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academic/treeviewx: Updated for version 1.18.4.2171_ac2afe5f8.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Kevin Matthew
Willy Sudiarto Raharjo
parent
d2a745ae39
commit
99f155ea31
7 changed files with 91 additions and 85 deletions
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@ -15,7 +15,8 @@ Some of its features include:
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Note!
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This program is different from Michael Eisen's TreeView for matrix-
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like display of expression data.
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like display of expression data. Also, we build the sources distributed
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by Debian.
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For details and citation:
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Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic
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@ -1,71 +0,0 @@
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--- tv-0.5.1/ncl-2.0/src/charactersblock.cpp.orig 2017-08-13 08:38:11.451581249 +0700
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+++ tv-0.5.1/ncl-2.0/src/charactersblock.cpp 2017-08-13 08:38:25.267599533 +0700
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@@ -8,6 +8,7 @@
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#include "discretematrix.h"
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#include "assumptionsblock.h"
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#include "charactersblock.h"
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+#include <cstring>
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using namespace std;
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--- tv-0.5.1/ncl-2.0/src/nexus.cpp.orig 2017-08-13 08:40:07.443734383 +0700
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+++ tv-0.5.1/ncl-2.0/src/nexus.cpp 2017-08-13 08:40:17.625747774 +0700
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@@ -2,6 +2,7 @@
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#include "xnexus.h"
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#include "nexustoken.h"
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#include "nexus.h"
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+#include <cstring>
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#define NCL_NAME_AND_VERSION "NCL version 2.01"
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#define NCL_COPYRIGHT "Copyright (c) 2000 by Paul O. Lewis"
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--- tv-0.5.1/ncl-2.0/src/nexustoken.cpp.orig 2017-08-13 08:41:41.569857692 +0700
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+++ tv-0.5.1/ncl-2.0/src/nexustoken.cpp 2017-08-13 08:41:52.463871895 +0700
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@@ -1,6 +1,7 @@
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#include "nexusdefs.h"
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#include "xnexus.h"
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#include "nexustoken.h"
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+#include <cstring>
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using namespace std;
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--- tv-0.5.1/ncl-2.0/src/nxsstring.cpp.orig 2017-08-13 08:42:36.847929712 +0700
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+++ tv-0.5.1/ncl-2.0/src/nxsstring.cpp 2017-08-13 08:42:48.870945321 +0700
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@@ -20,6 +20,7 @@
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#include <stdio.h>
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#include <assert.h>
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#include <math.h>
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+#include <cstring>
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#include "nxsstring.h"
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nxsstring& nxsstring::operator+=( const double d )
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--- tv-0.5.1/TreeLib/Parse.cpp.orig 2017-08-13 08:43:50.188024809 +0700
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+++ tv-0.5.1/TreeLib/Parse.cpp 2017-08-13 08:44:00.407038015 +0700
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@@ -23,6 +23,7 @@
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#include <ctype.h>
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#include "Parse.h"
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+#include <cstring>
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// Return the next token in the string
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tokentype Parser::NextToken ()
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--- tv-0.5.1/TreeLib/TreeLib.cpp.orig 2017-08-13 08:45:24.898146879 +0700
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+++ tv-0.5.1/TreeLib/TreeLib.cpp 2017-08-13 08:45:33.518157938 +0700
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@@ -23,6 +23,7 @@
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#include "TreeLib.h"
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#include "Parse.h"
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+#include <cstdlib>
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#include <vector>
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--- tv-0.5.1/TreeLib/treereader.cpp.orig 2017-08-13 08:47:09.041280171 +0700
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+++ tv-0.5.1/TreeLib/treereader.cpp 2017-08-13 08:51:04.192577614 +0700
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@@ -22,6 +22,8 @@
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// $Id: treereader.cpp,v 1.5 2003/09/10 12:58:16 rdmp1c Exp $
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#include "treereader.h"
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+#include <cstring>
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+#include <stdlib.h>
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#if __MWERKS__
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#include <string.h>
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@ -11,7 +11,7 @@ treeviewx:
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treeviewx: TreeView X provides a simple way to view the contents of a NEXUS,
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treeviewx: PHYLIP, Hennig86, Clustal, or other format tree file.
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treeviewx:
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treeviewx: Home: http://code.google.com/p/treeviewx/
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treeviewx:
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treeviewx:
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treeviewx:
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treeviewx:
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65
academic/treeviewx/treeviewx.1
Normal file
65
academic/treeviewx/treeviewx.1
Normal file
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@ -0,0 +1,65 @@
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'\" t
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.\" Title: TREEVIEW X
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.\" Author: [see the "AUTHOR" section]
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.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
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.\" Date: 06/23/2011
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.\" Manual: User Manuals
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.\" Source: TreeView X 0.5
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.\" Language: English
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.\"
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.TH "TREEVIEW X" "1" "06/23/2011" "TreeView X 0.5" "User Manuals"
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.\" -----------------------------------------------------------------
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.\" * Define some portability stuff
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.\" -----------------------------------------------------------------
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.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.\" http://bugs.debian.org/507673
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.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
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.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.ie \n(.g .ds Aq \(aq
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.el .ds Aq '
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.\" -----------------------------------------------------------------
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.\" * set default formatting
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.\" -----------------------------------------------------------------
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.\" disable hyphenation
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.nh
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.\" disable justification (adjust text to left margin only)
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.ad l
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.\" -----------------------------------------------------------------
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.\" * MAIN CONTENT STARTS HERE *
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.\" -----------------------------------------------------------------
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.SH "NAME"
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TreeView_X \- displays and prints phylogenetic trees
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.SH "SYNOPSIS"
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.HP \w'\fBtv\fR\ 'u
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\fBtv\fR [\fIfilename\fR]
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.SH "DESCRIPTION"
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.PP
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\fBtv\fR
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is the program that starts the TreeView X GUI\&.
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.PP
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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 one to order the branches of the trees, and to export the trees in SVG format\&.
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.PP
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If started from the command line with
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filename
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as an argument, TreeView X will open the tree stored in
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filename\&.
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.SH "SEE ALSO"
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.PP
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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
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.SH "REFERENCE"
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.PP
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Page, R\&. D\&. M\&. 1996\&. TREEVIEW: An application to display phylogenetic trees on personal computers\&. Computer Applications in the Biosciences 12: 357\-358\&.
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.SH "AUTHOR"
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.PP
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TreeView X
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was written by Rod Page (r\&.page@bio\&.gla\&.ac\&.uk) URL: http://darwin\&.zoology\&.gla\&.ac\&.uk/~rpage/treeviewx\&.
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.PP
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This manual page was written by Charles Plessy (plessy@debian\&.org) for the
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Debian(TM)
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system (but may be used by others)\&.
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.PP
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Permission is granted to copy, distribute and/or modify TreeView\ \&X and this document under the terms of the
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GNU
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General Public License, Version 2 or any later version published by the Free Software Foundation\&.
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.PP
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On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common\-licenses/GPL\-2\&.
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@ -5,7 +5,7 @@
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# Renamed to from "treeview" to "treeviewx" in 2018 to avoid confusion
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# with Michael Eisen's TreeView for matrix-like display of expression data.
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# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com
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# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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@ -27,7 +27,9 @@
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PRGNAM=treeviewx
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SRCNAM=tv
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VERSION=${VERSION:-0.5.1}
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SRCVER=0.5
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VERSION=${VERSION:-0.5.1_20100723}
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SRCDATE=20100823
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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@ -63,9 +65,9 @@ set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $SRCNAM-$VERSION
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tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
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cd $SRCNAM-$VERSION
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rm -rf $SRCNAM-$SRCVER
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tar xvf $CWD/${PRGNAM}_${SRCVER}.1+${SRCDATE}.orig.tar.gz
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cd $SRCNAM-$SRCVER
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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@ -78,8 +80,6 @@ find -L . \
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# Then, of course comment the next line.
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sed "s:USE_SVG=1:USE_SVG=0:" -i configure
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patch -p1 < $CWD/cstring.patch
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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS -fpermissive" \
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./configure \
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@ -93,9 +93,20 @@ CXXFLAGS="$SLKCFLAGS -fpermissive" \
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make
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make install DESTDIR=$PKG
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# Let's rename the executable
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cd $PKG/usr/bin
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mv $SRCNAM $PRGNAM
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cd -
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# Thanks Debian for the man page
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install -D -m644 $CWD/$PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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find $PKG/usr/man -type f -exec gzip -9 {} \;
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for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
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mkdir -p $PKG/usr/share/{applications,pixmaps}
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cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
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cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
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@ -1,6 +1,6 @@
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[Desktop Entry]
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Categories=Education;
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Exec=tv
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Exec=treeviewx
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Icon=treeviewx
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Name=TreeView X
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StartupNotify=false
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@ -1,8 +1,8 @@
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PRGNAM="treeviewx"
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VERSION="0.5.1"
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HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/"
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DOWNLOAD="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz"
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MD5SUM="07e1ed8873c5f19ded7294668233bae1"
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VERSION="0.5.1_20100723"
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HOMEPAGE="https://github.com/rdmpage"
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DOWNLOAD="http://deb.debian.org/debian/pool/main/t/treeviewx/treeviewx_0.5.1+20100823.orig.tar.gz"
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MD5SUM="8059a306b723e6fb4d3befcf302b2920"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="wxPython"
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