[med-svn] r839 - in trunk/packages/treeviewx/trunk/debian: . patches
hanska-guest at alioth.debian.org
hanska-guest at alioth.debian.org
Sun Nov 18 15:06:06 UTC 2007
Author: hanska-guest
Date: 2007-11-18 15:06:06 +0000 (Sun, 18 Nov 2007)
New Revision: 839
Added:
trunk/packages/treeviewx/trunk/debian/patches/80_missing_includes.dpatch
trunk/packages/treeviewx/trunk/debian/tv.1
Modified:
trunk/packages/treeviewx/trunk/debian/changelog
trunk/packages/treeviewx/trunk/debian/install
trunk/packages/treeviewx/trunk/debian/mime-info.keys
trunk/packages/treeviewx/trunk/debian/mime-info.mime
trunk/packages/treeviewx/trunk/debian/patches/00list
trunk/packages/treeviewx/trunk/debian/rules
trunk/packages/treeviewx/trunk/debian/treeviewx.desktop
trunk/packages/treeviewx/trunk/debian/treeviewx.mime
Log:
* Fixing missing #includes
* Added statically generated tv.1 (to save buildd time)
* Other minor fixes
* Added Italian to the .desktop file
Modified: trunk/packages/treeviewx/trunk/debian/changelog
===================================================================
--- trunk/packages/treeviewx/trunk/debian/changelog 2007-11-18 14:40:57 UTC (rev 838)
+++ trunk/packages/treeviewx/trunk/debian/changelog 2007-11-18 15:06:06 UTC (rev 839)
@@ -7,8 +7,12 @@
[ David Paleino ]
* Added support for MIME types (.phb is now associated to treeviewx)
(still to be tested)
+ * Fixing missing #includes
+ * Added statically generated tv.1 (to save buildd time)
+ * Other minor fixes
+ * Added Italian to the .desktop file
- -- David Paleino <d.paleino at gmail.com> Sun, 18 Nov 2007 12:46:46 +0100
+ -- David Paleino <d.paleino at gmail.com> Sun, 18 Nov 2007 15:45:12 +0100
treeviewx (0.5.1-4) unstable; urgency=low
Modified: trunk/packages/treeviewx/trunk/debian/install
===================================================================
--- trunk/packages/treeviewx/trunk/debian/install 2007-11-18 14:40:57 UTC (rev 838)
+++ trunk/packages/treeviewx/trunk/debian/install 2007-11-18 15:06:06 UTC (rev 839)
@@ -1,2 +1 @@
-bitmaps/treeviewx.xpm /usr/share/pixmaps/
debian/treeviewx.desktop /usr/share/applications/
Modified: trunk/packages/treeviewx/trunk/debian/mime-info.keys
===================================================================
--- trunk/packages/treeviewx/trunk/debian/mime-info.keys 2007-11-18 14:40:57 UTC (rev 838)
+++ trunk/packages/treeviewx/trunk/debian/mime-info.keys 2007-11-18 15:06:06 UTC (rev 839)
@@ -1,2 +1,3 @@
-application/x-clustalw-tree:
+text/clustalw-tree:
open=tv %f
+ icon-filename=/usr/share/pixmaps/treeviewx.xpm
Modified: trunk/packages/treeviewx/trunk/debian/mime-info.mime
===================================================================
--- trunk/packages/treeviewx/trunk/debian/mime-info.mime 2007-11-18 14:40:57 UTC (rev 838)
+++ trunk/packages/treeviewx/trunk/debian/mime-info.mime 2007-11-18 15:06:06 UTC (rev 839)
@@ -1,2 +1,2 @@
-application/x-clustalw-tree
+text/clustalw-tree
ext: phb
Modified: trunk/packages/treeviewx/trunk/debian/patches/00list
===================================================================
--- trunk/packages/treeviewx/trunk/debian/patches/00list 2007-11-18 14:40:57 UTC (rev 838)
+++ trunk/packages/treeviewx/trunk/debian/patches/00list 2007-11-18 15:06:06 UTC (rev 839)
@@ -3,3 +3,4 @@
51_wxT_tview.cpp.dpatch
60_LGPLtoGPL.dpatch
70_choose_tree.dpatch
+80_missing_includes.dpatch
Added: trunk/packages/treeviewx/trunk/debian/patches/80_missing_includes.dpatch
===================================================================
--- trunk/packages/treeviewx/trunk/debian/patches/80_missing_includes.dpatch (rev 0)
+++ trunk/packages/treeviewx/trunk/debian/patches/80_missing_includes.dpatch 2007-11-18 15:06:06 UTC (rev 839)
@@ -0,0 +1,76 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 80_strlen_charactersblock.cpp.dpatch by David Paleino <d.paleino at gmail.com>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Fixes "error: ‘strlen’ was not declared in this scope" during compilation
+
+ at DPATCH@
+diff -urNad trunk~/TreeLib/Parse.cpp trunk/TreeLib/Parse.cpp
+--- trunk~/TreeLib/Parse.cpp 2007-11-18 14:39:17.000000000 +0100
++++ trunk/TreeLib/Parse.cpp 2007-11-18 14:39:18.000000000 +0100
+@@ -19,8 +19,9 @@
+ */
+
+ // $Id: Parse.cpp,v 1.9 2002/02/23 12:22:32 rdmp1c Exp $
+-
++
+ #include <ctype.h>
++#include <cstring>
+ #include "Parse.h"
+
+ // Return the next token in the string
+diff -urNad trunk~/TreeLib/treereader.cpp trunk/TreeLib/treereader.cpp
+--- trunk~/TreeLib/treereader.cpp 2007-11-18 14:39:17.000000000 +0100
++++ trunk/TreeLib/treereader.cpp 2007-11-18 14:39:36.000000000 +0100
+@@ -22,6 +22,7 @@
+
+ #include "treereader.h"
+ #include <cstdlib>
++#include <cstring>
+
+ #if __MWERKS__
+ #include <string.h>
+diff -urNad trunk~/ncl-2.0/src/charactersblock.cpp trunk/ncl-2.0/src/charactersblock.cpp
+--- trunk~/ncl-2.0/src/charactersblock.cpp 2007-11-18 14:14:43.000000000 +0100
++++ trunk/ncl-2.0/src/charactersblock.cpp 2007-11-18 14:39:18.000000000 +0100
+@@ -8,6 +8,7 @@
+ #include "discretematrix.h"
+ #include "assumptionsblock.h"
+ #include "charactersblock.h"
++#include <cstring>
+
+ using namespace std;
+
+diff -urNad trunk~/ncl-2.0/src/nexus.cpp trunk/ncl-2.0/src/nexus.cpp
+--- trunk~/ncl-2.0/src/nexus.cpp 2007-10-02 09:51:43.000000000 +0200
++++ trunk/ncl-2.0/src/nexus.cpp 2007-11-18 14:39:18.000000000 +0100
+@@ -2,6 +2,7 @@
+ #include "xnexus.h"
+ #include "nexustoken.h"
+ #include "nexus.h"
++#include <cstring>
+
+ #define NCL_NAME_AND_VERSION "NCL version 2.01"
+ #define NCL_COPYRIGHT "Copyright (c) 2000 by Paul O. Lewis"
+diff -urNad trunk~/ncl-2.0/src/nexustoken.cpp trunk/ncl-2.0/src/nexustoken.cpp
+--- trunk~/ncl-2.0/src/nexustoken.cpp 2007-10-02 09:51:43.000000000 +0200
++++ trunk/ncl-2.0/src/nexustoken.cpp 2007-11-18 14:39:18.000000000 +0100
+@@ -1,6 +1,7 @@
+ #include "nexusdefs.h"
+ #include "xnexus.h"
+ #include "nexustoken.h"
++#include <cstring>
+
+ using namespace std;
+
+diff -urNad trunk~/ncl-2.0/src/nxsstring.cpp trunk/ncl-2.0/src/nxsstring.cpp
+--- trunk~/ncl-2.0/src/nxsstring.cpp 2007-10-02 09:51:43.000000000 +0200
++++ trunk/ncl-2.0/src/nxsstring.cpp 2007-11-18 14:39:18.000000000 +0100
+@@ -20,6 +20,7 @@
+ #include <stdio.h>
+ #include <assert.h>
+ #include <math.h>
++#include <cstring>
+ #include "nxsstring.h"
+
+ nxsstring& nxsstring::operator+=( const double d )
Property changes on: trunk/packages/treeviewx/trunk/debian/patches/80_missing_includes.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Modified: trunk/packages/treeviewx/trunk/debian/rules
===================================================================
--- trunk/packages/treeviewx/trunk/debian/rules 2007-11-18 14:40:57 UTC (rev 838)
+++ trunk/packages/treeviewx/trunk/debian/rules 2007-11-18 15:06:06 UTC (rev 839)
@@ -32,22 +32,22 @@
manpages: tv.1
-config.status: patch configure
+config.status: patch
dh_testdir
CFLAGS="$(CFLAGS) -Wl,-z,defs" ./configure --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man
+ touch configure-stamp
build: config.status
build-stamp:
dh_testdir
$(MAKE)
- install -m0644 bitmaps/treeview.xpm bitmaps/treeviewx.xpm
touch $@
clean: clean-patched unpatch
clean-patched:
dh_testdir
dh_testroot
- rm -f build-stamp
+ rm -f build-stamp configure-stamp
[ ! -f Makefile ] || $(MAKE) -i distclean
dh_clean
@@ -55,11 +55,12 @@
dh_testdir
dh_testroot
dh_clean -k
- dh_installdirs usr/share/mime-info/
+ dh_installdirs usr/share/mime-info/ usr/share/pixmaps/treeviewx/
$(MAKE) install DESTDIR=$(CURDIR)/debian/treeviewx
install -m 644 debian/mime-info.mime $(CURDIR)/debian/treeviewx/usr/share/mime-info/treeviewx.mime
install -m 644 debian/mime-info.keys $(CURDIR)/debian/treeviewx/usr/share/mime-info/treeviewx.keys
+ install -m 644 bitmaps/treeview.xpm $(CURDIR)/debian/treeviewx/usr/share/pixmaps/treeviewx.xpm
binary-indep: build install
@@ -84,4 +85,4 @@
dh_builddeb
binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
+.PHONY: build clean binary-indep binary-arch binary install
Modified: trunk/packages/treeviewx/trunk/debian/treeviewx.desktop
===================================================================
--- trunk/packages/treeviewx/trunk/debian/treeviewx.desktop 2007-11-18 14:40:57 UTC (rev 838)
+++ trunk/packages/treeviewx/trunk/debian/treeviewx.desktop 2007-11-18 15:06:06 UTC (rev 839)
@@ -8,10 +8,12 @@
GenericName[en]=Tree Plotter
GenericName[fr]=Traceur d'arbres
GenericName[pt_BR]=Plotador de árvores
+GenericName[it]=Plotter di Alberi
Comment=Displays, modifies, prints and exports in SVG format phylogenetic trees
Comment[en]=Displays, modifies, prints and exports in SVG format phylogenetic trees
Comment[fr]=Affiche, modifie, imprime et exporte au format SVG des arbres phyolgénétiques
Comment[pt_BR]=Exibe, modifica e exporta em formato SVG árvores filogenéticas
+Comment[it]=Mostra, modifica, stampa ed esporta in formato SVG alberi filogenetici
Type=Application
Categories=Biology;Science;Education;
Modified: trunk/packages/treeviewx/trunk/debian/treeviewx.mime
===================================================================
--- trunk/packages/treeviewx/trunk/debian/treeviewx.mime 2007-11-18 14:40:57 UTC (rev 838)
+++ trunk/packages/treeviewx/trunk/debian/treeviewx.mime 2007-11-18 15:06:06 UTC (rev 839)
@@ -1 +1 @@
-application/x-clustalw-tree; /usr/bin/tv '%s'; description=ClustalW Phylogenetic Tree
+text/clustalw-tree; /usr/bin/tv '%s'; description=ClustalW Phylogenetic Tree
Added: trunk/packages/treeviewx/trunk/debian/tv.1
===================================================================
--- trunk/packages/treeviewx/trunk/debian/tv.1 (rev 0)
+++ trunk/packages/treeviewx/trunk/debian/tv.1 2007-11-18 15:06:06 UTC (rev 839)
@@ -0,0 +1,49 @@
+.\" Title: TREEVIEW X
+.\" Author:
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 2005-02-18
+.\" Manual:
+.\" Source:
+.\"
+.TH "TREEVIEW X" "1" "2005\-02\-18" "" ""
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+tv - displays and prints phylogenetic trees
+.SH "SYNOPSIS"
+.HP 3
+\fBtv\fR [\fIfilename\fR]
+.SH "DESCRIPTION"
+.PP
+\fBtv\fR
+is the program that starts the TreeView X GUI\.
+.PP
+TreeView X is an open source and multi\-platform program to display phylogenetic trees\. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE\-PUZZLE, and other programs)\. It allows to order the branches of the trees, and to export the trees in SVG format\.
+.PP
+If started from the command line with
+\fIfilename\fR
+as an argument, TreeView X will open the tree stored in
+\fIfilename\fR\.
+.SH "SEE ALSO"
+.PP
+At present there is is no documentation for TreeView X\. In the meantime please see the online documentation for TreeView (remember that TreeView X has only a subset of the features of TreeView)\. http://taxonomy\.zoology\.gla\.ac\.uk/rod/treeview/treeview_manual\.html
+.SH "REFERENCE"
+.PP
+Page, R\. D\. M\. 1996\. TREEVIEW: An application to display phylogenetic trees on personal computers\. Computer Applications in the Biosciences 12: 357\-358\.
+.SH "AUTHOR"
+.PP
+TreeView X
+was written by Rod Page (r\.page at bio\.gla\.ac\.uk) URL: http://darwin\.zoology\.gla\.ac\.uk/~rpage/treeviewx\.
+.PP
+This manual page was written by Charles Plessy (<charles\-debian\-nospam at plessy\.org>) for the
+Debian(TM)
+system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document under the terms of the
+GNU
+General Public License, Version 2 any later version published by the Free Software Foundation\.
+.PP
+On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\.
+.SH "COPYRIGHT"
+Copyright \(co 2006 Charles Plessy
+.br
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