Add Gitpod configuration with custom Dockerfile

[jasonratcliff]

Gitpod

Configure Gitpod workspace to use a custom base image from version stable R image maintained by The Rocker Project.

To test updates, create a workspace image from the branch context for gitpod/dockerfile with the following URL:

gitpod.io/#https://github.com/jasonratcliff/thesis/tree/gitpod/dockerfile

Note the image Linux distribution given Gitpod support for Debian/Ubuntu based Docker images:

/workspace/thesis$ cat /etc/issue
Ubuntu 22.04.2 LTS \n \l

Rocker

Version-stable Rocker image bundles R v4.3.0 with geospatial dependencies:

• https://github.com/rocker-org/rocker-versioned2/wiki/geospatial_58e506b335db

Quarto Markdown

Quarto release v1.3.340 is installed from a Debian (.deb) package:

• https://docs.posit.co/resources/install-quarto/#quarto-deb-file-install

Checks

Verify Quarto version and binary path:

/workspace/thesis$ quarto check install

[✓] Checking Quarto installation......OK
      Version: 1.3.340
      Path: /opt/quarto/bin

[✓] Checking basic markdown render....OK

Note disconnect between renv.lock versioning and R v4.3.0 installation:

/workspace/thesis$ quarto check knitr

(/) Checking R installation...........Warning messages:
1: This project is configured to use R version '4.1.2', but '4.3.0' is currently being used. 
2: This project is configured to use Bioconductor '3.14', which is not compatible with R '4.3.0'.
Use 'renv::init(bioconductor = TRUE)' to re-initialize this project with the latest Bioconductor release. 
[✓] Checking R installation...........OK
      Version: 4.3.0
      Path: /usr/local/lib/R
      LibPaths:
        - /home/gitpod/.cache/R/renv/library/thesis-a03aafbd/R-4.3/x86_64-pc-linux-gnu
        - /usr/local/lib/R/library
      knitr: (None)
      rmarkdown: (None)

      The rmarkdown package is not available in this R installation.
      Install with install.packages("rmarkdown")

Currently, limited package installations in user library:

/workspace/thesis$ Rscript -e 'list.files(.libPaths()[1])'
Warning messages:
1: This project is configured to use R version '4.1.2', but '4.3.0' is currently being used. 
2: This project is configured to use Bioconductor '3.14', which is not compatible with R '4.3.0'.
Use 'renv::init(bioconductor = TRUE)' to re-initialize this project with the latest Bioconductor release. 
[1] "BiocManager" "renv"