Debugging your Binder

choldgraf · 2018-11-02 17:12:52 UTC

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

betatim · 2018-11-02 17:10:14 UTC

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 · 2018-11-02 17:13:04 UTC

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 · 2019-01-28 19:01:20 UTC

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 · 2019-01-29 03:07:55 UTC

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   |

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

diyadas · 2019-02-06 06:29:04 UTC

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 · 2019-02-06 11:54:56 UTC

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.