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Using R with Jupyter / RStudio on Binder

License: BSD 3-Clause "New" or "Revised" License

Jupyter Notebook 96.52% R 3.48%

binder binder-ready

r's Introduction

Specifying an R environment with a runtime.txt file

Jupyter+R:

RStudio:

RShiny:

Binder supports using R and RStudio, with libraries pinned to a specific snapshot on packagemanager.rstudio.com.

Requirements and suggestions

You need to have a runtime.txt file that is formatted like:

r-<r-version>-<YYYY>-<MM>-<DD>

where <r-version> is a version of R (like 4.1, 4.0, etc) you want to use, and <YYYY>-<MM>-<DD> is the date for a snapshot from packagemanager.rstudio.com that will be used for installing your R packages.

Try using a date newer than 2022-01-01, as you'll get faster package installs thanks to binary packages from rstudio.packagemanager.com!

To install R libraries, add install.package("<package-name>") calls to install.R. If you want to pin to a specific version of the library, you can also do devtools::install_version("<package-name>", "<version>").

For some R packages, you might need to install system packages via apt - you can do so by writing out a list of apt package names in apt.txt. You can find the list of such packages in the page for your package at packagemanager.rstudio.com. Make sure to select "Ubuntu 18.04 (Bionic)" in the dropdown on the top right.

Both RStudio and IRKernel are installed by default, so you can use either the Jupyter notebook interface or the RStudio interface.

This repository also contains an example of a Shiny app.

Alternatives

There are many ways to use R in mybinder.org!

rocker/binder - this uses a base image from the R community's excellent rocker project - you get a lot of curated base packages, faster binary package installs as well as ability to pin to a specific version of R (>4.0).

r-conda - mybinder.org also supports using the conda package manager to manage R and R packages. This gives you access to specific R versions as well as fast installs of R packages available in conda-forge

Another alternative is to use the holepunch package for R.

URL addresses for RStudio and Shiny environments

The Binder repository can be used to allow anyone to access an RStudio environment containing our code and data right in their web browser. It also allows hosting a Shiny app. For those purposes, we have to append a bit of text to the URL of our Binder repository, which we can find out at mybinder.org when we enter the URL of our original repository from GitHub or Figshare, etc.

For the RStudio environment, we must add the following at the end of the URL: ?urlpath=rstudio
- Example: http://mybinder.org/v2/gh/binder-examples/r/master?urlpath=rstudio
For the Shiny app environment, we must add the following at the end of the URL: ?urlpath=shiny. In this case, we also have to note that if the Shiny app files are located in a folder, this folder should be specified in the URL, after a slash. We would then also have to put in a trailing slash at the end of the URL, and to avoid spaces in the name of the repository, placing instead a hyphen (the reason is that spaces are converted to %20).
- Example: http://mybinder.org/v2/gh/binder-examples/r/master?urlpath=shiny/bus-dashboard/

r's People

Contributors

Stargazers

Watchers

Forkers

aculich cbahlai henchc rareseas federicomarini betatim efsilvaa kaitai zhuozhih raoofphysics fhoces christophm zkamvar gbonomib proxor fadhlyemen afcarl idocs apoterie marwahaha upendrak tomsing1 rociotmartinez jthmiller karenword crazyhottommy u2ng repositorian ctb kellieotto reedacartwright aisaaco tracykteal anelda aahowel3 fpsom s-canchi jgarciamesa crivaldi nikolayvoronchikhin amabdallah brooksambrose jclauneuro russ-white soltaniehha taotao20180808 andrewcheny hlshao yuvipanda kirstiejane punama bentut libretexts heidiseibold hancjozef gedankenstuecke sebkopf prussia harvardinformatics giswqs aspiekiwi aclorena luizhnlorena santandermetgroup imccommons cboettig ngs-docs didi9 lmfeist mryap lennertschepers agilly crsuzh fusiakja proflewis dmgt kcompher dwelkie marskar christofseiler ncypris thomasdenecker python-oilgains iamciera marijastanojcic geoheil rkingdc kratos997 klainfo frycast sahirbhatnagar rodriguesdossantosvincent cochranteck gerrydito olexandr-konovalov robsalasco yoshitok jeffblackadar sneumann geoff-marine

r's Issues

Should we add an example for DESCRIPTION?

Maybe create a new repository instead of using this one.

@gedankenstuecke just added support for DESCRIPTION files to repo2docker

Is it possible to build a binder with RStudio-latest?

Hi,

Following the addition of the quarto format to Jupytext at mwouts/jupytext#837, I'd like to add RStudio latest (& quarto) to my project's binder.

Is there an easy way to do so?

Thanks!

RStudio not working with repo2docker

[I'm not sure if this is the right place to file this issue, so please point me to the best repo in which to do so.]

I pulled the latest version of this repo to my machine and ran jupyter-repo2docker .. The container got built successfully and I received the token to launch the Jupyter notebooks. However, when I tried going to New → RStudio Session, I got the following error:

This was, I think, the relevant error on the console:

14 Jul 2018 08:36:23 [rsession-achintya] ERROR system error 13 (Permission denied) [message=User 'achintya' has id 501, which is lower than the minimum user id of 1000 (this is controlled by the the auth-minimum-user-id rserver option)];
OCCURRED AT: int main(int, char* const*) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:1631; LOGGED FROM: int main(int, char* const*) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:1639

What's the best way to resolve this without tinkering with one's system configuration?

Does mybinder.org supports R 4.2?

My runtime.txt has

r-4.2-2023-03-01

and launch https://mybinder.org/v2/gh/GESIS-Methods-Hub/minimal-example-qmd-rstats-xml2/HEAD gives me

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerbwntvooj'...
HEAD is now at d1435a6 Replace xml2 example output
Error during build: Extra data: line 1 column 5 (char 4)

R examples fail to build on myBinder

The examples at https://github.com/binder-examples/r all fail for me with the error

debconf:%20delaying%20package%20configuration,%0Asince%20apt-utils%20is%20not%20installed

Step to reproduce:

open https://mybinder.org/v2/gh/binder-examples/r/master?urlpath=shiny/bus-dashboard/

Start binder a rocker Dockerfile, running jupyter

From project root:

jupyter-repo2docker verse

Howto install additional linux packages now that runtime.txt replaces docker file

Great resource!
For a teaching project, we need to install an R/Bioconductor package that requires the libnetcdf-dev linux package. I was wondering how to do that as there is no docker anymore. Is the runtime.txt approach compatible with a docker file?

Thx,

Lieven

RStudio version is failing to launch

I've tried loading the instance here but it seems to be down: https://mybinder.org/v2/gh/binder-examples/r/master?urlpath=rstudio

Apologies for unsolicited issue and lack of detail (it's fairly self explanatory), hope this is of use/interest.

Is there a way to set the R version?

Ideally binder would just match the R version current with the MRAN date (likewise for the RStudio version; this is what we do in Rocker: https://github.com/rocker-org/rocker-versioned/blob/master/VERSIONS.md) Are you installing R from default Ubuntu repos, CRAN-hosted Ubuntu binaries, or from source?

LICENSE?

Can we add the standard Jupyter License here?

Shiny dashboards no longer rendering

I am using the Shiny feature to render dashboards. The shiny link shown here was working for me about a week and a half ago, but it's not working now: https://github.com/binder-examples/r
http://beta.mybinder.org/v2/gh/binder-examples/r/master?urlpath=shiny/bus-dashboard/

native repo2docker example with no Dockerfile

runtime.txt: specify MRAN date
install.r installation script

R example not working when copied to personal repo

I cloned the binder-example/r repo on my own github and updated the binder badge to point at my new repo instead of the original one and the load is crapping out.
https://github.com/binder-examples/r (works)
https://github.com/bentut/bdac-grad (error- clone of above)

This worked for me last week

shiny binder link is off

Not sure what exactly, but here's what I see:

The link has resolved to:

https://hub.mybinder.org/hub/bus-dashboard/?token=<MYTOKEN>

which seems wrong, since there is no pod URL in there...

Here's what the binder link in the readme points to:

https://mybinder.org/v2/gh/binder-examples/r/master?urlpath=shiny/bus-dashboard

If I do not include urlPath in the url, then it directs me to the correct URL. I can also confirm that urlPath still works fine on the jupyterlab demo repository.

cc @betatim !

R installation

R is mainly used for data analysis task thanks to the huge number of packages and readily usable tests that often provide you with the necessary results.
When getting started with R, a good first step is to install the amazing RStudio IDE.
https://www.rstudio.com/products/rstudio/download/
https://www.r-project.org/

Getting Started with R for Data Analysis.

•Introduction to R :
R is a powerful tool for data analysis, offering a vast array of packages and tests for efficient and effective data exploration.

•Installing RStudio :
RStudio is an exceptional integrated development environment (IDE) for R.
It enhances your R coding experience and provides a user-friendly interface.
Download RStudio

•Setting Up R
Install R on your system.
Download R

Shiny Binder for Apps in Nested Folders

For this R package:

https://github.com/cytoscape/cyjShiny

I have a demo Shiny application in a sub-folder:

https://github.com/cytoscape/cyjShiny/tree/master/inst/demos/tinyApp

How can I link to it? The link below does not appear to work:

https://mybinder.org/v2/gh/cytoscape/cyjShiny/master?urlpath=shiny/inst/demos/tinyApp/

Unable to install tmap and tmap dependencies

Following the example, I expected that all I would have to do install tmap would be to use the following in my install.R file:

install.packages('tmap')

However, when I open the notebook, I receive the following error:

Error in library(tmap): there is no package called ‘tmap’
Traceback:

library(tmap)
stop(txt, domain = NA)

I have tried many variations but none have been successful.
https://github.com/RAJohansen/BindeR

Any ideas?

How to run container with rstudio or shiny?

Hey binder team! Could you provide an example of how to run the container using rstudio or shiny? I see where the server is located, and in testing (I think) you would just run the server.R with Rscript or similar, but I'm not sure how it should be done properly from outside the container, with a docker command. To start us off, here is a quick reference for how to get the (notebook) running:

docker run --rm -it -p 8888:8888 vanessa/repo2docker-r jupyter notebook --ip 0.0.0.0

Thank you!

MRAN - package ‘devtools’ is not available

Hello,

New compilation for R repositories based on MRAN are giving this error (including mybinder example https://mybinder.org/v2/gh/binder-examples/binder-r-description/master?urlpath=rstudio)

I'm using runtime.txt with the following string: r-3.6-2020-04-20, and I changed to r-3.6-2020-07-22 (last devtools snapshot on MRAN is 07-21) and the error persists.

> install.packages('devtools', repos='https://mran.microsoft.com/snapshot/2018-02-01', method='libcurl')
Installing package into ‘/srv/rlibs’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository https://mran.microsoft.com/snapshot/2018-02-01/src/contrib:
  Line starting '<!doctype html><html ...' is malformed!
Warning message:
package ‘devtools’ is not available (for R version 3.6.3)

Bbbb

Image fails to launch?

Not sure what I'm doing wrong, could be a chance error. Image seemed to have built (after some time) and pushed successfully, but fails to launch server:

https://mybinder.org/v2/gh/cboettig/geocompr/master?urlpath=rstudio

error message in the log isn't particularly informative:

Image gcr.io/binder-prod/r2d-05168b0-cboettig-2dgeocompr-38e476:d1bd8016f74bb9b56e982fe9eca7a08a5d9f2a5c for user cboettig-geocompr-r5xgth94 failed to launch

Any ideas?

install.R does not appear to run when launching the RStudio instance

If you head to http://beta.mybinder.org/v2/gh/binder-examples/r/master?urlpath=rstudio from the README file and try to play with index.Rmd, you get an error when attempting to execute the first code chunk:

Error in library(ggplot2) : there is no package called ‘ggplot2’

It seems that the packages from install.R don't get installed when launching the RStudio instance.

If I first run install.R within RStudio (running source("install.R") in the Console, the error message doesn't appear and all works well.

Can this file be made to run when the RStudio instance is launched?

run R with Python 2.7

I there a way to run both R and Python 2.7 at jupyter-repo2docker,
since you can not put both of them into runtime.txt