academic/treeviewx: Added (Program to display phylogenetic trees).
Renamed from academic/treeview, to avoid confusion with a different package also named Treeview. Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Petar Petrov
David Spencer
parent
646d20b456
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Rod Page's TreeView X is a simple program for displaying phylogenies.
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Some of its features include:
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- reads many different tree file formats (including NEXUS, PHYLIP,
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Hennig86, NONA, MEGA, and ClustalW/X)
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- supports standard the TrueType and Postscript fonts
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- supports native graphics file format for copying pictures into
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other applications, and for saving graphics files
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- print preview
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- can print multiple trees per page and/or one tree over more than
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one page
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- has drag-and-drop facility for easy opening of files
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- Web-based online help
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- tree editor
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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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For details and citation:
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Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic
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trees on personal computers. Computer Applications in the Biosciences
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12: 357-358.
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Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic
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trees on personal computers. Computer Applications in the Biosciences
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12: 357-358
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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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if [ -x /usr/bin/update-desktop-database ]; then
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/usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
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fi
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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treeviewx: treeviewx (Program to display phylogenetic trees)
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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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treeviewx:
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#!/bin/sh
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# Slackware build script for treeviewx
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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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# 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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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=treeviewx
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SRCNAM=tv
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VERSION=${VERSION:-0.5.1}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) export ARCH=i586 ;;
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arm*) export ARCH=arm ;;
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*) export ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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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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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Disable SVG support. If you want it, you should build
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# wxGTK or wxPython including svg from contrib/src/svg
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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="$SLKCFLAGS -fpermissive" \
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./configure \
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--prefix=/usr \
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--libdir=/usr/lib${LIBDIRSUFFIX} \
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--sysconfdir=/etc \
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--localstatedir=/var \
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--mandir=/usr/man \
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--build=$ARCH-slackware-linux
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make
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make install DESTDIR=$PKG
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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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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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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a COPYING INSTALL $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cat $CWD/doinst.sh > $PKG/install/doinst.sh
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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[Desktop Entry]
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Categories=Education;
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Exec=tv
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Icon=treeviewx
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Name=TreeView X
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StartupNotify=false
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Type=Application
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GenericName=
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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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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="wxPython"
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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