Rmagic | Deconstructing the & quot ; black magic & quot ; in R language

First of all, I’m new to rpy2 / jupyter so please don’t judge me if this isn’t the correct place to ask my question.

I am trying to set up an integrated workflow for data analysis using R and Python and I encounter the following error:

I am on Ubuntu 19.04. running a conda environment using Jupyter 1.0.0, Python 3.7.4, R 3.5.1, r-irkernel 1.0.2 and rpy2 3.1.0 and I installed the R-package Seurat through R.

When I create a Jupyter notebook using the R-kernel, I can load Seurat with library(Seurat) just fine.

I can also use R code in python using rpy2 and the rmagic such as:

I'm learning to use rpy2 in Jupyter notebook. I'm having troubles with the plotting. When I use this example from the rpy2 docs for interactive work:

I am trying to use the built-in R progress-bar (txtProgressBar) with %%R magic in Jupyter. While it does produce a nice animation when executed in the R console or RStudio, it does not produce the desired output in the Jupyter (notebook or lab) with an rpy2 extension instead, printing all the steps at once after finishing (which makes the progress bar useless). Two questions:

• How could I make it work?
• If it is not possible yet, how do I approach implementing this functionality on the rpy2 side (I already know how to make the interactive output/widgets on the Jupyter/IPython side)?

Here is a simple snippet of a progress bar from rfunction.com:

Just created a registration form, and I want to extend a label text to be shown into one line. With CSS inspector found that class is:

I know google colaboratory doesn't yet support an R kernel. What about rmagic? Can I use rpy2?

I tried :

This is supposed to be simple given recent stage of anaconda should be quite compatible with R. I am following this tutorial,

https://www.statsmodels.org/stable/examples/notebooks/generated/mixed_lm_example.html

However, at this 3rd line,

While I'm trying to install rmagic, it shows following error

I am using rpy2 through the rmagic to interleave R code with python3 code in a jupyter notebook. A simple code cell as this:

I want to install Redmine on my Raspberry Pi2. When I tried to run the command sudo bundle install --without development test rmagic I got this as output:

Don't run Bundler as root. Bundler can ask for sudo if it is needed, and installing your bundle as root will break this application for all non-root users on this machine. The dependency tzinfo-data (>= 0) will be unused by any of the platforms Bundler is installing for. Bundler is installing for ruby but the dependency is only for x86-mingw32, x64-mingw32, x86-mswin32, java. To add those platforms to the bundle, run bundle lock --add-platform x86-mingw32 x64-mingw32 x86-mswin32 java. The dependency activerecord-jdbc-adapter (~> 1.3.2) will be unused by any of the platforms Bundler is installing for. Bundler is installing for ruby but the dependency is only for java. To add those platforms to the bundle, run bundle lock --add-platform java. The dependency activerecord-jdbcmysql-adapter (>= 0) will be unused by any of the platforms Bundler is installing for. Bundler is installing for ruby but the dependency is only for java. To add those platforms to the bundle, run bundle lock --add-platform java. Fetching gem metadata from https://rubygems.org/.. Retrying dependency api due to error (2/4): Bundler::HTTPError Network error while fetching https://index.rubygems.org/api/v1/dependencies?gems=actionpack-xml_parser%2Cactiverecord-jdbc-adapter%2Cactiverecord-jdbcmysql-adapter%2Ccapybara%2Ccoderay%2Ci18n%2Cjquery-rails%2Cmime-types%2Cmimemagic%2Cminitest%2Cmocha%2Cmysql2%2Cnet-ldap%2Cnokogiri%2Cprotected_attributes%2Crack-openid%2Crails%2Crails-dom-testing%2Crails-html-sanitizer%2Crbpdf%2Crdoc%2Credcarpet%2Crequest_store%2Crmagick%2Croadie-rails%2Cruby-openid%2Cselenium-webdriver%2Csimplecov%2Ctzinfo-data%2Cyard.......... Fetching version metadata from https://rubygems.org/... Fetching dependency metadata from https://rubygems.org/.. Resolving dependencies........................... Using erubis 2.7.0 Using bundler 1.14.6 Gem::RemoteFetcher::UnknownHostError: no such name (https://rubygems.org/gems/rake-12.0.0.gem) An error occurred while installing rake (12.0.0), and Bundler cannot continue. Make sure that gem install rake -v '12.0.0' succeeds before bundling.

Gem::RemoteFetcher::UnknownHostError: no such name (https://rubygems.org/gems/i18n-0.7.0.gem) An error occurred while installing i18n (0.7.0), and Bundler cannot continue. Make sure that gem install i18n -v '0.7.0' succeeds before bundling.

And when I wanted to run gem install rake -v '12.0.0' or gem install i18n -v '0.7.0' the command did not started and I got only > symbol on the start of the row, like when I want to edit something on mySQL through CLI.

What I missed? I didn't found this in the Documentation. I installed followed by these steps.