Docker + R + checkpointで再現可能な解析プロジェクトを作る

.
├── .Rprofile          【R：セッション開始時に実行するスクリプト】
├── .checkpoint/       【R：checkpointによるパッケージキャッシュ】
├── .env.example       【Docker Compose：環境変数の設定テンプレート】
├── .git/
├── .gitignore
├── LICENSE
├── Makefile           【Make：起動コマンド短縮】
├── README.md
├── codes/
│   ├── .gitignore
│   ├── README.md
│   ├── analysis.qmd   【Quarto:解析コードと結果の解釈】
│   ├── analysis_cache/
│   ├── analysis_files/
│   ├── datasets/      【Quarto:データセット】
│   ├── figures/       【Quarto:プロットの画像データ(.svg)】
│   └── templates/     【Quarto：引用文献の書誌要素とスタイル定義】
├── compose.yml        【Docker Compose：設定ファイル】
├── dev/
│   ├── docker/
│   │   ├── .Renviron
│   │   ├── .ssh/
│   │   ├── Dockerfile 【Docker：設定ファイル】
│   │   └── startup.sh*
│   └── dotfiles/　    【RStudio：設定ファイル】
└── research.Rproj     【R：Rプロジェクトファイル】

.DEFAULT_GOAL := help

.PHONY: help
help: ## show a command list ## N/A
	@echo "Command list:"
	@printf "\033[36m%-9s\033[0m %-48s %s\n" "[Target]" "[Description]" "[Product]"
	@grep -E '^[/a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | perl -pe 's%^([/a-zA-Z_-]+):.*?(##)%$$1 $$2%' | awk -F " *?## *?" '{printf "\033[36m%-9s\033[0m %-48s %s\n", $$1, $$2, $$3}'

.PHONY: up
up: ## build and run RStudio Server in the background ## docker compose up -d --build
	@docker compose up -d --build
	@echo "💡 Access: http://localhost:8787/"

.PHONY: down
down: ## stop and remove running containers and networks ## docker compose down
	@docker compose down

.PHONY: stop
stop: ## stop running containers without deleting it ## docker compose stop
	@docker compose stop

.PHONY: start
start: ## (re-)start stopped containers ## docker compose start
	@docker compose start

.PHONY: ps
ps: ## list containers for the compose-project ## docker compose ps
	@docker compose ps

.PHONY: prune
prune: ## delete unused Docker objects ## docker system prune -f
	@docker system prune -f

.PHONY: bash
bash: ## start bash in the rstudio container ## docker compose exec rstudio /bin/bash
	@docker compose exec rstudio /bin/bash

make up

[+] Building 0.3s (12/12) FINISHED
[+] Running 1/0
 ⠿ Container r-project-rstudio-1  Running        0.0s
💡 Access: http://localhost:8787/

make down

[+] Running 2/2
 ⠿ Container r-project-rstudio-1  Removed       11.8s
 ⠿ Network r-project_default      Removed        0.7s

make

Command list:
[Target]  [Description]                                    [Product]
help      show a command list                              N/A
up        build and run RStudio Server in the background   docker compose up -d --build
down      stop and remove running containers and networks  docker compose down
stop      stop running containers without deleting it      docker compose stop
start     (re-)start stopped containers                    docker compose start
ps        list containers for the compose-project          docker compose ps
prune     delete unused Docker objects                     docker system prune -f
bash      start bash in the rstudio container              docker compose exec rstudio /bin/bash

# Time zone of the Docker host machine
# Default value is "UTC"
LOCAL_TZ="UTC"

# The path to your universal dotfiles directory 
# on the Docker host machine.
# Default value is "./dev/dotfiles"
DOTFILES_ROOT="./dev/dotfiles"

# The path to your SSH private key file to connect GitHub.
# Default value is "/dev/null"
GITHUB_SSH_IDENTITY="/dev/null"

services:
  rstudio:
    build: dev/docker
    ports:
      - "8787:8787"
    environment:
      - TZ=${LOCAL_TZ:-UTC}
      - PASSWORD=password
      - DISABLE_AUTH=true
    volumes:
      - type: bind
        source: "."
        target: "/home/rstudio/project"
      - type: bind
        source: "${DOTFILES_ROOT:-./dev/dotfiles}"
        target: "/home/rstudio/dotfiles"
      - type: bind
        source: "${GITHUB_SSH_IDENTITY:-/dev/null}"
        target: "/home/rstudio/.ssh/id_github"
        read_only: true

FROM rocker/rstudio:4.1.3

# Install apt packages (including Japanese fonts)
RUN apt-get update \
  && apt-get install -y --no-install-recommends \
     ssh \
     libxt-dev \
     libxml2-dev \
     libgit2-dev \
     libfontconfig1-dev \
     fonts-ipaexfont \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*

# Install R packages
RUN install2.r -e -s -n -1 \
     checkpoint \
     pacman \
     rmarkdown \
  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds

# Add github.com to known_hosts in SSH
RUN mkdir -p /home/rstudio/.ssh \
  && ssh-keyscan -t rsa, ed25519 github.com > /home/rstudio/.ssh/known_hosts \
  && chown -R rstudio:rstudio /home/rstudio \
  && chmod 700 /home/rstudio/.ssh

# Copy the configuration files
COPY --chown=rstudio:rstudio .Renviron /home/rstudio/.Renviron
COPY --chown=rstudio:rstudio .ssh/config /home/rstudio/.ssh/config

# Copy the startup script
COPY startup.sh /startup

# Change the startup command
CMD [ "/startup" ]

options(
  warn = 1, 
  warnPartialMatchArgs = TRUE, 
  warnPartialMatchAttr = TRUE, 
  warnPartialMatchDollar = TRUE, 
  showWarnCalls = TRUE, 
  showErrorCalls = TRUE
)

---
title: "Analysis report"
subtitle: " `r Sys.time() ` "
author: "Your Name"
format: 
  html: 
    toc: true
    number-sections: true
    theme: simplex
    backgroundcolor: "#e3e3e3"
    monobackgroundcolor: "#ffffff"
    highlight-style: solarized
    code-block-bg: "#dcd6d2"
    mainfont: Times New Roman, YuMincho, Hiragino Mincho ProN, Yu Mincho,  
              MS PMincho, serif;
    linestretch: "2.5"
    self-contained: true
    code-tools: true
    code-fold: true
    link-external-icon: true
    link-external-newwindow: true
    fig-format: svg
    fig-width: 10
extract-media: "./figures"
bibliography: "./templates/0000_r-project.bib"
csl: "./templates/sage-vancouver.csl"
---

```{r}
#| label: setup
#| code-fold: false

# attach the package 'checkpoint'
library(checkpoint)

# set checkpoint date
checkpoint("2022-04-01", checkpoint_location = "../", scan_now = FALSE)

# attach packages
library(pacman)
pacman::p_load(kableExtra, tidyverse)

# save default graphics parameters
oldpar <- par(no.readonly = TRUE) 

# load data sets
df_01 <- read.csv("datasets/01_bcg.csv", na.strings = c("", "NULL"))

```