A docker image to keep this site alive

Step 1: download docker

go to https://www.docker.com/products/docker-desktop/

to install docker.

Step 2 build a docker image

build a docker image from scratch with the help of chatGPT. Below is the docker file:

# Use the Rocker RStudio image
FROM rocker/rstudio:4


# Install system dependencies, including fontconfig and freetype
RUN apt-get update && apt-get install -y \
    tzdata \
    libcurl4-openssl-dev \
    libssl-dev \
    libxml2-dev \
    libsqlite3-0 \
    libclang-dev \
    psmisc \
    sudo \
    wget \
    zlib1g-dev \
    libgit2-dev \
    libfontconfig1-dev \
    libfreetype6-dev \
    pkg-config \
    libharfbuzz-dev \
    libfribidi-dev \
    libpng-dev \
    libjpeg-dev \
    libtiff5-dev \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

RUN apt-get update && apt-get install -y libbz2-dev

# Set the timezone to avoid interactive mode
ENV DEBIAN_FRONTEND=noninteractive

# Set the timezone to Boston (EST)
RUN echo "America/New_York" > /etc/timezone && \
    ln -snf /usr/share/zoneinfo/America/New_York /etc/localtime && \
    dpkg-reconfigure -f noninteractive tzdata


# Install Hugo (ARM64)
RUN wget https://github.com/gohugoio/hugo/releases/download/v0.42/hugo_0.42_Linux-ARM64.tar.gz && \
    tar -xvzf hugo_0.42_Linux-ARM64.tar.gz hugo && \
    mv hugo /usr/local/bin/ && \
    rm hugo_0.42_Linux-ARM64.tar.gz

#make a directory to be mounted to the host machine for installing R packages
RUN mkdir /usr/local/lib/R/host-site-library

RUN echo '.libPaths(c("/usr/local/lib/R/host-site-library", .libPaths()))' > /home/rstudio/.Rprofile

# Install blogdown package
RUN R -e "install.packages('blogdown', version = '1.0', repos='http://cran.rstudio.com/')" 
RUN R -e "install.packages('devtools')"
RUN R -e "install.packages('tidyverse')"



# Expose ports for RStudio Server and Hugo
EXPOSE 8787 1313

build the image

docker build -t my-rstudio-blogdown .

use the pre-built rstudio image which contains rstudio server to avoid install it from scratch.

I tried to install Rstudio server inside the docker image and it gave me errors. common problem is the rstudio server deb file url is not correct.

Make sure it is ARM architechture compatible since I am using a macbook pro with M3 chip.

common errors are missing libraries during apt-get install for devtools. Even it did not error out during the image building process, the devtools does not work inside the Rstudio.

library(devtools) shows the package is not installed.

so I installed manually inside Rstudio:

install.packges("devtools")

and get error messages for missing libraries. I then gave the error messages to ChatGPT, and it added the libraires:

     zlib1g-dev \
    libgit2-dev \
    libfontconfig1-dev \
    libfreetype6-dev \
    pkg-config \
    libharfbuzz-dev \
    libfribidi-dev \
    libpng-dev \
    libjpeg-dev \
    libtiff5-dev \

I then iterate several times until I have devtools installed correctly during the image building process.

run the docker container

In your host machine, mkdir ~/R/host-site-library.

docker run -d -p 8787:8787 -p 8080:8080 \
    -v ~/githup_repo/DivingIntoGeneticsAndGenomics:/home/rstudio/my_blog \
    -v ~/R/host-site-library:/usr/local/lib/R/host-site-library \
    -e USER=rstudio \
    -e PASSWORD=test \
    --name my-rstudio-hugo-container my-rstudio-blogdown

-v ~/R/host-site-library:/usr/local/lib/R/host-site-library will mount the ~/R/host-site-library folder to the /usr/local/lib/R/host-site-library inside the container. All your newly installed R packages will be stored there so you do not need to re-install them.

Go to localhost:8787 to log in the Rstudio server. User name: rstudio, password: test.

Within Rstudio, you need to specify the port (which we mapped to local 8080) and the host. If you do not specify the host to be 0.0.0.0, you can not access the website either.

blogdown::serve_site(port = 8080, host = '0.0.0.0')

Now, go to your web browser and type localhost:8080 you should see the blogdown website!

additional glitch

My blog uses hugo0.42, and blogdown1.0 can render the website, but the Rstudio add-in for creating a new post does not work.

Manually create a post inside the content/post folder using file name format “2024-08-11-my-test.Rmd” and use the yaml header with a format below:

---
title: "Your Post Title"
author: "Your Name"
date: "2024-08-11"
output:
  blogdown::html_page:
    self_contained: false
tags: ["tag1", "tag2"]
categories: ["category1"]
---

push the docker image to dockerhub

I pushed the container to dockerhub so I can pull it on another macbook pro.

docker login

docker tag my-rstudio-blogdown crazyhottommy/my-rstudio-blogdown:latest

docker push crazyhottommy/my-rstudio-blogdown:latest

Final tips:

remove all containers and images

docker rm -vf $(docker ps -aq)
docker rmi -f $(docker images -aq)

You can git clone the docker file at https://github.com/crazyhottommy/blogdown1.0_hug0.4_docker

Happy Learning!

Tommy