R Environment

Default environments for R 3.6.

This notebook describes and creates the default R environment in Nextjournal. Check out the showcase if you want to see what the environment contains. To see how it’s built, see setup.

Showcase

These packages are included in Nextjournal's R 3.6 environment.

suppressMessages(library(dplyr))

installed.packages() %>%

  as_tibble() %>%

  select(Package, Version) %>%

  arrange(Package)

System Packages and Basics

A number of support libraries are installed, as well as gcc v7 for installing Rcpp and other packages that require compilation.

The Rcpp package version

R packages are installed using install.packages() or devtools::install_github() in an R cell. Please refer to the R section of Installing Software and Packages for more detailed information.

Plotting

Three plotting methods are available in the default environment. The built-in R plotting system works automatically to create static plots, Plotly v

R

x <- seq(-10, 10, length= 60); y <- x

f <- function(x, y) { r <- sqrt(x^2+y^2); sin(r)/r }

z <- outer(x, y, f)

persp(x, y, z, theta = 30, phi = 30, expand = 0.5, col = "#009caa"); NULL

0.5s

Showcase (R)

R

Plotly

This syntax allows full access to the functionality of Plotly on R.

library(plotly)

d <- diamonds[sample(nrow(diamonds), 1000), ]

plot_ly(d, x = ~carat, y = ~price,

  # Hover text:

  text = ~paste("Price: ", price, '$<br>Cut:', cut),

  color = ~carat, size = ~carat, type='scatter', mode='markers')

ggplot2

Plot with the ggplot2 package.

library(ggplot2)

qplot(speed, dist, data=cars) + geom_smooth()

0.5s

Showcase (R)

R

Data Structures

In addition to standard R functionality, Nextjournal's default R environment contains several packages for data manipulation and parsing.

Data Frames

The standard R data structure is the data.frame. This is a table with named columns, numbered rows, and can have columns with enumerated factors. Nextjournal will automatically attempt to display a data frame when it is the final return value of a cell.

iris

Tibbles

One of the many packages from the Tidyverse provides tibbles: a modification of data frames that are lazy (do not modify input data) and surly (complain more about errors). Any data.frame object can easily be converted to a tibble, and will display in much the same way:

library(tibble)

as_tibble(mtcars)

JSONlite

The jsonlite package provides simple (de)serialization functions.

toJSON(iris, pretty=TRUE)

Setup

The full setup starting from a minimal Ubuntu installation is below

Build a Minimal R Environment

Install R from the R 3.5/3.6 repository for Ubuntu. The build-essential package (which includes gcc) is a necessary prerequisite for installation of some R packages.

echo 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' > \

  /etc/apt/sources.list.d/r35.list

key_id=`curl -s https://cloud.r-project.org/bin/linux/ubuntu/README \

  | grep "sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys" \

  | sed 's/.* //'`

apt-key adv --keyserver keyserver.ubuntu.com --recv-keys $key_id

apt-get -qq update

DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends \

  r-base

apt-get clean

rm -r /var/lib/apt/lists/* # Clear package list so it isn't stale

Setup package install options.

echo 'local({

  r <- getOption("repos")

  r["CRAN"] <- "https://cloud.r-project.org"

  options(repos = r, download.file.method = "libcurl")

})' > /etc/R/Rprofile.site

Install two necessary packages for R to work on Nextjournal.

R -e 'install.packages(c("base64enc", "jsonlite"), Ncpus=4)'

Build the Default R Environment

Install

Install libraries that R needs for compilation of packages.

apt-get -qq update

DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends \

  libssh2-1 libcurl4-openssl-dev libssl-dev libxml2-dev \

  r-base-dev libcairo2-dev libpango1.0-dev libpangocairo-1.0

apt-get clean

rm -r /var/lib/apt/lists/*

Install the conda Jupyter package, then ensure jupyter-client and jupyter-core are the latest releases. Jupyter-core devel used to address connection file permissions issue, revert when 4.6.2 is released. —MPD 15 Dec 2019

conda install jupyter

conda clean -qtipy

pip install --upgrade jupyter-client \

  git+https://github.com/jupyter/jupyter_core

This default image has support for tidyverse, plotly, svglite, and shiny. The package also makes some basic utilities available, as well as devtools to help facilitate the use of certain packages, and packrat and renv for installations. Remaining packages are installed to support the Jupyter IRkernel.

install.packages(c("devtools", "remotes", "packrat", "renv", 

                   "tidyverse", "uuid", "digest", 

                   "plotly", "svglite", "shiny",

                   "feather", "arrow", "R.matlab", "repr", "future", "evaluate", 

                   "pbdZMQ", "crayon", "IRdisplay", "IRkernel"), 

                 Ncpus=4)

IRkernel::installspec()

Setup default fonts for built-in plots, and when ggplot2 and/or svglite are loaded. This .Rprofile will be mounted to root's home directory, and saved with the environment.

local({

  if (file.exists("/usr/share/fonts/truetype/Fira_Sans") || 

      file.exists("/usr/share/fonts/truetype/dejavu")) {

    fonts <- "Fira Sans,PT Sans,Open Sans,DejaVu Sans,sans-serif"

  } else {

    fonts <- "sans"

  }

  options(nextjournal.svg.device.default.fonts = fonts)

})

setHook(packageEvent("ggplot2", "onLoad"), 

  function(pkgname,pkgpath) {

    if (file.exists("/usr/share/fonts/truetype/Fira_Sans") || 

        file.exists("/usr/share/fonts/truetype/dejavu")) {

      fonts <- "Fira Sans,PT Sans,Open Sans,DejaVu Sans,sans-serif"

    } else {

      fonts <- "sans"

    }

    options(nextjournal.ggplot.device.default.fonts = fonts)

    ggplot2::theme_update(text = ggplot2::element_text(family = fonts))

  })

setHook(packageEvent("svglite", "onLoad"), 

  function(pkgname,pkgpath) {

    # Function to build a font alias with all four standard faces, 

    # needed because font filenames are not standardized.

    faces <- function(fam,base,r,i,b,bi) {

      list(plain = list(alias = fam, file = paste0(base,r)),

          italic = list(alias = fam, file = paste0(base,i)),

            bold = list(alias = fam, file = paste0(base,b)),

      bolditalic = list(alias = fam, file = paste0(base,bi)))

    }

    if (file.exists("/usr/share/fonts/truetype/Fira_Sans") && 

        file.exists("/usr/share/fonts/truetype/PT_Serif")) {

      fonts <- list(

        sans = faces("Fira Sans,PT Sans,Open Sans,DejaVu Sans,sans-serif",

                     "/usr/share/fonts/truetype/Fira_Sans/FiraSans-",

                     "Regular.ttf","Italic.ttf",

                     "Bold.ttf","BoldItalic.ttf"),

       serif = faces("PT Serif,Noto Serif,DejaVu Serif,serif",

                     "/usr/share/fonts/truetype/PT_Serif/PT_Serif-Web-",

                     "Regular.ttf","Italic.ttf",

                     "Bold.ttf","BoldItalic.ttf"))

    } else { # Fallback for older environments which only had DejaVu fonts

      fonts <- list(

        sans = faces("DejaVu Sans,Fira Sans,PT Sans,Open Sans,sans-serif",

                     "/usr/share/fonts/truetype/dejavu/DejaVuSans",

                     ".ttf","-Oblique.ttf",

                     "-Bold.ttf","-BoldOblique.ttf"),

       serif = faces("DejaVu Serif,PT Serif,Noto Serif,serif",

                    "/usr/share/fonts/truetype/dejavu/DejaVuSerif",

                    ".ttf","-Italic.ttf",

                     "-Bold.ttf","-BoldItalic.ttf"))

    }

    options(nextjournal.svglite.device.default.fonts = fonts)

  })

Cleanup.

rm -rf /tmp/*

Checks.

du -hsx /

jupyter kernelspec list

Test

strsplit(R.version.string," ")[[1]][[3]]

jupyter kernelspec list

jupyter --version

jupyter --paths

cat /usr/local/share/jupyter/kernels/ir/kernel.json

cp /usr/local/share/jupyter/kernels/ir/logo-64x64.png /results/logo.png

1.6s

Showcase (Bash in R)

R

packageDescription("Rcpp")[["Version"]]

packageDescription("tidyverse")[["Version"]]

packageDescription("plotly")[["Version"]]

packageDescription("ggplot2")[["Version"]]

packageDescription("jsonlite")[["Version"]]

packageDescription("svglite")[["Version"]]

packageDescription("feather")[["Version"]]