data */
++ } dynamic;
++
++extern char *new_string();
++extern int add_data();
++extern char *freeze_string();
+diff -ubrN tree.orig/Makefile tree/Makefile
+--- tree.orig/Makefile 1994-05-02 23:15:58.000000000 +0200
++++ tree/Makefile 2006-09-10 18:59:24.000000000 +0200
+@@ -20,7 +20,7 @@
+ ${CC} -c memory.c ${DBG} ${INC}
+
+ %.o: %.c treestruct.h list.h
+- ${CC} -c $*.c ${DBG} ${INC}
++ ${CC} ${CFLAGS} -c $*.c ${DBG} ${INC}
+
+ build:
+ cp *.c ${BLD}
Added: trunk/packages/treetool/trunk/debian/patches/treetool.diff
===================================================================
--- trunk/packages/treetool/trunk/debian/patches/treetool.diff (rev 0)
+++ trunk/packages/treetool/trunk/debian/patches/treetool.diff 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,73 @@
+diff -ubrN treetool.orig/Makefile treetool/Makefile
+--- treetool.orig/Makefile 1994-05-02 23:04:28.000000000 +0200
++++ treetool/Makefile 2006-09-10 18:59:24.000000000 +0200
+@@ -59,7 +59,7 @@
+ HOBJS=${OBJDIR}/treelib.o ${OBJDIR}/graphics.o
+
+
+-LIBS=-lX11 -lm -lxview -lolgx
++LIBS=-L/usr/X11R6/lib -lX11 -lm -lxview -lolgx
+
+ all: t
+
+@@ -76,7 +76,7 @@
+ ${CC} -c help.c ${DBG} ${INC}
+
+ %.o: %.c treedata.h
+- ${CC} -c $*.c ${DBG} ${INC}
++ ${CC} ${CFLAGS} -c $*.c ${DBG} ${INC}
+
+ clean:
+ rm -f *.o
+diff -ubrN treetool.orig/README treetool/README
+--- treetool.orig/README 1994-05-02 23:08:27.000000000 +0200
++++ treetool/README 2006-09-10 18:59:24.000000000 +0200
+@@ -79,8 +79,8 @@
+ Third, it will look for the "font_map" file (no leading '.') in the user's
+ home directory.
+
+-4. /usr/lib/font_map
+- Fourth, it will look for the "font_map" file in the /usr/lib directory.
++4. /usr/share/treetool/font_map
++ Fourth, it will look for the "font_map" file in the /usr/share/treetool directory.
+
+ If you get an error message like "Could not open font file, only Helvetica-12
+ font will be available", you've forgotten to install the font_map.
+diff -ubrN treetool.orig/saveframe.c treetool/saveframe.c
+--- treetool.orig/saveframe.c 1994-05-02 22:35:24.000000000 +0200
++++ treetool/saveframe.c 2006-09-10 18:59:24.000000000 +0200
+@@ -38,7 +38,7 @@
+ int savefile_exists(s)
+ char *s;
+ {
+- struct stat buf;
++ struct stat *buf;
+
+ if(stat(s, buf)==0)
+ return(1);
+diff -ubrN treetool.orig/size.c treetool/size.c
+--- treetool.orig/size.c 1994-05-02 22:35:24.000000000 +0200
++++ treetool/size.c 2006-09-10 18:59:24.000000000 +0200
+@@ -419,7 +419,9 @@
+ a=0.0;
+ else
+ a=atan2(dy,dx);
+- sincos(a,&s,&c); /* s=sin, c=cos */
++ /* sincos(a,&s,&c); */ /* s=sin, c=cos */
++ s = sin(a);
++ c = cos(a);
+
+ /* find vector from center of text to an edge, in the same direction
+ as the branch vector */
+diff -ubrN treetool.orig/treetool.c treetool/treetool.c
+--- treetool.orig/treetool.c 1994-05-02 22:35:24.000000000 +0200
++++ treetool/treetool.c 2006-09-10 18:59:24.000000000 +0200
+@@ -225,7 +225,7 @@
+
+ globals->sel_type=NoSel;
+ globals->selection=NULL;
+- globals->clip_type=NULL;
++ /* globals->clip_type=NULL; */
+ globals->clipboard=NULL;
+ globals->filename=(char *)strdup("Untitled");
+ globals->filenames=newlist();
Added: trunk/packages/treetool/trunk/debian/rules
===================================================================
--- trunk/packages/treetool/trunk/debian/rules (rev 0)
+++ trunk/packages/treetool/trunk/debian/rules 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,17 @@
+#!/usr/bin/make -f
+# debian/rules for treetool using cdbs
+# Andreas Tille <tille at debian.org>, GPL
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+clean::
+ rm -rf obj
+
+install/treetool::
+ cp -a treetool/t `pwd`/debian/`dh_listpackages`/usr/bin/treetool
+
+get-orig-source:
+ . debian/get-orig-source
+
\ No newline at end of file
Property changes on: trunk/packages/treetool/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/treetool/trunk/debian/sample.tree
===================================================================
--- trunk/packages/treetool/trunk/debian/sample.tree (rev 0)
+++ trunk/packages/treetool/trunk/debian/sample.tree 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1 @@
+((((((Human,Chimp),Gorilla),Orang),Gibbon),Mouse),Bovine);
Added: trunk/packages/treetool/trunk/debian/treetool.1
===================================================================
--- trunk/packages/treetool/trunk/debian/treetool.1 (rev 0)
+++ trunk/packages/treetool/trunk/debian/treetool.1 2008-03-09 20:46:35 UTC (rev 1544)
@@ -0,0 +1,48 @@
+.TH TREETOOL 1 "April 16, 2001"
+.SH NAME
+treetool \- interactive tool for displaying trees
+.SH SYNOPSIS
+.B treetool
+.RI [filename] \ [options]
+.SH DESCRIPTION
+This manual page documents briefly the
+.B treetool
+utility.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program did not have a manual page.
+.PP
+\fBtreetool\fP is an interactive tool for displaying, editing, and printing
+phylogenetic trees. The tree is displayed visually on screen, in
+various formats, and the user is able to modify the format, structure,
+and characteristics of the tree. Trees may be viewed, compared,
+formatted for printing, constructed from smaller trees, etc.
+.SH OPTIONS
+This program is usually started under X from the menu, or with the command
+treetool, but also has the following commandline options:
+.TP
+.B \-h
+Display brief help and this list of options.
+.TP
+.B \-p, \-phenogram
+Specifies phenogram (boxed) tree format.
+.TP
+.B \-r, \-radial
+Specifies radial (flower) tree format.
+.TP
+.B \-auto
+Start with automatic formatting.
+.TP
+.B \-noauto
+Start without automatic formatting.
+.TP
+.B \-merge
+Start with automatic node merging.
+.TP
+.B \-nomerge
+Start without automatic node merging.
+.SH SEE ALSO
+.BR phylip (1),
+.br
+.SH AUTHOR
+This manual page was written by Dr. Guenter Bechly <gbechly at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
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