Debugging your Binder

**choldgraf** · April 15, 2019, 9:04pm

Are you having problems getting your Binder repository to work? Feel free to ask questions here!

Note: please don’t post in this thread any more. Instead use the http://discourse.jupyter.org/c/questions category for your questions. Thank you

**betatim** · November 2, 2018, 5:10pm

I think of “a Binder” as a repository on GitHub or GitLab that works on a site like mybinder.org. Is this also what you have in mind?

**choldgraf** · November 2, 2018, 5:13pm

Yep - I think of “a Binder” as “a repository that’s meant to run on a BinderHub”. (edited the top comment to be a bit more clear)

**diyadas** · January 28, 2019, 7:01pm

I’m trying to launch app.R on my repo’s shiny branch with Binder: https://github.com/diyadas/vizresume/tree/shiny

And for some reason: https://mybinder.org/v2/gh/diyadas/vizresume/shiny?urlpath=shiny
is failing to build.

I’m basing the URL on the binder example, though I’m not sure it’s correct.

At this point would you recommend trying a Dockerfile instead?

I ran a dependency check on the 10 packages I’m loading using miniCRAN’s pkgDep and apparently there are 178 depends and suggests.
Is there a way to force it only to install the 72 depends? Or is it doing that by default?
It’s hard for me to tell because the buffer on the log (that I can see) isn’t very long. Is there a way to see the full log somewhere?

Thanks very much!

**choldgraf** · January 29, 2019, 3:07am

Ahh so the package / dependency management thing is still really tricky IMO. I’m not sure how the R packaging world works to fix that problem :-/ could you past the full error message though?

One idea: some folks in the R community have been playing around with ways to make it easier to create Binder-ready repositories using the Rocker stack of Docker images. I believe that @karthik even threw together a little helper R library to do this:

github.com

karthik/rstudio2019/blob/6c2ff0e6400e7c3af52098bf9b09812823766ced/binder-notes.md

![](https://mybinder.org/static/logo.svg?v=f9f0d927b67cc9dc99d788c822ca21c0)

# How to set up a My Binder for your R project

[My Binder](https://mybinder.org/) has had R support for about a year but it is getting better. When passed a Git repo (hosted on GitHub, Gitlab or from any arbitrary location), it will look for patterns (such as the presence of a DESCRIPTION file, `install.R` etc) and create a Dockerfile and start to build an instance from a pre-configured build pack (there is one for R projects and this is extensible to meet other needs).

## ⚙ Simplest  setup

For the simplest setup, you'll just need two files in your repo. 
- `runtime.txt` Here you can specify your R version by date (e.g. `r-2018-12-31`) and also versions of Python and Julia. In the case of R, this will also lock down CRAN packages to this R release (Rocker takes care of pulling packages from MRAN matching this date. You should specify the version based on a date:

- Select a MRAN date corresponding to your desired R version or just choose latest.  

|R version | MRAN date  | RStudio version | RStudio date |
|----------|------------|-----------------|--------------|
| 3.1.0    | 2014-09-17 | NA              | NA           |
| 3.2.0    | 2015-06-18 | NA              | NA           |
| 3.2.5    | 2016-05-03 | NA              | NA           |
| 3.3.0    | 2016-06-21 | NA              | NA           |
| 3.3.1    | 2016-10-31 | 1.0.44          | 2016-11-01   |

This file has been truncated. show original

Wanna follow those instructions and see if that can solve your problem?

**diyadas** · February 6, 2019, 6:29am

Karthik helped me get up and running with a Dockerfile, thanks for the suggestion.

I was wondering if there’s a way to go directly to a Shiny app if I’m going the Docker route, or if my only option is https://mybinder.org/v2/gh/diyadas/vizresume/shiny?urlpath=rstudio and then “Run app.” Extrapolating from the example repo, I think that link would be https://mybinder.org/v2/gh/diyadas/vizresume/shiny?urlpath=shiny but now instead of “failed to build” I get a 404 page.

Thanks.

**betatim** · February 6, 2019, 11:54am

When you use the standard R setup from repo2docker you can have a link like http://mybinder.org/v2/gh/binder-examples/r/master?urlpath=shiny/bus-dashboard/ that takes you directly to the Shiny app.

**marija** · April 9, 2019, 6:10am

Hi, I’m having problems with getting my shiny app to run with the binder.
I was using an example from binder-examples/r github, the building part seems to work, however, I’m getting a Not Found page when I want to run the app https://mybinder.org/v2/gh/MarijaStanojcic/RDatasets/master?urlpath=shiny/APP/

Any advice?
Thanks

**fomightez** · April 9, 2019, 3:52pm

My guess would be the way to trigger a call runApp() isn’t compatible with the App directory approach?
The example has the two file method described here and here. Maybe someone else can comment if it only works with the Two-file method?

**marija** · April 15, 2019, 8:16am

Thank you for the response. I tried doing this, but it is still not working. I still get Not Found page.

**fomightez** · April 15, 2019, 3:08pm

Hi Marja,
I see that you tried to convert it to the two files system. And I see the still 503 error too.
I was going to suggest then you try forking the example and converting it to use your data so you can see when the Shiny dashabord breaks. (Or if it doesn’t break use the code.) However…
I see your fork of the example and the example itself failing to work right now. Albeit this is different than the error you are having. The shiny dashboard opens but it is darkened out and unable to be used.
So you could work on getting your fork to at least work with your code and data up to that point. Since the example has the problem and it hasn’t been changed in 20 days, I think it is something in the infrastructure that is out of the typical users hands that is causing the problem. Or it is my browser. Do you see the example failing to work too?

**betatim** · April 15, 2019, 7:56pm

For me the example also does exactly what @fomightez describes. From looking at the network inspector in my browser I think it is a problem with proxying the websocket.

**betatim** · April 15, 2019, 9:03pm

I made a Pull Request to repo2docker which I think will fix this: https://github.com/jupyter/repo2docker/pull/646 if any of you have a moment to test drive this locally that would be great.

I think you’d need to run repo2docker --uid 1000 --user jovyan https://github.com/binder-examples/r to do so. It will take quite a while as it has to compile all of the tidyverse :-/

**betatim** · April 16, 2019, 6:36am

The change has been deployed. After triggering a rebuild of the repository by hand http://mybinder.org/v2/gh/binder-examples/r/master?urlpath=shiny/bus-dashboard/ now works again for me.