Set up GitHub Codespace

Generic steps to make the codespace my style

Easiest Way

The easiest way to set up a GitHub Codespace with your preferred configuration is to use a .devcontainer configuration. This approach lets you define your development environment as code:

1. Create a .devcontainer folder in your repository
2. Add a devcontainer.json file with your configuration

For example, the eddelbuettel/r2u repository provides a ready-to-use configuration when launching a Codespace from the repository. You can find detailed instructions in their Codespaces documentation.

Prompts instruct the GitHub Agent

- When there are syntax errors that cannot be easily fixed, the issue seems if often incomplete or fragmented code. Write clean versions instead, also, try to delete the version non-clean afterwards with the confirmation from me. 
- 

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Here’s a sample configuration for R and Quarto manually set by my self:

Basics for R

• Install R and Quarto

sudo apt-get update && sudo apt-get install -y r-base

wget https://quarto.org/download/latest/quarto-linux-amd64.deb
sudo apt-get install -y ./quarto-linux-amd64.deb
rm quarto-linux-amd64.deb

• Install Pandoc

sudo apt-get update && sudo apt-get install -y pandoc

• Install Extension: REditorSupport
  • install the requred packages: sudo Rscript -e "install.packages('languageserver', repos='https://cloud.r-project.org/')" sudo Rscript -e "install.packages('httpgd', repos='https://cloud.r-project.org/')"
• Install often used R packages

Note for certain packages, some additional system packages are required. From example, for PMCMRplus package, libmpfr need to be installed.

sudo apt update
sudo apt install libmpfr-dev

sudo Rscript -e "install.packages('devtools', repos='https://cloud.r-project.org/')"

## Example: dependencies for drcHelper
install.packages("Rmpfr")
install.packages(c(
   "multcomp", "PMCMRplus", "dplyr", "tidyselect", "lme4", "bmd",
  "ggplot2", "scales", "metafor", "rstatix", "DescTools", "isotone"
))
install.packages("remotes") # if not already installed

remotes::install_github("DoseResponse/bmd@a3bd9c6113e35d43e0990614469dabb10cd409bd")
remotes::install_github("DoseResponse/drc")
remotes::install_github("DoseResponse/drcData")

To clean up lock files and install a package: rm -f /home/codespace/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-ragg && Rscript -e "install.packages('ragg', repos='https://cloud.r-project.org/')"

For rendering the pkgdown website, additional packages are neede

install.packages(c(
  "GLMcat", "kableExtra", "emmeans", "outliers", "drda", "pander", "ggnewscale", "patchwork", "ggprism", "plyr","MCPMpd"
))

• Install radian

## Ubuntu 23.04 or above, my current code space is 4.24
lsb_release -a
sudo apt update
sudo apt install pipx
pipx ensurepath

# install released version
pipx install radian
# or the dev version
pipx install git+https://github.com/randy3k/radian
# to run radian
radian

To find out the path of radian: which radian.

To associate R code execution in VS Code with radian instead of the default R terminal, follow these steps:

1. Install the VS Code R extension (if not already installed).
2. Set radian as the R terminal in VS Code settings:

• Open VS Code settings (Ctrl+,).
• Search for r.rterm.linux.
• Set its value to the path of radian

Install R 4.5 or higher

Here are step-by-step instructions to upgrade R to version 4.5 or higher on Ubuntu 24.04:

Remove the old R version (optional):

sudo apt remove --purge r-base r-base-core r-recommended r-base-dev

Install required dependencies:

sudo apt update
sudo apt install -y --no-install-recommends software-properties-common dirmngr gnupg apt-transport-https ca-certificates

Add the CRAN GPG key:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 'E298A3A825C0D65DFD57CBB651716619E084DAB9'

Add the CRAN repository for R (for Ubuntu 24.04 “Noble”):

echo "deb https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" | sudo tee /etc/apt/sources.list.d/cran.list

Update package list:

sudo apt update

Install the latest R version:

sudo apt install -y r-base

Verify the R version:

R --version

This should install R 4.5.x or newer.

Get around CRAN checks

Github pages publishing workflow