academic/PhyTime: Removed (Included in PhyML).

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

academic/PhyTime/PhyTime.SlackBuild

@@ -1,113 +0,0 @@
-#!/bin/sh
-
-# Slackware build script for PhyTime
-
-# Copyright 2016 Petar Petrov slackalaxy@gmail.com
-# All rights reserved.
-#
-# Redistribution and use of this script, with or without modification, is
-# permitted provided that the following conditions are met:
-#
-# 1. Redistributions of this script must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#
-#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
-#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
-#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-PRGNAM=PhyTime
-VERSION=${VERSION:-20131112}
-BUILD=${BUILD:-1}
-TAG=${TAG:-_SBo}
-
-SRCNAM=phyml
-SRCVER=20120412
-
-if [ -z "$ARCH" ]; then
-  case "$( uname -m )" in
-    i?86) ARCH=i586 ;;
-    arm*) ARCH=arm ;;
-       *) ARCH=$( uname -m ) ;;
-  esac
-fi
-
-CWD=$(pwd)
-TMP=${TMP:-/tmp/SBo}
-PKG=$TMP/package-$PRGNAM
-OUTPUT=${OUTPUT:-/tmp}
-
-if [ "$ARCH" = "i586" ]; then
-  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
-  LIBDIRSUFFIX=""
-elif [ "$ARCH" = "i686" ]; then
-  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
-  LIBDIRSUFFIX=""
-elif [ "$ARCH" = "x86_64" ]; then
-  SLKCFLAGS="-O2 -fPIC"
-  LIBDIRSUFFIX="64"
-else
-  SLKCFLAGS="-O2"
-  LIBDIRSUFFIX=""
-fi
-
-set -e
-
-rm -rf $PKG
-mkdir -p $TMP $PKG $OUTPUT
-cd $TMP
-rm -rf $SRCNAM-$SRCVER
-tar xvf $CWD/${SRCNAM}_${SRCVER}.orig.tar.gz
-cd $SRCNAM-$SRCVER
-chown -R root:root .
-find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
-  -o -perm 511 \) -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
- -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
-
-# Apply version patch
-cd src
-  patch -i $CWD/$VERSION.patch
-cd ..
-
-./configure \
-  --prefix=/usr \
-  --libdir=/usr/lib${LIBDIRSUFFIX} \
-  --sysconfdir=/etc \
-  --localstatedir=/var \
-  --enable-phytime \
-  --mandir=/usr/man \
-  --docdir=/usr/doc/$PRGNAM-$VERSION \
-  --build=$ARCH-slackware-linux
-
-# Use our CFLAGS
-sed -i "/^CFLAGS/s/=/+=/" src/Makefile
-sed -i "/^CFLAGS/s/=/+=/" Makefile
-
-CFLAGS="$SLKCFLAGS" \
-CXXFLAGS="$SLKCFLAGS" \
-make
-make install DESTDIR=$PKG
-
-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
-
-mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
-cp -a \
-  AUTHORS ChangeLog COPYING INSTALL README \
-  $PKG/usr/doc/$PRGNAM-$VERSION
-cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
-cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
-
-mkdir -p $PKG/install
-cat $CWD/slack-desc > $PKG/install/slack-desc
-
-cd $PKG
-/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}

academic/PhyTime/PhyTime.info

@@ -1,10 +0,0 @@
-PRGNAM="PhyTime"
-VERSION="20131112"
-HOMEPAGE="https://github.com/stephaneguindon/phyml/"
-DOWNLOAD="http://http.debian.net/debian/pool/main/p/phyml/phyml_20120412.orig.tar.gz"
-MD5SUM="d2207a3d6caf633c43239a01ce70f244"
-DOWNLOAD_x86_64=""
-MD5SUM_x86_64=""
-REQUIRES=""
-MAINTAINER="Petar Petrov"
-EMAIL="slackalaxy@gmail.com"

academic/PhyTime/README

@@ -1,2 +0,0 @@
-PhyTime is a PhyML - related software, that estimates maximum likelihood
-phylogenies from alignments of nucleotide or amino acid sequences.

academic/PhyTime/References

@@ -1,8 +0,0 @@
-New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies:
-Assessing the Performance of PhyML 3.0. Guindon S., Dufayard J.F.,
-Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology,
-59(3):307-21, 2010.
-
-Bayesian estimation of divergence times from large sequence alignments.
-Mol Biol Evol. 2010 Aug;27(8):1768-81. doi: 10.1093/molbev/msq060.
-Epub 2010 Mar 1.

academic/PhyTime/slack-desc

@@ -1,19 +0,0 @@
-# HOW TO EDIT THIS FILE:
-# The "handy ruler" below makes it easier to edit a package description.
-# Line up the first '|' above the ':' following the base package name, and
-# the '|' on the right side marks the last column you can put a character in.
-# You must make exactly 11 lines for the formatting to be correct.  It's also
-# customary to leave one space after the ':' except on otherwise blank lines.
-
-       |-----handy-ruler------------------------------------------------------|
-PhyTime: PhyTime (Phylogenetic estimation using Maximum Likelihood)
-PhyTime:
-PhyTime: PhyTime estimates maximum likelihood phylogenies from alignments
-PhyTime: of nucleotide or amino acid sequences.
-PhyTime:
-PhyTime:
-PhyTime:
-PhyTime:
-PhyTime:
-PhyTime:
-PhyTime: