<commit_before>#!/bin/bash
set -e

echo
echo "*****************************************"
echo "*** Installing R packages ***"
echo "*****************************************"

# libudunits2-dev required for udunits, needed by mapview
apt-get install -y \
    r-cran-rmpi \
    libudunits2-dev

export JAVA_CPPFLAGS="-I${JAVA_HOME}/include -I${JAVA_HOME}/include/linux"
export JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/jre/lib/amd64/server:${JAVA_HOME}/jre/lib/amd64
R CMD javareconf

R -e "install.packages('pacman', dependencies=TRUE, repos='http://cran.rstudio.com/')"
R -e "pacman::p_load_gh(\
        'verbe039/bfast', \
        'loicdtx/bfastSpatial'\
    )"
R -e "pacman::p_load(\
        'corrplot',\
        'devtools',\
        'dismo',\
        'dplyr',\
        'DT',\
        'ggmap',\
        'ggplot2',\
        'htmltools',\
        'knitr',\
        'leaflet',\
        'lubridate',\
        'mapview',\
        'plyr',\
        'random',\<commit_msg>Changed to optimized BFAST implementation.<commit_after>#!/bin/bash
set -e

echo
echo "*****************************************"
echo "*** Installing R packages ***"
echo "*****************************************"

# libudunits2-dev required for udunits, needed by mapview
apt-get install -y \
    r-cran-rmpi \
    libudunits2-dev

export JAVA_CPPFLAGS="-I${JAVA_HOME}/include -I${JAVA_HOME}/include/linux"
export JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/jre/lib/amd64/server:${JAVA_HOME}/jre/lib/amd64
R CMD javareconf

R -e "install.packages('pacman', dependencies=TRUE, repos='http://cran.rstudio.com/')"
R -e "pacman::p_load_gh(\
        'appelmar/bfast',\
        'appelmar/strucchange',\
        'loicdtx/bfastSpatial'\
    )"
R -e "pacman::p_load(\
        'corrplot',\
        'devtools',\
        'dismo',\
        'dplyr',\
        'DT',\
        'ggmap',\
        'ggplot2',\
        'htmltools',\
        'knitr',\
        'leaflet',\
        'lubridate',\
        'mapview',\
        'plyr',\
        'random',\
{'fraction_non_alphanumeric': 0.24557857503789793, 'fraction_numerical': 0.008590197069226882, 'mean_word_length': 2.680297397769517, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4625102', 'n_tokens_mistral': 760, 'n_tokens_neox': 680, 'n_words': 118}