From 0a3c56553633f2af5933a6a86ba231bb27588c97 Mon Sep 17 00:00:00 2001
From: Petar Petrov
Date: Sat, 7 Oct 2017 16:05:35 +0100
Subject: academic/PhyML: Updated for version 3.3.20170530.

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
---
 academic/PhyML/PhyML.SlackBuild | 41 +++++++++++++++++++++++++++--------------
 academic/PhyML/PhyML.info       |  6 +++---
 academic/PhyML/README           | 11 +++--------
 academic/PhyML/slack-desc       |  2 +-
 4 files changed, 34 insertions(+), 26 deletions(-)

(limited to 'academic/PhyML')

diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild
index d4b3d67cae..d82f9370f5 100644
--- a/academic/PhyML/PhyML.SlackBuild
+++ b/academic/PhyML/PhyML.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for PhyML
 
-# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com
+# Copyright 2011-2017 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -25,13 +25,11 @@
 # Thanks to Niels Horn for some handy modifications and corrections.
 
 PRGNAM=PhyML
-VERSION=${VERSION:-3.2.20160530}
+SRCNAM=$(echo $PRGNAM | tr A-Z a-z)
+VERSION=${VERSION:-3.3.20170530}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
-SRCNAM=$(echo $PRGNAM | tr A-Z a-z)
-SRCVER=3.2.20160530
-
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
     i?86) ARCH=i586 ;;
@@ -64,15 +62,9 @@ set -e
 rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
-rm -rf $SRCNAM-$SRCVER
-
-if [ -e $CWD/v${SRCVER}.tar.gz ]; then
-  tar xvf $CWD/v${SRCVER}.tar.gz
-else
-  tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz
-fi
-
-cd $SRCNAM-$SRCVER
+rm -rf $SRCNAM-$VERSION
+tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
+cd $SRCNAM-$VERSION
 chown -R root:root .
 find -L . \
  \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
@@ -145,6 +137,27 @@ CXXFLAGS="$SLKCFLAGS" \
 make
 make install DESTDIR=$PKG
 
+# This is PhyTime
+./autogen.sh
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --mandir=/usr/man \
+  --enable-phytime \
+  --docdir=/usr/doc/$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
 
diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info
index 739d1befc0..3a44d2b2b0 100644
--- a/academic/PhyML/PhyML.info
+++ b/academic/PhyML/PhyML.info
@@ -1,8 +1,8 @@
 PRGNAM="PhyML"
-VERSION="3.2.20160530"
+VERSION="3.3.20170530"
 HOMEPAGE="https://github.com/stephaneguindon/phyml/"
-DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.2.20160530.tar.gz"
-MD5SUM="7a4689e2de3ac9efd7586980b07331f0"
+DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20170530/phyml-3.3.20170530.tar.gz"
+MD5SUM="8801c23dbdb295b6bbcd417f0010bb6a"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="openmpi"
diff --git a/academic/PhyML/README b/academic/PhyML/README
index fd66cda123..b6ce38f0bd 100644
--- a/academic/PhyML/README
+++ b/academic/PhyML/README
@@ -9,16 +9,11 @@ It also implements two methods to evaluate branch supports in a sound
 statistical framework (the non-parametric bootstrap and the
 approximate likelihood ratio test).
 
-NOTE 1: This also builds Phyrex and the MPI (using multiple processors)
-version of PhyML. The executable of the latter is called phyml-mpi and
-requires openmpi. If you do not want them to be built in the package,
+This also builds MPI (using multiple processors) version of PhyML, which
+requires 'openmpi'. Other additional programs built by the script are
+Phyrex and PhyTime. If you do not want them to be built in the package,
 check the SlackBuild script.
 
-NOTE 2: PhyTime used to be part of the PhyML package. However, PhyTime
-from the latest releases of PhyML does not build anymore. meanwhile,
-PhyTime is available separately, which installs the latest version that
-builds.
-
 For details and citation
 New Algorithms and Methods to Estimate Maximum-Likelihood
 Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S.,
diff --git a/academic/PhyML/slack-desc b/academic/PhyML/slack-desc
index ae498120bb..e03cd2812c 100644
--- a/academic/PhyML/slack-desc
+++ b/academic/PhyML/slack-desc
@@ -14,6 +14,6 @@ PhyML: wide range of options that were designed to facilitate standard
 PhyML: phylogenetic analyses.
 PhyML:
 PhyML: Home: http://code.google.com/p/phyml/
-PhyML: References: /usr/doc/PhyML-3.2.20160530/References
+PhyML: References: /usr/doc/PhyML-3.3.20170530/References
 PhyML:
 PhyML:
-- 
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