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NOTES.md

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TODO

  • bekijk werking renv, misschien betere oplossing om per project versioned R-libraries te bepalen?
  • maak een aparte image met de system libraries, waar R-images op gebaseerd worden, met system libraries versioned en niet-versioned.
  • maak een versioned versie aan, met ook de system libraries versioned
  • na opkuist van rbleeding en rversioned, push naar docker hub
  • probeer op Diskstation image via docker hub op te starten

Versioned and mostly modularized R environments

  • mhermans/rversioned: base image with R, tidyverse and common R packages versioned
  • mhermans/rspatial: base image + geo/gis R-packages & required libraries such as GDAL
  • mhermans/rnetwork: base image + R network analysis libraries (+ bindings to mapequation)
  • mhermans/rstats: base image + various regression, modeling, stats packages

quid R + Python + reticulate + Jupyter + Rstudio image?

quid blogdown docker image met packages om posts steeds hetzelfde te hergenereren?

Docker/Rstudio combo issues

  • Rstudio does not keep track of projects (open project)
  • Git push/pull ok over HTTP, maar geen SSH?
  • Docker images starten zonder internetverbinding: docker: Error response from daemon: open /etc/resolv.conf: no such file or directory.

Docker setup

In folder wiht Dockerfile:

docker build -t mhermans/rgistest:1.0.1 --file Dockerfile .
docker build -t mhermans/rversioned:0.1.1 --file Dockerfile-rversioned-0.1.1 .
docker build -t mhermans/rlatest --no-cache --file Dockerfile . 2>&1 | tee log.txt 
sudo docker build -t mhermans/rbleeding --no-cache --file Dockerfile . 2>&1 | tee log.txt

List available images

Run image (port required for Rstudio):

docker run -v /home/mhermans/projects/hiking_vis/:/home/rstudio/hiking_vis -p 8787:8787 mhermans/rgistest

Open localhost:8787, rstudio/rstudio login

List (running) containers

docker images

Run interactive shell

docker run -i -t mhermans/rgistest /bin/bash

Docker resource use

docker stats containerid

Stop container

docker stop container_id

login to Dockerhub

docker login --username=yourhubusername --password=yourpassword --email=[email protected]

password is stored in config.json (but hashed)

List orphaned volumes

docker volume ls -qf dangling=true

Delete orphaned volumes

docker volume rm $(docker volume ls -qf dangling=true)

Docker disk usage

docker system df

Clean everything

docker system prune

... or individual aspects

docker images prune

R docker envirnonment

docker run --rm -ti -d -p 8787:8787 -v $HOME/var/data:/home/rstudio/data -v $HOME/projects/:/home/rstudio/projects/ rocker/rstudio

Docker run flags

-d daemon mode
-e environment variable. Voor Rstudie: PASSWORD=XXX ROOT=true
-v map volumes external_path:internal_path
-p map port external_port:internal_port