System dependencies and R packages for installing on a fresh Ubuntu installation

r-packages

#!/usr/bin/env bash

sudo apt-get update -y && sudo apt-get --with-new-pkgs upgrade -y

sudo apt-get install -y \
    build-essential \
    libcurl4-openssl-dev \
    libssl-dev \
    libfreetype6-dev \
    libmagick++-dev \
    cargo \
    libxml2-dev \
    xorg \
    libx11-dev \
    libglu1-mesa-dev \
    libatlas-base-dev \
    gfortran \
    libblas-dev \
    liblapack-dev \
    python-autopep8 \
    libftgl2 \
    libcgal-dev \
    libclang-dev \
    libpq5 \
    python3-pip \
    libffi-dev \
    python3-dev \
    python3-venv \
    git \
    pandoc \
    cmake \
    g++ \
    dos2unix

# packages for TwoSampleMR
sudo apt-get install -y \
    libcurl4-openssl-dev \
    gfortran \
    libgmp-dev \
    r-cran-ggplot2 \
    r-cran-gridextra \
    r-cran-cowplot \
    r-cran-plyr \
    r-cran-reshape2 \
    r-cran-stringr \
    r-cran-knitr \
    r-cran-markdown \
    r-cran-gtable \
    r-cran-rmarkdown \
    r-cran-mendelianrandomization \
    r-cran-dplyr \
    r-cran-psych \
    r-cran-magrittr \
    r-cran-car \
    r-cran-randomforest \
    r-cran-meta \
    r-cran-data.table \
    r-cran-glmnet \
    r-cran-lattice \
    r-cran-pbapply \
    r-cran-mass \
    r-cran-cairo \
    r-cran-remotes \
    r-cran-knitr \
    r-cran-tidyverse \
    r-cran-bookdown \
    r-cran-devtools \
    r-cran-tinytex \
    r-cran-pkgdown \
    r-cran-pkgbuild \
    r-cran-markdown \
    r-cran-xfun

sudo R -e 'update.packages(ask = FALSE)'
sudo R -e "remotes::install_github('MRCIEU/TwoSampleMR')"

# install.packages(c('knitr', 'rmarkdown', 'bookdown', 'tidyverse', 'devtools', 'tinytex', 'pkgdown', 'remotes', 'markdown'), dependencies = TRUE)

sudo apt-get install -y \
    magick \
    kable \
    kableExtra

sudo R -e 'if (!requireNamespace("tinytex", quietly = TRUE)) install.packages("tinytex")'
sudo R -e 'if (!tinytex::is_tinytex()) tinytex::install_tinytex()'
sudo R -e "tinytex::tlmgr_install('fira')"

sudo R -e 'remotes::install_github("Hemken/Statamarkdown")'