academic/treeviewx: Updated for version 1.18.4.2171_ac2afe5f8.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

7 files changed, 91 insertions, 85 deletions

diff --git a/academic/treeviewx/README b/academic/treeviewx/README
index 9e1dcb3422..218f85f4cf 100644
--- a/academic/treeviewx/README
+++ b/academic/treeviewx/README
@@ -15,7 +15,8 @@ Some of its features include:
 
 Note!
 This program is different from Michael Eisen's TreeView for matrix-
-like display of expression data.
+like display of expression data. Also, we build the sources distributed
+by Debian.
 
 For details and citation:
 Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic
diff --git a/academic/treeviewx/cstring.patch b/academic/treeviewx/cstring.patch
deleted file mode 100644
index cae987703f..0000000000
--- a/academic/treeviewx/cstring.patch
+++ /dev/null
@@ -1,71 +0,0 @@
---- tv-0.5.1/ncl-2.0/src/charactersblock.cpp.orig	2017-08-13 08:38:11.451581249 +0700
-+++ tv-0.5.1/ncl-2.0/src/charactersblock.cpp	2017-08-13 08:38:25.267599533 +0700
-@@ -8,6 +8,7 @@
- #include "discretematrix.h"
- #include "assumptionsblock.h"
- #include "charactersblock.h"
-+#include <cstring>
- 
- using namespace std;
- 
---- tv-0.5.1/ncl-2.0/src/nexus.cpp.orig	2017-08-13 08:40:07.443734383 +0700
-+++ tv-0.5.1/ncl-2.0/src/nexus.cpp	2017-08-13 08:40:17.625747774 +0700
-@@ -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"
---- tv-0.5.1/ncl-2.0/src/nexustoken.cpp.orig	2017-08-13 08:41:41.569857692 +0700
-+++ tv-0.5.1/ncl-2.0/src/nexustoken.cpp	2017-08-13 08:41:52.463871895 +0700
-@@ -1,6 +1,7 @@
- #include "nexusdefs.h"
- #include "xnexus.h"
- #include "nexustoken.h"
-+#include <cstring>
- 
- using namespace std;
- 
---- tv-0.5.1/ncl-2.0/src/nxsstring.cpp.orig	2017-08-13 08:42:36.847929712 +0700
-+++ tv-0.5.1/ncl-2.0/src/nxsstring.cpp	2017-08-13 08:42:48.870945321 +0700
-@@ -20,6 +20,7 @@
- #include <stdio.h>
- #include <assert.h>
- #include <math.h>
-+#include <cstring>
- #include "nxsstring.h"
- 
- nxsstring& nxsstring::operator+=( const double d )
---- tv-0.5.1/TreeLib/Parse.cpp.orig	2017-08-13 08:43:50.188024809 +0700
-+++ tv-0.5.1/TreeLib/Parse.cpp	2017-08-13 08:44:00.407038015 +0700
-@@ -23,6 +23,7 @@
-  
- #include <ctype.h>
- #include "Parse.h"
-+#include <cstring>
- 
- // Return the next token in the string
- tokentype Parser::NextToken ()
---- tv-0.5.1/TreeLib/TreeLib.cpp.orig	2017-08-13 08:45:24.898146879 +0700
-+++ tv-0.5.1/TreeLib/TreeLib.cpp	2017-08-13 08:45:33.518157938 +0700
-@@ -23,6 +23,7 @@
- 
- #include "TreeLib.h"
- #include "Parse.h"
-+#include <cstdlib>
- 
- #include <vector>
- 
---- tv-0.5.1/TreeLib/treereader.cpp.orig        2017-08-13 08:47:09.041280171 +0700
-+++ tv-0.5.1/TreeLib/treereader.cpp     2017-08-13 08:51:04.192577614 +0700
-@@ -22,6 +22,8 @@
-  // $Id: treereader.cpp,v 1.5 2003/09/10 12:58:16 rdmp1c Exp $
- 
- #include "treereader.h"
-+#include <cstring>
-+#include <stdlib.h>
- 
- #if __MWERKS__
-        #include <string.h>
diff --git a/academic/treeviewx/slack-desc b/academic/treeviewx/slack-desc
index 3d1a87af6b..7130ac2dc0 100644
--- a/academic/treeviewx/slack-desc
+++ b/academic/treeviewx/slack-desc
@@ -11,7 +11,7 @@ treeviewx:
 treeviewx: TreeView X provides a simple way to view the contents of a NEXUS,
 treeviewx: PHYLIP, Hennig86, Clustal, or other format tree file.
 treeviewx:
-treeviewx: Home: http://code.google.com/p/treeviewx/
+treeviewx:
 treeviewx:
 treeviewx:
 treeviewx:
diff --git a/academic/treeviewx/treeviewx.1 b/academic/treeviewx/treeviewx.1
new file mode 100644
index 0000000000..e286165f47
--- /dev/null
+++ b/academic/treeviewx/treeviewx.1
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: TREEVIEW X
+.\"    Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\"      Date: 06/23/2011
+.\"    Manual: User Manuals
+.\"    Source: TreeView X 0.5
+.\"  Language: English
+.\"
+.TH "TREEVIEW X" "1" "06/23/2011" "TreeView X 0.5" "User Manuals"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+TreeView_X \- displays and prints phylogenetic trees
+.SH "SYNOPSIS"
+.HP \w'\fBtv\fR\ 'u
+\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 one to order the branches of the trees, and to export the trees in SVG format\&.
+.PP
+If started from the command line with
+filename
+as an argument, TreeView X will open the tree stored in
+filename\&.
+.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@bio\&.gla\&.ac\&.uk) URL: http://darwin\&.zoology\&.gla\&.ac\&.uk/~rpage/treeviewx\&.
+.PP
+This manual page was written by Charles Plessy (plessy@debian\&.org) for the
+Debian(TM)
+system (but may be used by others)\&.
+.PP
+Permission is granted to copy, distribute and/or modify TreeView\ \&X and this document under the terms of the
+GNU
+General Public License, Version 2 or any later version published by the Free Software Foundation\&.
+.PP
+On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common\-licenses/GPL\-2\&.
diff --git a/academic/treeviewx/treeviewx.SlackBuild b/academic/treeviewx/treeviewx.SlackBuild
index f229fe052f..5929e48f2d 100644
--- a/academic/treeviewx/treeviewx.SlackBuild
+++ b/academic/treeviewx/treeviewx.SlackBuild
@@ -5,7 +5,7 @@
 # Renamed to from "treeview" to "treeviewx" in 2018 to avoid confusion
 # with Michael Eisen's TreeView for matrix-like display of expression data.
 
-# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com
+# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -27,7 +27,9 @@
 
 PRGNAM=treeviewx
 SRCNAM=tv
-VERSION=${VERSION:-0.5.1}
+SRCVER=0.5
+VERSION=${VERSION:-0.5.1_20100723}
+SRCDATE=20100823
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -63,9 +65,9 @@ set -e
 rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
-rm -rf $SRCNAM-$VERSION
-tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
-cd $SRCNAM-$VERSION
+rm -rf $SRCNAM-$SRCVER
+tar xvf $CWD/${PRGNAM}_${SRCVER}.1+${SRCDATE}.orig.tar.gz
+cd $SRCNAM-$SRCVER
 chown -R root:root .
 find -L . \
  \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
@@ -78,8 +80,6 @@ find -L . \
 # Then, of course comment the next line.
 sed "s:USE_SVG=1:USE_SVG=0:" -i configure
 
-patch -p1 < $CWD/cstring.patch
-
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS -fpermissive" \
 ./configure \
@@ -93,9 +93,20 @@ CXXFLAGS="$SLKCFLAGS -fpermissive" \
 make
 make install DESTDIR=$PKG
 
+# Let's rename the executable
+cd $PKG/usr/bin
+mv $SRCNAM $PRGNAM
+cd -
+
+# Thanks Debian for the man page
+install -D -m644 $CWD/$PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1
+
 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
   | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
 
+find $PKG/usr/man -type f -exec gzip -9 {} \;
+for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
+
 mkdir -p $PKG/usr/share/{applications,pixmaps}
 cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
 cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
diff --git a/academic/treeviewx/treeviewx.desktop b/academic/treeviewx/treeviewx.desktop
index ab8e3727c3..2ef02ac0d0 100644
--- a/academic/treeviewx/treeviewx.desktop
+++ b/academic/treeviewx/treeviewx.desktop
@@ -1,6 +1,6 @@
 [Desktop Entry]
 Categories=Education;
-Exec=tv
+Exec=treeviewx
 Icon=treeviewx
 Name=TreeView X
 StartupNotify=false
diff --git a/academic/treeviewx/treeviewx.info b/academic/treeviewx/treeviewx.info
index 09997ad2b9..8de22d44fb 100644
--- a/academic/treeviewx/treeviewx.info
+++ b/academic/treeviewx/treeviewx.info
@@ -1,8 +1,8 @@
 PRGNAM="treeviewx"
-VERSION="0.5.1"
-HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/"
-DOWNLOAD="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz"
-MD5SUM="07e1ed8873c5f19ded7294668233bae1"
+VERSION="0.5.1_20100723"
+HOMEPAGE="https://github.com/rdmpage"
+DOWNLOAD="http://deb.debian.org/debian/pool/main/t/treeviewx/treeviewx_0.5.1+20100823.orig.tar.gz"
+MD5SUM="8059a306b723e6fb4d3befcf302b2920"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="wxPython"