r_spdep_dependency_install.sh_backup

#!/bin/bash
# Script to install udunits2 2.1.19, gdal 2.1.0, geos 3.6.2, proj 4.8.0 with nad and epsg
# Written by Ghanghoon "Will" Paik (gip5038@psu.edu)
# June 25 2019
# Updated: July 19 2019
# NOTE: Submit it as a job is recommended (takes long time to build ~2 hrs)

if [[ ! -z "$PBS_NODEFILE" ]]; then
	NP=$(wc -l $PBS_NODEFILE | awk '{print $1}')
else
	NP=1;
fi

cd ~/scratch
mkdir tmp_lib
cd tmp_lib
TMPDIR=~/scratch/tmp_lib

module load gcc/5.3.1

# "units" requires udunits2-devel
wget http://download-ib01.fedoraproject.org/pub/epel/6/x86_64/Packages/u/udunits2-2.1.19-1.el6.x86_64.rpm
wget http://download-ib01.fedoraproject.org/pub/epel/6/x86_64/Packages/u/udunits2-devel-2.1.19-1.el6.x86_64.rpm

rpm2cpio udunits2-2.1.19-1.el6.x86_64.rpm | cpio -idmv
rpm2cpio udunits2-devel-2.1.19-1.el6.x86_64.rpm | cpio -idmv

# "sf" requires GDAL >= 2.0.1, GEOS 3.6.2, PROJ >= 4.8, PROJ-NAD, and PROJ-EPSG
# Install GDAL
wget https://github.com/OSGeo/gdal/archive/v2.1.0.tar.gz
tar -xf v2.1.0.tar.gz
cd gdal-2.1.0/gdal
./configure --prefix=$TMPDIR/usr
make -j $NP && make install

cd $TMPDIR

# Install GEOS
wget http://download.osgeo.org/geos/geos-3.6.2.tar.bz2
tar -xf geos-3.6.2.tar.bz2
cd geos-3.6.2
./configure --prefix=$TMPDIR/usr
make -j $NP && make install

cd $TMPDIR

wget http://elgis.argeo.org/repos/6/elgis/x86_64//proj-4.8.0-3.el6.x86_64.rpm
wget http://elgis.argeo.org/repos/6/elgis/x86_64//proj-devel-4.8.0-3.el6.x86_64.rpm
wget http://elgis.argeo.org/repos/6/elgis/x86_64//proj-epsg-4.8.0-3.el6.x86_64.rpm
wget http://elgis.argeo.org/repos/6/elgis/x86_64//proj-nad-4.8.0-3.el6.x86_64.rpm

rpm2cpio proj-4.8.0-3.el6.x86_64.rpm | cpio -idmv
rpm2cpio proj-devel-4.8.0-3.el6.x86_64.rpm | cpio -idmv
rpm2cpio proj-epsg-4.8.0-3.el6.x86_64.rpm | cpio -idmv
rpm2cpio proj-nad-4.8.0-3.el6.x86_64.rpm | cpio -idmv

cd $TMPDIR

mv usr ~/spdep_dep

cd ~/scratch
rm -rf tmp_lib

echo "export PATH=$PATH:$HOME/spdep_dep/bin" >> ~/.bashrc
echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/spdep_dep/lib:$HOME/spdep_dep/lib64:/usr/lib64" >> ~/.bashrc
echo "export CPATH=$CPATH:$HOME/spdep_dep/include" >> ~/.bashrc


#install.packages("units", configure.args = "--with-udunits2-lib=$HOME/spdep_dep/lib64")
#install.packages("sf", configure.args = "--with-gdal-config=$HOME/spdep_dep/bin/gdal-config --with-gdal-lib=$HOME/spdep_dep/lib --with-proj-lib=$HOME/spdep_dep/lib64 --with-proj-include=$HOME/spdep_dep/include --with-proj-share=$HOME/spdep_dep/share/proj --with-geos-config=$HOME/spdep_dep/bin/geos-config")
#install.packages("spdep")

#install.packages("sf", configure.args = "--with-gdal-config=/gpfs/scratch/gip5038/test/r/usr/bin/gdal-config --with-gdal-lib=/gpfs/scratch/gip5038/test/r/usr/lib --with-proj-lib=/gpfs/scratch/gip5038/test/r/usr/lib64 --with-proj-include=/gpfs/scratch/gip5038/test/r/usr/include --with-proj-share=/gpfs/scratch/gip5038/test/r/usr/share/proj --with-geos-config=/gpfs/scratch/gip5038/test/r/usr/bin/geos-config")