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Romain Primet
@rprimet
sorry for the noise
Romain Primet
@rprimet

Still I'm still not yet understanding the config system changes, if I set up something like

config:
    Authenticator:
      enable_auth_state: true
    CryptKeeper:
      keys:
        - "secret"
    JupyterHub:
      authenticator_class: "GitLabOAuthenticator"
    GitLabOAuthenticator:
      callbackUrl: http://192.168.49.2:30902/hub/oauth_callback
      clientId: "client_id"
      clientSecret: "client_secret"

then in the minikube logs, I get

[C 2021-03-04 14:12:21.101 JupyterHub application:89] Bad config encountered during initialization: The 'authenticator_class' trait of <jupyterhub.app.JupyterHub object at 0x7f286b7eaeb0> instance must be a type, but 'GitLabOAuthenticator' could not be imported
Sarah Gibson
@sgibson91
@rprimet Can you try using just "gitlab" for authenticator_class? Here's my config for BinderHub with GitHub OAuth enabled https://github.com/alan-turing-institute/hub23-deploy/blob/d88a2e21a2f1cf615588416c21ec3762a758c62c/deploy/prod.yaml#L43
Romain Primet
@rprimet
@sgibson91 thanks, that did it! (I was confused by "must be a type") Also, IIUC, the camelCasing of attributes is gone as well?
Sarah Gibson
@sgibson91
Yes I think so - I think that's to make the JupyterHub config consistent with the BinderHub one
Romain Primet
@rprimet
thanks again! @sgibson91
Sarah Gibson
@sgibson91
No worries! :)
jelias1
@jelias1
Hello! New here and to binder so forgive me if this has been answered somewhere else. I am having trouble connecting to an MQTT broker (in AWS) using the paho mqtt client in my notebook. Is outgoing network traffic blocked on Binder?
Sarah Gibson
@sgibson91
@jelias1 yes. We've also recently blocked IP addresses associated with cloud providers as we were having issues with abuse.
jelias1
@jelias1
That is unfortunate, but I understand. Thank you for the quick reply!
Min RK
@minrk
We've recently blocked incoming traffic from datacenters, but not outgoing. My guess is this is the longstanding outgoing port blocking - only a few egress ports are allowed (basically HTTP(s) only with a couple exceptions).
Sarah Gibson
@sgibson91
Ah yes! ☝🏻
Romain Primet
@rprimet

Hi all, any hints on troubleshooting a dev install of binderhub (local bhub / minikube jhub) where after the build, the redirect to the jupyter server results in a redirect loop and accessing the server through the hub (hub/home and then click on 'my server') results in a 404?

The pods seem running, including the single-user server jupyter-username, the logs from the single-user server show some 404s, e.g.

[W 08:26:07.607 NotebookApp] 404 GET /user/username (172.17.0.2) 36.72ms referer=http://192.168.49.2:30902/hub/home

The proxy seems to show the redirect loop, i.e.

08:23:23.410 [ConfigProxy] debug: PROXY WEB /user/username/?token=token_value to http://172.17.0.7:8888
08:23:23.417 [ConfigProxy] debug: PROXY WEB /user/username/?token=token_value to http://172.17.0.7:8888
08:23:23.424 [ConfigProxy] debug: PROXY WEB /user/username/?token=token_value to http://172.17.0.7:8888
08:23:23.432 [ConfigProxy] debug: PROXY WEB /user/username/?token=token_value to http://172.17.0.7:8888
08:23:23.441 [ConfigProxy] debug: PROXY WEB /user/username/?token=token_value to http://172.17.0.7:8888
08:23:23.449 [ConfigProxy] debug: PROXY WEB /user/username/?token=token_value to http://172.17.0.7:8888
08:23:23.458 [ConfigProxy] debug: PROXY WEB /user/username/?token=token_value to http://172.17.0.7:8888
08:23:23.466 [ConfigProxy] debug: PROXY WEB /user/username/?token=token_value to http://172.17.0.7:8888
08:23:23.473 [ConfigProxy] debug: PROXY WEB /user/username/?token=token_value to http://172.17.0.7:8888
08:23:23.479 [ConfigProxy] debug: PROXY WEB /user/username/?token=token_value to http://172.17.0.7:8888

Nothing in particular about the jupyterhub pod logs excepts a few 404s on global contents (jquery etc.)

I am using an authenticated config, close to the one in #1169 but rebased to match the current config changes on master, which I can paste somewhere but I'm mainly looking for advice on where to look to debug this

Thanks!

ARafik
@ARafik
Hi, please there is a way to add an new apt-repo with the binder grammar ?
Sarah Gibson
@sgibson91
ARafik
@ARafik
Thank you @sgibson91
Erik Sundell
@consideRatio
What is "a binder", is it okay to describe it as a binder-ready git repo?
Sarah Gibson
@sgibson91
@consideRatio In one aspect, yes. I might also describe "a binder" as a shareable, computational environment in the cloud - since a binder-ready git repo could also be described as a repo that follows software best practices. The "launching your project with one click" part is the reward binder gives for following best practices.
Erik Sundell
@consideRatio
Thanks @sgibson91! :tada:
Loic Tetrel
@ltetrel

Hi all :)
I had two questions for you.
1) How can I increase the time for a user launch, before it hits the retry ? For now I am using retries and increasing this to a high number (obviously, it needs to re-try a lot of time before hitting a good scaled time), I also try retry_delay but this is just a delay and not what I need https://binderhub.readthedocs.io/en/latest/reference/launcher.html#id1
2) Is it possible to configure the start script server-side (not on a user repo?), maybe with the config c.Launcher.pre_launch_hook? I need this process to be run inside the user environment, so running python code in hub pod is not possible for example:

  hub:
    baseUrl: /jupyter/
    image:
...
    extraVolumes:
...
    extraVolumeMounts:
...
    extraConfig:
      myExtraConfig: |
        ... python code ....

Thank you!

3 replies
Romain Primet
@rprimet
Hi, I recently had an issue that took me a long time to figure out (mostly by trial and error) -- a missing singleuser/cmd value in the testing local binder / k8s jupyterhub authenticated yaml config file. Apparently that was throwing me in a redirect loop at notebook redirect time. What is the purpose of singleuser/cmd and why is it either missing or not required anymore in the current master? Thanks!
(there is a comment in the docs that says # to make notebook servers aware of hub but that's not much clearer to me :-) )
Thanks again!
Alexander Konovalov
@alex-konovalov
Hi all! I have a question about running R code on Binder. The problem is with installing dependencies for units and rgdal packages, described in rse-standrewscs/distance-binder-demo#1. I can't find where I can specify this.
syn4ps1s
@syn4ps1s

Hi!!, i have a little question... i have a repo with runtime.txt and install.R but I don't have access to /rstudio , the jupyter notebook is created but no access to R. this is happening on my own binder setup.. with is working properly for all python notrebooks.. the building output is different from mybinder.org with the same repo and works properly, I can land into the studio but my own is not.. 404 not found.. my runtime.txt has only this inside : r-3.6-2019-04-12 , and also my install.R

install.packages("tidyverse")
install.packages("rmarkdown")
install.packages("httr")
install.packages("shinydashboard")
install.packages('leaflet')

What could be the problem? I'm kind of lost ... for any advice... thank you!!

syn4ps1s
@syn4ps1s
my installed helm binderhub version is : --version=0.2.0-n465.hb35ec4e
Achintya Rao
@raoofphysics:matrix.org
[m]

Hi folks. Are Dockerfiles for R environments officially deprecated? If not, which is the best place to look for an example Dockerfile for RStudio use?

I see that https://github.com/binder-examples/r/ works (http://mybinder.org/v2/gh/binder-examples/r/master?urlpath=rstudio/) but https://github.com/rocker-org/binder does not (https://mybinder.org/v2/gh/rocker-org/binder/master?urlpath=rstudio/). Specifically the error is:

RStudio Server

The requested page was not found.

Please contact your system administrator for assistance, or click here to go back.

I tried using the Dockerfile from the rocker-org/binder repo (https://github.com/rocker-org/binder/blob/82a50434cddf87eb78ec20279120076ed4763be2/binder/Dockerfile/) with repo2docker but that doesn’t work either. In fact, I can't even open a Jupyter notebook with R (only Python3).

5 replies
Michał Krassowski
@krassowski
Hi everyone! I was looking to revive my binder for https://github.com/krassowski/multi-omics-state-of-the-field I am actually surprised to see that it installs RStudio and IRKernel, while I do not want them installed. I would like just JupyterLab + p7zip + conda packages from environment.yml. I think that IRkernel started conflicting with my package versions (I had just a partial freeze) and also it is taking ages to build for the first time. Can I have JupyterLab on binder without having RStudio and IRKernel?
I mean I do use R, but via rpy2 and not via IRKernel. I would appreciate some info on how binder decides when to install RStudio/IRKernel and how to suppress. From a very uneducated perspective it seems like it is trying to be clever about me environment and seeing that I install R it tries to make me happy, but it actually makes the experience worse for me - is this correct, or is it just that it will install all of it anyways? Or maybe I have some file that causes it?
Michał Krassowski
@krassowski
Or in which repo should I open an issue with feature request "disable automatic install of RStudio/IRkernel"?
Wolf Vollprecht
@wolfv
@krassowski maybe it's the renv.lock file?
especially r.py and _r_base.py
Michał Krassowski
@krassowski
Thank you! It is indeed what I was looking for! However, it seems to work differently to what the code says, so I am clearly still missing something. So the lines https://github.com/jupyterhub/repo2docker/blob/0eb7260f4760ebbaf4cf466bbb0d0be2276f330f/repo2docker/buildpacks/r.py#L117-L141 seem to say that it should only install RStudio if either runtime.txt or DESCRIPTION is present. Neither of those are included in my repo. renv.lock is not in use on binder either, but it should not matter. What am I missing?
Tim Head
@betatim
weird. when i attempt to build your repo it says that it picked the conda buildpack. which is "the right thing to do" and what you expect. but it doesn't explain how rstudio ends up being installed
Tim Head
@betatim
mystery solved: we install RStudio in addition to the packages from the environment.yml when the env includes r-base
Tim Head
@betatim

there is currently no way to tell repo2docker not to do this, mostly because there is no way to tell repo2docker to do this (no conda package for rstudio).

the reason we check for and install irkernel and rstudio if r-base is in the environment is that there is no good way to install a specific version of R without using conda. we thought that there are APT packages from a private PPA that look like you can use them to install a specific version of R but they aren't meant to be used (and hence sometimes break) when you use them to install R=3.5.3 or 3.6.23 or some such.

1 reply
Raphael Das Gupta
@das-g
Where's the source for https://mybinder.readthedocs.io/en/latest/using/config_files.html#default-nix-the-nix-package-manager ? The "On GitHub" links in the black expandable ReadTheDocs box go to https://github.com/jupyterhub/binder/blob/master/doc/using/config_files.rst (or the respective edit URL), but that file doesn't exist on that branch.
Nathan Weeks
@nathanweeks
Is there a mybinder.org outage?
Sarah Gibson
@sgibson91
Only on one of the clusters, but you should be directed to one of the other three https://mybinder.readthedocs.io/en/latest/about/status.html#federation-status
Sarah Gibson
@sgibson91
:grimacing:
Tim Head
@betatim
:-/
Tim Head
@betatim
@nathanweeks thanks for letting us know. in the process of banning some abusive users. thing should get back to normal soon (hopefully)
1 reply
Michał Krassowski
@krassowski
Just wanted to bring more eyes to the codecov issue ((https://about.codecov.io/security-update/) for: https://github.com/jupyterhub/binderhub. It would be reassuring to have some kind of confirmation that neither images nor packages were affected. I know that I am asking for a lot.
Min RK
@minrk
@krassowski thanks, we've been looking into it jupyterhub/team-compass#398. As I understand it, an action has access potentialy to anything in the workflow, but not secrets in or the repo general unless a secret appears in the workflow somewhere. Since our test workflows on affected repos do not have any references to secrets in them at all, I don't think it's possible for them to be compromised by this codecov issue, unless I misunderstand.
We are helped by the fact that our 'publish' workflows that do have credentials are run from separate workflows from tests. The codecov action was never run in a workflow with any secrets, as far as I can tell. We are looking at how to be a bit stricter about what actions we use in those workflows with credentials to avoid something like this actually hitting us in the future.
Michał Krassowski
@krassowski
Thank you for looking into this. I think that your assessment is accurate, but it would be ideal to see this confirmed by someone from the GitHub Actions team (or just official bit in the docs).
Also, I wish GHA could make sharing artifacts between workflows easier -it would allow to use the environment-limited secrets (that can be configured to require a manual approval for execution) for publishing images/packages. They are so close to making our lives easier, but kind of missing this one final step.
YoungDon Choi
@DavidChoi76
I have to use requirments.txt and environment.yml to create MyBinder JupyterHub computational environment. So I'm trying to use environment.yml that includes requirments.txt such as pip -r requirements.txt. Also, I want to use automatically generated requirement.txt from Python virtual environment. In this case, there is some error that there are no python libraries. Is there a way to pass when there is no library? I found some solutions to pass it using customed python code with requirements.txt, but I couldn't find a way to use MyBinder configuration options.
Aaron Curtis
@foobarbecue
hi all, I'm running a single-node binderhub (jupyterhub helm chart on k3s, binderhub run from git with testing/local-binder-k8s-hub/binderhub_config.py ) and able to build images but after the build it fails to launch, with Cannot assign requested address . Any ideas or debugging tips for this?