5 files changed, 0 insertions, 201 deletions
diff --git a/academic/bpp1.9-phyl/README b/academic/bpp1.9-phyl/README
deleted file mode 100644
index 292485c428638..0000000000000
--- a/academic/bpp1.9-phyl/README
+++ /dev/null
@@ -1,10 +0,0 @@
-Bio++ is a set of C++ libraries for Bioinformatics, including sequence
-analysis, phylogenetics, molecular evolution and population genetics.
-Bio++ is Object Oriented and is designed to be both easy to use and
-computer efficient. Bio++ intends to help programmers to write
-computer expensive programs, by providing them a set of re-usable
-tools.
-
-This contains the Bio++ 1.9 (April 2010) Phyl Library. It can be
-installed along the current Bio++ suite libraries, however they better
-not be present at compile time.
diff --git a/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild b/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild
deleted file mode 100644
index 94f338cef34f2..0000000000000
--- a/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild
+++ /dev/null
@@ -1,123 +0,0 @@
-#!/bin/bash
-
-# Slackware build script for bpp1.9-phyl
-
-# Copyright 2020-2021 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.
-
-cd $(dirname $0) ; CWD=$(pwd)
-
-PRGNAM=bpp1.9-phyl
-SRCNAM=bpp-phyl
-VERSION=${VERSION:-1.9.0}
-BUILD=${BUILD:-1}
-TAG=${TAG:-_SBo}
-PKGTYPE=${PKGTYPE:-tgz}
-
-if [ -z "$ARCH" ]; then
-  case "$( uname -m )" in
-    i?86) ARCH=i586 ;;
-    arm*) ARCH=arm ;;
-       *) ARCH=$( uname -m ) ;;
-  esac
-fi
-
-# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
-# the name of the created package would be, and then exit. This information
-# could be useful to other scripts.
-if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
-  echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
-  exit 0
-fi
-
-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 [ "$ARCH" = "x86_64" ]; then
-  SLKCFLAGS="-O2 -fPIC"
-  LIBDIRSUFFIX="64"
-else
-  SLKCFLAGS="-O2"
-  LIBDIRSUFFIX=""
-fi
-
-# This is needed for vCAPS to find its libraries at runtime. Thanks Urachlay!
-LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9"
-
-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
-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 {} \;
-
-# CAPS wants TreeTemplateTools to be modified a bit...
-patch -p1 -i $CWD/caps_TreeTemplateTools.patch
-
-# Use custom install place, so libs can coexist with latest bpp
-export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH"
-sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Phyl.spec
-
-mkdir -p build
-cd build
-  cmake \
-    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \
-    -DCMAKE_INSTALL_PREFIX=/usr \
-    -DCMAKE_BUILD_TYPE=Release ..
-
-  sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Phyl/cmake_install.cmake
-  sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Phyl/cmake_install.cmake
-
-  make
-  make DESTDIR=$PKG install
-cd ..
-
-# Remove static library
-rm -f $PKG/usr/lib64/Bpp1.9/libbpp-phyl.a
-
-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 \
-  $PKG/usr/doc/$PRGNAM-$VERSION
-cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
-
-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
diff --git a/academic/bpp1.9-phyl/bpp1.9-phyl.info b/academic/bpp1.9-phyl/bpp1.9-phyl.info
deleted file mode 100644
index 26d984b0c4c31..0000000000000
--- a/academic/bpp1.9-phyl/bpp1.9-phyl.info
+++ /dev/null
@@ -1,10 +0,0 @@
-PRGNAM="bpp1.9-phyl"
-VERSION="1.9.0"
-HOMEPAGE="http://biopp.univ-montp2.fr/"
-DOWNLOAD="http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-1.9.0.tar.gz"
-MD5SUM="1b100b688faca52419e9f782798b8add"
-DOWNLOAD_x86_64=""
-MD5SUM_x86_64=""
-REQUIRES="bpp1.9-seq"
-MAINTAINER="Petar Petrov"
-EMAIL="slackalaxy@gmail.com"
diff --git a/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch b/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch
deleted file mode 100644
index b4f79029de515..0000000000000
--- a/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-diff -pruN orig/Phyl/TreeTemplateTools.h new/Phyl/TreeTemplateTools.h
---- orig/Phyl/TreeTemplateTools.h	2010-04-01 16:37:04.000000000 +0300
-+++ new/Phyl/TreeTemplateTools.h	2017-02-03 14:33:11.000000000 +0200
-@@ -191,7 +191,7 @@ class TreeTemplateTools
-     static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
-     {
-       N* leaf = tree.getNode(leafName);
--      if (!leaf->hasfather())
-+      if (!leaf->hasFather())
-         throw Exception("TreeTemplateTools::dropLeaf(). Leaf is the only node in the tree, can't remove it.");
-       N* parent = leaf->getFather();
-       if (parent->getNumberOfSons() > 2)
-@@ -203,7 +203,7 @@ class TreeTemplateTools
-       else if (parent->getNumberOfSons() == 2)
-       {
-         //We have to delete the parent node as well:
--        N* brother = parent->getson(0);
-+        N* brother = parent->getSon(0);
-         if (brother == leaf) brother = parent->getSon(1);
-         if (!parent->hasFather())
-         {
-@@ -212,7 +212,7 @@ class TreeTemplateTools
-           {
-             brother->setDistanceToFather(brother->getDistanceToFather() + leaf->getDistanceToFather());
-           }
--          tree->setRootNode(brother);
-+          tree.setRootNode(brother);
-           delete parent;
-           delete leaf;
-         }
-@@ -223,7 +223,7 @@ class TreeTemplateTools
-           {
-             brother->setDistanceToFather(brother->getDistanceToFather() + parent->getDistanceToFather());
-           }
--          unsigned int pos = gParent->getsonPosition(parent);
-+          unsigned int pos = gParent->getSonPosition(parent);
-           gParent->setSon(pos, brother);
-           delete parent;
-           delete leaf;
diff --git a/academic/bpp1.9-phyl/slack-desc b/academic/bpp1.9-phyl/slack-desc
deleted file mode 100644
index 05245c02f105d..0000000000000
--- a/academic/bpp1.9-phyl/slack-desc
+++ /dev/null
@@ -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------------------------------------------------------|
-bpp1.9-phyl: bpp1.9-phyl (Bio++ 1.9 Phyl Library)
-bpp1.9-phyl:
-bpp1.9-phyl: Contains the Bio++ 1.9 Phyl Library.
-bpp1.9-phyl:
-bpp1.9-phyl:
-bpp1.9-phyl:
-bpp1.9-phyl:
-bpp1.9-phyl:
-bpp1.9-phyl:
-bpp1.9-phyl:
-bpp1.9-phyl: