From 08e0e1dd1b453f5b299e502cd876a70608db3339 Mon Sep 17 00:00:00 2001
From: Petar Petrov
Date: Sun, 4 Sep 2022 13:49:57 +0100
Subject: academic/PhyML: Updated for version 3.3.20220408.

Signed-off-by: Dave Woodfall <dave@slackbuilds.org>
---
 academic/PhyML/PhyML.SlackBuild | 68 ++++++++++++++++++++++-------------------
 academic/PhyML/PhyML.info       |  6 ++--
 2 files changed, 39 insertions(+), 35 deletions(-)

(limited to 'academic/PhyML')

diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild
index 41e235cda0..351fde6f1f 100644
--- a/academic/PhyML/PhyML.SlackBuild
+++ b/academic/PhyML/PhyML.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for PhyML
 
-# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com
+# Copyright 2011-2022 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -27,7 +27,7 @@
 cd $(dirname $0) ; CWD=$(pwd)
 
 PRGNAM=PhyML
-VERSION=${VERSION:-3.3.20200621}
+VERSION=${VERSION:-3.3.20220408}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 PKGTYPE=${PKGTYPE:-tgz}
@@ -123,45 +123,49 @@ sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile
 CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make
 make install DESTDIR=$PKG
 
-# This is Phyrex
-./autogen.sh
-./configure \
-  --prefix=/usr \
-  --libdir=/usr/lib${LIBDIRSUFFIX} \
-  --sysconfdir=/etc \
-  --localstatedir=/var \
-  --mandir=/usr/man \
-  --enable-phyrex \
-  --docdir=/usr/doc/$PRGNAM-$VERSION \
-  --build=$ARCH-slackware-linux
-
-# Use our CFLAGS
+# This is Phyrex but it breaks at the moment
+ ./autogen.sh
+ ./configure \
+   --prefix=/usr \
+   --libdir=/usr/lib${LIBDIRSUFFIX} \
+   --sysconfdir=/etc \
+   --localstatedir=/var \
+   --mandir=/usr/man \
+   --enable-phyrex \
+   --docdir=/usr/doc/$PRGNAM-$VERSION \
+   --build=$ARCH-slackware-linux
+
+ # Use our CFLAGS
 sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile
 
 CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" 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/=/+=/" Makefile src/Makefile
-
-CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" 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=$ARCH-slackware-linux
+#
+# # Use our CFLAGS
+# sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile
+#
+# CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make
+# make install DESTDIR=$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
 
+# fix permissions for docs
+chmod 0644 doc/*.{pdf,tex,bib}
+chmod 0644 doc/fig/*.pdf
+
 # Include some examples
 mkdir -p $PKG/usr/share/$PRGNAM
 cp -a examples $PKG/usr/share/$PRGNAM
diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info
index ec04310e99..9b34384c9f 100644
--- a/academic/PhyML/PhyML.info
+++ b/academic/PhyML/PhyML.info
@@ -1,8 +1,8 @@
 PRGNAM="PhyML"
-VERSION="3.3.20200621"
+VERSION="3.3.20220408"
 HOMEPAGE="https://github.com/stephaneguindon/phyml/"
-DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20200621/phyml-3.3.20200621.tar.gz"
-MD5SUM="12622e111c388bcb16696660033143b5"
+DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20220408/phyml-3.3.20220408.tar.gz"
+MD5SUM="b35e641af77d7f058cf1ddc73be5e0b7"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="openmpi"
-- 
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