academic/bpp-core: Added (Bio++ Core Library)

Signed-off-by: Dave Woodfall <dave@slackbuilds.org>

5 files changed, 156 insertions, 0 deletions

diff --git a/academic/bpp-core/README b/academic/bpp-core/README
new file mode 100644
index 000000000000..6210addd2eb5
--- /dev/null
+++ b/academic/bpp-core/README
@@ -0,0 +1,8 @@
+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++ Core Library.
diff --git a/academic/bpp-core/bpp-core.SlackBuild b/academic/bpp-core/bpp-core.SlackBuild
new file mode 100644
index 000000000000..ea5ae35b5200
--- /dev/null
+++ b/academic/bpp-core/bpp-core.SlackBuild
@@ -0,0 +1,106 @@
+#!/bin/bash
+
+# Slackware build script for bpp-core
+
+# Copyright 2017-2022 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=bpp-core
+VERSION=${VERSION:-2.4.1}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+PKGTYPE=${PKGTYPE:-tgz}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i586 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+if [ ! -z "${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
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
+cd $PRGNAM-$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 {} \;
+
+# thanks Debian
+patch -p1 -i $CWD/gcc11.patch
+
+sed -i "s|cmake-package-location lib/cmake|cmake-package-location lib${LIBDIRSUFFIX}/cmake|" CMakeLists.txt
+
+mkdir -p build
+cd build
+  cmake \
+    -DCMAKE_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_INSTALL_PREFIX=/usr \
+    -DCMAKE_BUILD_TYPE=Release ..
+  make
+  make install DESTDIR=$PKG
+cd ..
+
+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.txt ChangeLog COPYING.txt $PKG/usr/doc/$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/bpp-core/bpp-core.info b/academic/bpp-core/bpp-core.info
new file mode 100644
index 000000000000..a5d5073b1c29
--- /dev/null
+++ b/academic/bpp-core/bpp-core.info
@@ -0,0 +1,10 @@
+PRGNAM="bpp-core"
+VERSION="2.4.1"
+HOMEPAGE="https://github.com/BioPP/bpp-core/"
+DOWNLOAD="https://github.com/BioPP/bpp-core/archive/v2.4.1/bpp-core-2.4.1.tar.gz"
+MD5SUM="25040b547ca63e57cb79de5815ef2584"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/bpp-core/gcc11.patch b/academic/bpp-core/gcc11.patch
new file mode 100644
index 000000000000..d4db303a25bb
--- /dev/null
+++ b/academic/bpp-core/gcc11.patch
@@ -0,0 +1,13 @@
+Description: Including limits lib to fix gcc-11 FTBFS
+Author: Nilesh Patra <nilesh@debian.org>
+Last-Update: 2021-04-15
+--- a/src/Bpp/Graph/GlobalGraph.cpp
++++ b/src/Bpp/Graph/GlobalGraph.cpp
+@@ -42,6 +42,7 @@
+ #include <sstream>
+ #include <string>
+ #include <vector>
++#include <limits>
+ 
+ #include "../Exceptions.h"
+ #include "../Text/TextTools.h"
diff --git a/academic/bpp-core/slack-desc b/academic/bpp-core/slack-desc
new file mode 100644
index 000000000000..c26a09a44335
--- /dev/null
+++ b/academic/bpp-core/slack-desc
@@ -0,0 +1,19 @@
+# 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------------------------------------------------------|
+bpp-core: bpp-core (Bio++ Core Library)
+bpp-core:
+bpp-core: Contains the Bio++ Core Library.
+bpp-core:
+bpp-core: Git: https://github.com/BioPP/bpp-core
+bpp-core:
+bpp-core:
+bpp-core:
+bpp-core:
+bpp-core:
+bpp-core: