configure

#!/usr/bin/env bash 

source ~/.profile

# get directory where this file is in and set as directory
JMB="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
cd $JMB

echo "i config starting"
echo "i jmb is here: $JMB"

export HERE=$JMB/bin

if [[ ${JMB} == '' ]]
then
    echo "i exporting JMB"
    echo "export JMB=$HERE" >> ~/.profile
    export JMB=$HERE
fi

if [[ $(echo "$PATH" | grep "$JMB" -F) == '' ]]
then
    echo "i updating PATH"
    echo "export PATH="$JMB${PATH:+:${PATH}}"" >> ~/.profile
    export PATH="$JMB${PATH:+:${PATH}}"
fi

echo "i making bin/ executable"
chmod +x bin/*

echo "i running dos2unix"
dos2unix bin/dos2unix-dir
./bin/dos2unix-dir bin

echo "i installing pak and scribe"

R_LIB_PAK=$(Rscript --vanilla \
    -e "cat(file.path(dirname(.Library.site[1]), 'pak-library'))"
)

R --vanilla <<EOF
lib_pak <- "$R_LIB_PAK"
stopifnot(nzchar(lib_pak))
dir.create(lib_pak, recursive = TRUE, showWarnings = FALSE)
Sys.chmod(lib_pak, "777")
if (!requireNamespace("pak", lib.loc = lib_pak, quietly = TRUE)) {
  utils::install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/", lib = lib_pak)
}
EOF

echo "i installing pack and scribe again"
./bin/pak-install source --lib-path $R_LIB_PAK

# TODO replace SCRIBE_VERSION with cran version
SCRIBE_VERSION=$(Rscript --vanilla \
    -e "lines <- readLines('https://cran.r-project.org/web/packages/scribe/index.html')" \
    -e "version <- lines[grep('Version', lines) + 1L]" \
    -e "m <- gregexpr('[0-9]?[.][0-9]?([.][0-9]?)?', version)" \
    -e "cat(as.character(numeric_version(regmatches(version, m)[[1]])))"
)

# update line in bin/pak
sed -i "s/SCRIBE_VERSION <- .*/SCRIBE_VERSION <- \"$SCRIBE_VERSION\"/g" bin/pak

# add symbolic link on linux and when in sudo
if [[ $(uname) == 'Linux' ]]
then
    # warn when not root
    if [[ $(whoami) != 'root' ]]
    then
        echo "w not root, will not add symbolic link"
    else
        echo "i adding symbolic link"
        mkdir -p /usr/local/jmb/bin
        sudo ln -s -f $JMB/bin/ /usr/local/jmb || true
        sudo chmod +x -R /usr/local/jmb/bin

        # check secure_path
        if [[ $(sudo cat /etc/sudoers | grep secure_path | grep -c $JMB/bin) == 0 ]]
        then
            echo "i adding jmb/bin to secure_path"
            sudo sed -i.bak '/secure_path/ s|$|:'$JMB'/bin|' /etc/sudoers
        fi
    fi
fi

echo "i done"
echo "i best to restart console"