R runtime not working/installing even if in runtime.txt

Bug description

Setting up a fresh install of BinderHub (z2bh) using the helm chart binderhub-0.2.0-n361.h6f57706 doesn’t work for R environments e.g. using the binder-examples/r doesn’t install the R kernel and only allows Python.

Expected behaviour

When using repo with R runtime, JupyterHub should have R kernel and be able to run R code like mybinder.org.

Actual behaviour

If I go the the link http://<my-domain>/v2/gh/binder-examples/r/master?filepath=index.ipynb I get no option for R as seen:

How to reproduce

Follow the Zero to JupyterHub guide for Kubernetes on Google Cloud (GKE) then following Zero to BinderHub but using BinderHub helm chart version binderhub-0.2.0-n361.h6f57706 instead of the older version in the guide.

Your personal set up

Using Google Kubernetes Engine

• Version: binderhub-0.2.0-n361.h6f57706
• Configuration:

config:
  BinderHub:
    hub_url: <http://hub-url>
    use_registry: true
    image_prefix: <image/prefix>-
    template_path: /etc/binderhub/custom/templates
    extra_static_path: /etc/binderhub/custom/static
    extra_static_url_prefix: /extra_static/
    template_variables:
        EXTRA_STATIC_URL_PREFIX: "/extra_static/"

initContainers:
  - name: git-clone-templates
    image: alpine/git
    args:
      - clone
      - --single-branch
      - --branch=master
      - --depth=1
      - --
      - https://github.com/<repo>
      - /etc/binderhub/custom
    securityContext:
      runAsUser: 0
    volumeMounts:
      - name: custom-templates
        mountPath: /etc/binderhub/custom
extraVolumes:
  - name: custom-templates
    emptyDir: {}
extraVolumeMounts:
  - name: custom-templates
    mountPath: /etc/binderhub/custom

cors: &cors
  allowOrigin: '*'

jupyterhub:
  custom:
    cors: *cors
  cull:
    timeout: 300
    every: 60

Maybe I’m missing something during setup? Any help would be ver much appreciated. Thank you!

[AppsusUK]

@manics thank you, your suggestion to use a recent version of repo2docker worked!

Here is the updated config for anyone else who faces the same issue:

config:
  BinderHub:
    hub_url: <http://hub-url>
    use_registry: true
    build_image: jupyter/repo2docker:0.11.0-184.g30ef220
    image_prefix: <image/prefix>-
    template_path: /etc/binderhub/custom/templates
    extra_static_path: /etc/binderhub/custom/static
    extra_static_url_prefix: /extra_static/
    template_variables:
        EXTRA_STATIC_URL_PREFIX: "/extra_static/"

initContainers:
  - name: git-clone-templates
    image: alpine/git
    args:
      - clone
      - --single-branch
      - --branch=master
      - --depth=1
      - --
      - https://github.com/<repo>
      - /etc/binderhub/custom
    securityContext:
      runAsUser: 0
    volumeMounts:
      - name: custom-templates
        mountPath: /etc/binderhub/custom
extraVolumes:
  - name: custom-templates
    emptyDir: {}
extraVolumeMounts:
  - name: custom-templates
    mountPath: /etc/binderhub/custom

cors: &cors
  allowOrigin: '*'

jupyterhub:
  custom:
    cors: *cors
  cull:
    timeout: 300
    every: 60

[manics]

@AppsusUK BinderHub uses repo2docker under the hood. The version used by mybinder.org is almost always ahead of the last tagged release: https://github.com/jupyterhub/mybinder.org-deploy/blob/1bb53c3dea862c6cf18bd0b09a77007837631297/mybinder/values.yaml#L83

In your gist logs it looks like your version of repo2docker is quite old, could you perhaps try a more recent version? https://gist.github.com/AppsusUK/cb88be934ca03b97fbb3f02d310a4254#file-gistfile1-txt-L175

{"message": "Step 42/46 : LABEL repo2docker.version=\"0.10.0+0.g69c09ae.dirty\"", "phase": "building"}

If you want you can install repo2docker locally to build your repo.