galaaz 2.1.7 → 2.1.9

data/blogs/manual/manual.tex

@@ -145,7 +145,7 @@
 \usepackage[utf8]{inputenc}
 
 \usepackage{geometry}
-\geometry{a4paper, top=1in}
+\geometry{a4paper, top=1.05in, headheight=30pt, headsep=14pt}
 
 % needed for kableExtra
 \usepackage{longtable}
@@ -166,29 +166,60 @@
 \usepackage{graphicx}
 
 \usepackage{fancyhdr}
-% set the header and foot style
-% style 'fancy' adds the section name on the header
-% and the page number on the footer
+% Header: small Galaaz mark (left); page number + section title (right),
+% matching classic LaTeX style: "4  AN EXTENSION TO THE EXAMPLE"
+% (upright page number, uppercase italic section name).
+% Logo paths cover repo blogs (../../sty/), installed ~/sty/, and local images/.
+% Blogs may delay headers with \renewcommand{\galaazheaderfrompage}{3} after this sty
+% (e.g. skip title/TOC and a logo splash page).
+\newcommand{\galaazheaderfrompage}{1}
+\newcommand{\galaazheaderlogo}{%
+  \raisebox{-0.12\height}{%
+    \IfFileExists{../../sty/galaaz-header.png}{%
+      \includegraphics[height=0.32in]{../../sty/galaaz-header.png}%
+    }{%
+      \IfFileExists{galaaz-header.png}{%
+        \includegraphics[height=0.32in]{galaaz-header.png}%
+      }{%
+        \IfFileExists{images/galaaz-header.png}{%
+          \includegraphics[height=0.32in]{images/galaaz-header.png}%
+        }{}%
+      }%
+    }%
+  }%
+}
+% Section title only in marks (no \thesection); page number is separate.
+\renewcommand{\sectionmark}[1]{\markboth{#1}{}}
+\renewcommand{\subsectionmark}[1]{}% keep the current section in the header
+\newcommand{\galaazmaybeheaderlogo}{%
+  \ifnum\value{page}<\galaazheaderfrompage\relax\else\galaazheaderlogo\fi}
+\newcommand{\galaazmayberighthead}{%
+  \ifnum\value{page}<\galaazheaderfrompage\relax
+  \else
+    \textup{\thepage}\hspace{1em}\textit{\MakeUppercase{\leftmark}}%
+  \fi
+}
 \pagestyle{fancy}
-
-% style 'fancyhf' leaves header and footer empty
-%\fancyhf{}
-
-% sets the left head element to \rightmark, which contains the
-% current section (\leftmark is the current chapter)
-%\fancyhead[L]{\rightmark} .
-
-% sets the right head element to the page number.
-% \fancyhead[R]{\thepage}
-
-% lets the head rule disappear.
-% \renewcommand{\headrulewidth}{0pt}
-% Possible selectors for the optional argument of \fancyhead/\fancyfoot
-% are L (left), C (center) or R (right) for the position of the element
-% and E (even) or O (odd) to distinguish even and odd pages. If you omit
-% E/O the element is set for all pages.
-
-% \usepackage{lipsum}
+\fancyhf{}
+\fancyhead[L]{\galaazmaybeheaderlogo}
+\fancyhead[R]{\galaazmayberighthead}
+\renewcommand{\headrulewidth}{0.3pt}
+\makeatletter
+\renewcommand{\headrule}{%
+  \ifnum\value{page}<\galaazheaderfrompage\relax
+  \else
+    \hrule\@height\headrulewidth\@width\headwidth
+    \vskip-\headrulewidth
+  \fi
+}
+\makeatother
+% First page often uses plain; same conditional header logic.
+\fancypagestyle{plain}{%
+  \fancyhf{}%
+  \fancyhead[L]{\galaazmaybeheaderlogo}%
+  \fancyhead[R]{\galaazmayberighthead}%
+  \renewcommand{\headrulewidth}{0.3pt}%
+}
 
 % make available command lastpage
 \usepackage{lastpage}
@@ -209,8 +240,34 @@
 % Command to import an R variable to latex
 \newcommand{\RtoLatex}[2]{\newcommand{#1}{#2}}
 
+% Soft-wrap Pandoc highlighted code/output boxes (Shaded + Highlighting).
+% This runs after Pandoc's default \DefineVerbatimEnvironment{Highlighting}
+% (header includes come later in the generated .tex). Prefer manual line
+% breaks in Rmd sources; breaklines is a safety net for leftovers/output.
+% Requires TinyTeX/TeX Live package: tlmgr install fvextra
+\IfFileExists{fvextra.sty}{%
+  \usepackage{fvextra}%
+  \DefineVerbatimEnvironment{Highlighting}{Verbatim}{%
+    breaklines=true,
+    breakanywhere=true,
+    breakindent=1.5em,
+    fontsize=\small,
+    commandchars=\\\{\}%
+  }%
+}{%
+  % fancyvrb is already loaded by Pandoc; shrink code so more fits per line.
+  \DefineVerbatimEnvironment{Highlighting}{Verbatim}{%
+    fontsize=\small,
+    commandchars=\\\{\}%
+  }%
+}
+
 % 
 %\newcommand{\atraso}[1]{\color{red} \textbf {Tempo desde a Assinatura do Contrato: #1 dias}}
+% No header on title/TOC (p.1) or splash logo page (p.2);
+% logo + page number + section title from page 3 onward.
+% Load after galaaz.sty.
+\renewcommand{\galaazheaderfrompage}{3}
 \usepackage{booktabs}
 \usepackage{longtable}
 \usepackage{array}
@@ -241,7 +298,7 @@
   \apptocmd{\@title}{\par {\large #1 \par}}{}{}
 }
 \makeatother
-\subtitle{Coupling Ruby (JRuby) and GNU R for data science}
+\subtitle{R-on-Rails: GNU R meets Ruby for the web}
 \author{Rodrigo Botafogo}
 \date{2026}
 
@@ -252,6 +309,8 @@
 \setcounter{tocdepth}{3}
 \tableofcontents
 }
+\begin{center}\includegraphics[width=0.45\linewidth]{images/galaaz-lockup-stacked} \end{center}
+
 \section{Introduction}\label{introduction}
 
 Galaaz is a system for tightly coupling Ruby and R. Ruby is a powerful
@@ -295,22 +354,26 @@ Until recently, there was no real perspective for Ruby to bridge this
 gap. Implementing a complete scientific computing infrastructure would
 take too long.
 
-\textbf{Galaaz 2.0} couples \textbf{JRuby} (Ruby on the JVM) with
-\textbf{GNU R}---the same R you use for CRAN and Bioconductor. Ruby and
-R run in \textbf{separate processes}; the \textbf{Galaaz bridge} sends
-requests to R and returns results to Ruby. From your point of view you
-still write Ruby: \texttt{R.c(...)},
+\textbf{Galaaz 2.0} supports \textbf{JRuby} and \textbf{CRuby} equally
+for the same NewBridge protocol. Pick the Ruby that fits your app: JRuby
+when you want real multithreading for web and I/O; CRuby when you prefer
+MRI. R remains the same \textbf{GNU R} you use interactively---including
+compiled extensions and Bioconductor. Ruby and R run in \textbf{separate
+processes}; the \textbf{Galaaz bridge} sends requests to R and returns
+results to Ruby. From your point of view you still write Ruby:
+\texttt{R.c(...)},
 \texttt{R.library(\textquotesingle{}ggplot2\textquotesingle{})},
-\texttt{\textasciitilde{}:mtcars}, and dplyr-style chains on R objects.
-You do not need to learn R syntax to get a lot done, though reading R
-documentation for individual packages remains useful.
+\texttt{\textasciitilde{}R{[}:mtcars{]}}, and dplyr-style chains on R
+objects. You do not need to learn R syntax to get a lot done, though
+reading R documentation for individual packages remains useful.
 
 Earlier experiments with Galaaz used Oracle's \textbf{GraalVM} with
 TruffleRuby and FastR so that Ruby and R could share one runtime. That
 path is no longer the focus: \textbf{standard GNU R} gives full
 compatibility with the R package ecosystem (including compiled
-extensions and Bioconductor) while JRuby gives a mature Ruby with
-\textbf{real multithreading} for application and I/O code.
+extensions and Bioconductor) while either Ruby engine talks to R over
+NewBridge (JRuby for mature multithreading on the application side;
+CRuby when you prefer MRI).
 
 The bridge handles \textbf{communication and typing} between the two
 worlds; large tables can also flow through \textbf{Apache Arrow} on the
@@ -356,12 +419,15 @@ the gemspec: \textbf{\texttt{galaaz}}, \textbf{\texttt{gstudio}},
 \textbf{\texttt{gknit-draft}}); for development and CI, prefer the
 \textbf{\texttt{bin/}} copies so JVM flags and paths stay correct.
 
-Below, \textbf{current (Galaaz 2.0 + JRuby + GNU R)} means the tool is
-wired to \textbf{\texttt{jruby}} and
-\textbf{\texttt{bin/galaaz\_jruby\_env.inc.sh}} (or equivalent logic in
-Ruby via \texttt{lib/galaaz\_jruby.rb}). \textbf{Legacy} means the
-script still targets \textbf{GraalVM} polyglot Ruby / FastR-era
-invocation and is \textbf{not} expected to work on a typical JRuby-only
+Below, \textbf{current (Galaaz 2.0 + JRuby or CRuby + GNU R)} means the
+tool uses \textbf{\texttt{bin/galaaz-ruby}} /
+\textbf{\texttt{GALAAZ\_RUBY}} (default: \texttt{ruby} on \texttt{PATH})
+and applies JVM flags only when the interpreter is JRuby
+(\texttt{bin/galaaz\_jruby\_env.inc.sh} /
+\texttt{lib/galaaz\_jruby.rb}). \textbf{\texttt{bin/galaaz-jruby}}
+forces JRuby. \textbf{Legacy} means the script still targets
+\textbf{GraalVM} polyglot Ruby / FastR-era invocation and is
+\textbf{not} expected to work on a typical JRuby or CRuby NewBridge
 setup.
 
 \textbf{Table layout:} names in the first column are
@@ -371,8 +437,8 @@ options and examples sit \textbf{outside} the tables so PDF columns stay
 readable.
 
 \begin{verbatim}
-## Warning in styling_latex_scale(out, table_info, "down"): Longtable cannot be
-## resized.
+## Warning in styling_latex_scale(out, table_info, "down"): Longtable
+## cannot be resized.
 \end{verbatim}
 
 \begingroup\fontsize{9}{11}\selectfont
@@ -381,9 +447,9 @@ readable.
 \toprule
 Script & Role & 2.0?\\
 \midrule
-galaaz-bootstrap & WSL2 helper: Docker checks; optional TinyTeX or poppler for gKnit PDF. & Yes*\\
-galaaz-jruby & JRuby with repo lib/ on LOAD\_PATH and required JVM flags (e.g. Arrow). & Yes\\
-galaaz\_jruby\_env.inc.sh & Sourced by bash wrappers; sets GALAAZ\_REQUIRED\_JRUBY\_J\_ARGS. & Yes†\\
+galaaz-bootstrap & WSL2 helper: Docker checks; optional TinyTeX/poppler. & Yes*\\
+galaaz-jruby & JRuby with repo lib/ on LOAD\_PATH and JVM flags. & Yes\\
+galaaz\_jruby\_env.inc.sh & Sourced by bash wrappers; sets JRUBY\_J\_ARGS. & Yes†\\
 install-tinytex & Install TinyTeX for PDF output. & Yes\\
 \bottomrule
 \end{longtable}
@@ -409,8 +475,8 @@ install-tinytex & Install TinyTeX for PDF output. & Yes\\
 Rake}\label{interactive-use-examples-and-rake}
 
 \begin{verbatim}
-## Warning in styling_latex_scale(out, table_info, "down"): Longtable cannot be
-## resized.
+## Warning in styling_latex_scale(out, table_info, "down"): Longtable
+## cannot be resized.
 \end{verbatim}
 
 \begingroup\fontsize{9}{11}\selectfont
@@ -429,8 +495,8 @@ galaaz & Forward arguments to rake (needs rake; usually JRuby). & Yes\\
 \subsection{gKnit and document drafts}\label{gknit-and-document-drafts}
 
 \begin{verbatim}
-## Warning in styling_latex_scale(out, table_info, "down"): Longtable cannot be
-## resized.
+## Warning in styling_latex_scale(out, table_info, "down"): Longtable
+## cannot be resized.
 \end{verbatim}
 
 \begingroup\fontsize{9}{11}\selectfont
@@ -440,7 +506,7 @@ galaaz & Forward arguments to rake (needs rake; usually JRuby). & Yes\\
 Script & Role & 2.0?\\
 \midrule
 gknit & Knit .Rmd via JRuby and R Markdown render. & Yes\\
-gknit-draft & Drafts from rticles-style templates; wrapper still uses legacy polyglot ruby. & Legacy\\
+gknit-draft & Drafts from rticles templates; legacy polyglot wrapper. & Legacy\\
 gknit-draft.rb & Ruby entry: GKnit.draft (use with JRuby + LOAD\_PATH). & JRuby\\
 gknit\_Rscript & Polyglot Rscript launcher; hard-coded LOAD\_PATH sample. & No\\
 \bottomrule
@@ -459,8 +525,8 @@ workflows until that wrapper matches the \textbf{\texttt{gknit}} stack.
 \subsection{Tests}\label{tests}
 
 \begin{verbatim}
-## Warning in styling_latex_scale(out, table_info, "down"): Longtable cannot be
-## resized.
+## Warning in styling_latex_scale(out, table_info, "down"): Longtable
+## cannot be resized.
 \end{verbatim}
 
 \begingroup\fontsize{9}{11}\selectfont
@@ -470,7 +536,7 @@ workflows until that wrapper matches the \textbf{\texttt{gknit}} stack.
 Script & Role & 2.0?\\
 \midrule
 run\_rspec & Top-level specs/*\_spec.rb with spec\_helper (see docs/testing.md). & Yes\\
-run\_all\_rspec & Compile ext/new\_bridge; run specs/ and new\_bridge\_specs/ together. & Yes\\
+run\_all\_rspec & Compile ext/new\_bridge; run specs/ and new\_bridge\_specs/. & Yes\\
 run\_slow\_rspec & Suites under slow-specs/ (read script header for spec\_helper). & Yes\\
 run\_old\_rspec & Legacy suites under old\_specs/. & Yes\\
 run\_rspec\_subset & Numbered subset 1–18 (Documentation/Spec\_Subsets.md). & Yes\\
@@ -481,8 +547,8 @@ run\_rspec\_subset & Numbered subset 1–18 (Documentation/Spec\_Subsets.md). &
 \subsection{Other}\label{other}
 
 \begin{verbatim}
-## Warning in styling_latex_scale(out, table_info, "down"): Longtable cannot be
-## resized.
+## Warning in styling_latex_scale(out, table_info, "down"): Longtable
+## cannot be resized.
 \end{verbatim}
 
 \begingroup\fontsize{9}{11}\selectfont
@@ -491,14 +557,15 @@ run\_rspec\_subset & Numbered subset 1–18 (Documentation/Spec\_Subsets.md). &
 \toprule
 Script & Role & 2.0?\\
 \midrule
-grun & Graal-era launcher: polyglot ruby with --jvm. Use galaaz-jruby -S instead. & No\\
+grun & Graal-era launcher: polyglot ruby --jvm; prefer galaaz-jruby. & No\\
 gstudio\_irb.rb / gstudio\_pry.rb & Loaded by gstudio; not meant to be run standalone. & Yes\\
 \bottomrule
 \end{longtable}
 \endgroup{}
 
 For day-to-day \textbf{2.0} use, rely on
-\textbf{\texttt{bin/galaaz-jruby}}, \textbf{\texttt{bin/gstudio}},
+\textbf{\texttt{bin/galaaz-ruby}} (or \textbf{\texttt{bin/galaaz-jruby}}
+when you want to force JRuby), \textbf{\texttt{bin/gstudio}},
 \textbf{\texttt{bin/gknit}}, \textbf{\texttt{bin/run\_example}},
 \textbf{\texttt{bin/run\_rspec}} /
 \textbf{\texttt{bin/run\_all\_rspec}}, and
@@ -506,7 +573,7 @@ For day-to-day \textbf{2.0} use, rely on
 Treat \textbf{\texttt{grun}}, \textbf{\texttt{gknit\_Rscript}}, and the
 polyglot \textbf{\texttt{ruby}} invocation in
 \textbf{\texttt{gknit-draft}} as \textbf{legacy} until they are ported
-to the same JRuby path as \textbf{\texttt{gknit}}.
+to the same launcher path as \textbf{\texttt{gknit}}.
 
 \section{System Compatibility}\label{system-compatibility}
 
@@ -518,7 +585,8 @@ Typical development and CI targets:
   \textbf{Linux} --- recent Ubuntu LTS or comparable distributions
   (x86\_64).
 \item
-  \textbf{macOS} --- recent releases with JRuby and GNU R available.
+  \textbf{macOS} --- recent releases with JRuby or CRuby and GNU R
+  available.
 \item
   \textbf{Windows} --- use \textbf{WSL2} (same Linux stack as above);
   native Windows is not the primary target.
@@ -533,16 +601,19 @@ is built with \texttt{make} and a C++ toolchain; see the project
 \begin{itemize}
 \tightlist
 \item
-  \textbf{JRuby} --- Ruby implementation on the JVM (Galaaz 2.0 is
-  developed and tested with JRuby).
+  \textbf{Ruby} --- \textbf{JRuby} or \textbf{CRuby} (both supported for
+  NewBridge). Tested with \textbf{JRuby 10.1.1.0} (+ \textbf{JDK 21})
+  and \textbf{CRuby 3.3.12}. Use \texttt{bin/galaaz-ruby} (honors
+  \texttt{GALAAZ\_RUBY}) or plain \texttt{gem\ install\ galaaz} under
+  the Ruby you choose.
 \item
-  A \textbf{Java runtime} (JDK) compatible with your JRuby version.
+  \textbf{GNU R} --- \texttt{R} and \texttt{Rscript} on your
+  \texttt{PATH} (tested with \textbf{4.3.3}), plus a C++ toolchain
+  (\texttt{g++}, \texttt{make}) and the \textbf{Rcpp} package to compile
+  the gatekeeper.
 \item
-  \textbf{GNU R} --- \texttt{R} on your \texttt{PATH}, with ability to
-  install packages (CRAN / Bioconductor as needed).
-\item
-  \textbf{Ruby gems} --- from the Galaaz repository,
-  \texttt{bundle\ install} (see the \texttt{Gemfile} / gemspec).
+  \textbf{galaaz gem} --- runtime dependency \texttt{msgpack} is pulled
+  in by \texttt{gem\ install}.
 \item
   Optional: \textbf{Docker} --- if you run R in a container (common on
   WSL2); see bootstrap below.
@@ -555,43 +626,93 @@ is built with \texttt{make} and a C++ toolchain; see the project
 
 \section{Installation}\label{installation}
 
-From a clone of the Galaaz repository:
+The supported install is \textbf{\texttt{gem\ install} + compile the
+gatekeeper}. You do not need a git clone.
 
 \begin{enumerate}
 \def\labelenumi{\arabic{enumi}.}
-\tightlist
 \item
-  Install \textbf{JRuby} and \textbf{GNU R} using your preferred package
-  manager or Ruby version manager.
+  Install \textbf{JRuby} (and a compatible \textbf{JDK}) \textbf{or
+  CRuby 3.3+}, plus \textbf{GNU R} (with \texttt{Rscript} and a C++
+  compiler).
 \item
-  Install \textbf{bundler} if needed, then run
-  \textbf{\texttt{bundle\ install}} in the repository root.
+  In R, install \textbf{Rcpp}: \texttt{install.packages("Rcpp")}.
 \item
-  Build the bridge native code:
-  \textbf{\texttt{make\ -C\ ext/new\_bridge\ all}} (or
-  \textbf{\texttt{rake\ compile\_gatekeeper}}).
+  Install the gem: \texttt{jruby\ -S\ gem\ install\ galaaz} (or
+  \texttt{gem\ install\ galaaz} under CRuby).
 \item
-  Run Ruby scripts with the project load path and JVM flags the project
-  expects --- the \textbf{\texttt{bin/galaaz-jruby}} wrapper sources
-  \textbf{\texttt{bin/galaaz\_jruby\_env.inc.sh}} and adds
-  \textbf{\texttt{-I\ lib}}. This matters especially for \textbf{Apache
-  Arrow} integration (see \texttt{docs/testing.md}).
+  Compile the native gatekeeper from the installed gem:
+
+\begin{verbatim}
+gem_dir="$(ruby -e \
+  "puts Gem::Specification.find_by_name('galaaz').full_gem_path")"
+# under JRuby: use jruby -e instead of ruby -e
+make -C "${gem_dir}/ext/new_bridge" all
+\end{verbatim}
 \item
   Ensure \textbf{\texttt{R}} starts GNU R and can install packages
-  (network access to CRAN mirrors when you first call
-  \texttt{R.install\_and\_loads}).
+  (network access to CRAN when you first call
+  \texttt{R.install\_and\_loads}). For \textbf{Apache Arrow} on
+  \textbf{JRuby} (Java 9+), the child JVM needs
+  \texttt{-\/-add-opens=java.base/java.nio=ALL-UNNAMED} via
+  \textbf{\texttt{JAVA\_OPTS}} (from a checkout,
+  \texttt{bin/galaaz-jruby} and \texttt{mise.toml} set this; a leading
+  \texttt{jruby\ -J...\ -S\ bundle\ exec} does \textbf{not} pass
+  \texttt{-J} to rspec). On \textbf{CRuby}, install Apache Arrow GLib
+  (\texttt{libarrow-glib-dev} from the
+  \href{https://arrow.apache.org/install/}{Apache Arrow APT} repo) and
+  \texttt{gem\ install\ red-arrow} matching
+  \texttt{pkg-config\ -\/-modversion\ arrow-glib}. Do not install the
+  unrelated Rubygems package named \texttt{arrow}.
 \end{enumerate}
 
 For \textbf{gKnit}, \textbf{knitr}, \textbf{rmarkdown}, and LaTeX (PDF
-output), install the corresponding R packages and a TeX distribution if
-you need PDF; the repository includes helpers such as
-\textbf{\texttt{bin/install-tinytex}} where appropriate.
+output), install the corresponding R packages, \textbf{Pandoc}, and a
+TeX distribution if you need PDF; the repository includes helpers such
+as \textbf{\texttt{bin/install-tinytex}} where appropriate.
 
-A \textbf{table of all \texttt{bin/} scripts} (bootstrap, JRuby wrapper,
+A \textbf{table of all \texttt{bin/} scripts} (bootstrap, Ruby launcher,
 gstudio, gknit, test runners, and which ones are legacy) is in the
 section \textbf{Command-line tools (\texttt{bin/})} earlier in this
 manual.
 
+\subsubsection{From a repository checkout
+(contributors)}\label{from-a-repository-checkout-contributors}
+
+\begin{enumerate}
+\def\labelenumi{\arabic{enumi}.}
+\tightlist
+\item
+  Install \textbf{bundler} if needed, then run
+  \textbf{\texttt{bundle\ install}} with your chosen Ruby
+  (\texttt{jruby\ -S\ bundle\ install} or CRuby
+  \texttt{bundle\ install}) in the repository root.
+\item
+  Build the bridge native code:
+  \textbf{\texttt{make\ -C\ ext/new\_bridge\ all}} (or
+  \textbf{\texttt{rake\ compile\_gatekeeper}}).
+\item
+  Run scripts with \textbf{\texttt{bin/galaaz-ruby}} (uses \texttt{ruby}
+  on \texttt{PATH}; set \textbf{\texttt{GALAAZ\_RUBY=jruby}} or
+  \textbf{\texttt{GALAAZ\_RUBY=ruby}} to force an engine). Spec runners:
+  \textbf{\texttt{bin/run\_rspec}} /
+  \textbf{\texttt{bin/run\_all\_rspec}} (same \texttt{GALAAZ\_RUBY}
+  rule). \textbf{\texttt{bin/galaaz-jruby}} remains a thin wrapper that
+  forces JRuby.
+\end{enumerate}
+
+A \textbf{gstudio} try image with Galaaz already installed is available
+for both engines: \textbf{JRuby} ---
+\texttt{docker\ run\ -\/-rm\ -it\ ghcr.io/rbotafogo/galaaz-try:gstudio}
+(or \texttt{./docker/try-gstudio/run.sh} from a checkout);
+\textbf{CRuby} ---
+\texttt{docker\ run\ -\/-rm\ -it\ ghcr.io/rbotafogo/galaaz-try:cruby}
+(or \texttt{./docker/try-cruby/run.sh}). Maintainers can prove a
+RubyGems install on a throwaway Ubuntu machine (no repo inside the
+container) with \texttt{./docker/cold-install/run.sh\ published-specs}
+(JRuby) or \texttt{./docker/cold-install-cruby/run.sh\ published-specs}
+(CRuby).
+
 \subsection{Windows + WSL2 (optional: Docker / R in a
 container)}\label{windows-wsl2-optional-docker-r-in-a-container}
 
@@ -651,12 +772,42 @@ installed.
 \begin{Highlighting}[]
 \NormalTok{  vec }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{1}\NormalTok{, }\DecValTok{2}\NormalTok{, }\DecValTok{3}\NormalTok{, }\DecValTok{4}\NormalTok{)}
   \FunctionTok{puts}\NormalTok{ vec}
+
+  \CommentTok{\# R.foo(...) calls an R *function*. Datasets are objects — fetch with}
+  \CommentTok{\# \textasciitilde{}:}
+\NormalTok{  df }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}
+  \FunctionTok{puts} \ConstantTok{R}\AttributeTok{.summary}\NormalTok{(df)}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
 ## [1] 1 2 3 4
-\end{verbatim}
+##       mpg             cyl             disp             hp       
+##  Min.   :10.40   Min.   :4.000   Min.   : 71.1   Min.   : 52.0  
+##  1st Qu.:15.43   1st Qu.:4.000   1st Qu.:120.8   1st Qu.: 96.5  
+##  Median :19.20   Median :6.000   Median :196.3   Median :123.0  
+##  Mean   :20.09   Mean   :6.188   Mean   :230.7   Mean   :146.7  
+##  3rd Qu.:22.80   3rd Qu.:8.000   3rd Qu.:326.0   3rd Qu.:180.0  
+##  Max.   :33.90   Max.   :8.000   Max.   :472.0   Max.   :335.0  
+##       drat             wt             qsec             vs        
+##  Min.   :2.760   Min.   :1.513   Min.   :14.50   Min.   :0.0000  
+##  1st Qu.:3.080   1st Qu.:2.581   1st Qu.:16.89   1st Qu.:0.0000  
+##  Median :3.695   Median :3.325   Median :17.71   Median :0.0000  
+##  Mean   :3.597   Mean   :3.217   Mean   :17.85   Mean   :0.4375  
+##  3rd Qu.:3.920   3rd Qu.:3.610   3rd Qu.:18.90   3rd Qu.:1.0000  
+##  Max.   :4.930   Max.   :5.424   Max.   :22.90   Max.   :1.0000  
+##        am              gear            carb      
+##  Min.   :0.0000   Min.   :3.000   Min.   :1.000  
+##  1st Qu.:0.0000   1st Qu.:3.000   1st Qu.:2.000  
+##  Median :0.0000   Median :4.000   Median :2.000  
+##  Mean   :0.4062   Mean   :3.688   Mean   :2.812  
+##  3rd Qu.:1.0000   3rd Qu.:4.000   3rd Qu.:4.000  
+##  Max.   :1.0000   Max.   :5.000   Max.   :8.000
+\end{verbatim}
+
+(\texttt{R.mtcars} is wrong: it becomes \texttt{mtcars()} in R and
+fails. With \texttt{using\ Galaaz::SymbolDSL}, the short form
+\texttt{\textasciitilde{}:mtcars} also works.)
 
 \begin{itemize}
 \item
@@ -697,13 +848,16 @@ installed.
   \end{quote}
 \end{itemize}
 
-\section{JRuby, multithreading, and the R
-bridge}\label{jruby-multithreading-and-the-r-bridge}
+\section{JRuby, CRuby, multithreading, and the R
+bridge}\label{jruby-cruby-multithreading-and-the-r-bridge}
 
-Galaaz 2.0 runs Ruby on \textbf{JRuby}, so your application can use
-\textbf{real parallel threads} for I/O-bound work (HTTP clients,
-database connections, message consumers, and so on). R itself is still
-executed in a \textbf{single GNU R process} behind the Galaaz bridge.
+Galaaz 2.0 supports \textbf{JRuby} and \textbf{CRuby} equally for
+NewBridge. On \textbf{JRuby}, your application can use \textbf{real
+parallel threads} for I/O-bound work (HTTP clients, database
+connections, message consumers, and so on). On \textbf{CRuby}, prefer
+multi-process scaling for CPU-bound concurrency. R itself is still
+executed in a \textbf{single GNU R process} behind the Galaaz bridge
+(use multiple R workers when you need more R throughput).
 
 When several Ruby threads call into R at the same time, the bridge
 \textbf{serializes} those calls: each request is matched to a reply
@@ -739,9 +893,15 @@ bridge itself, see \texttt{specs/bridge\_concurrent\_spec.rb} and
 \subsection{Long-running R calls and a completion
 block}\label{long-running-r-calls-and-a-completion-block}
 
-For R work that can take a long time, the bridge can avoid a Ruby-side
-\textbf{wait timeout} by scheduling the call and resuming in a
-\textbf{block} when the \texttt{RET} arrives.
+For R work that can take a long time \textbf{on the bridge}, the bridge
+can avoid a Ruby-side \textbf{wait timeout} by scheduling the call and
+resuming in a \textbf{block} when the \texttt{RET} arrives.
+
+\textbf{Important distinction:} this keeps the \textbf{same} GNU R
+process busy. Other sync \texttt{eval\_r} / gknit chunks still wait on
+that R. For CRAN installs and other work that must \textbf{not}
+monopolize the bridge (or that can OOM a small VM if abandoned
+mid-compile), use \textbf{\texttt{R::Job}} in the next section instead.
 
 \begin{itemize}
 \tightlist
@@ -789,9 +949,11 @@ error.)
 
 \ConstantTok{R}\AttributeTok{.eval\_r\_async}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}(\{ Sys.sleep(0.3); 42L \})\textquotesingle{}}\NormalTok{, }\WarningTok{timeout:} \DecValTok{nil}\NormalTok{) }\ControlFlowTok{do} \OperatorTok{|}\NormalTok{result}\OperatorTok{|}
   \ControlFlowTok{if}\NormalTok{ result}\AttributeTok{.ok?}
-    \FunctionTok{puts} \StringTok{"[completion] R finished; eval\_r{-}style value: }\SpecialCharTok{\#\{}\NormalTok{result}\AttributeTok{.value.inspect}\SpecialCharTok{\}}\StringTok{"}
+    \FunctionTok{puts} \StringTok{"[completion] R finished; value: "} \OperatorTok{+}
+         \StringTok{"}\SpecialCharTok{\#\{}\NormalTok{result}\AttributeTok{.value.inspect}\SpecialCharTok{\}}\StringTok{"}
   \ControlFlowTok{else}
-    \FunctionTok{puts} \StringTok{"[completion] R/bridge error: }\SpecialCharTok{\#\{}\NormalTok{result}\AttributeTok{.error.class}\SpecialCharTok{\}}\StringTok{: }\SpecialCharTok{\#\{}\NormalTok{result}\AttributeTok{.error.message}\SpecialCharTok{\}}\StringTok{"}
+    \FunctionTok{puts} \StringTok{"[completion] R/bridge error: "} \OperatorTok{+}
+         \StringTok{"}\SpecialCharTok{\#\{}\NormalTok{result}\AttributeTok{.error.class}\SpecialCharTok{\}}\StringTok{: }\SpecialCharTok{\#\{}\NormalTok{result}\AttributeTok{.error.message}\SpecialCharTok{\}}\StringTok{"}
   \ControlFlowTok{end}
 \NormalTok{  completion}\AttributeTok{.push}\NormalTok{(}\WarningTok{:done}\NormalTok{)}
 \ControlFlowTok{end}
@@ -810,7 +972,7 @@ error.)
 ## [main] other Ruby work step 1
 ## [main] other Ruby work step 2
 ## [main] other Ruby work step 3
-## [completion] R finished; eval_r-style value: "[1] 42"
+## [completion] R finished; value: "[1] 42"
 ## [main] R completion has run; exiting.
 \end{verbatim}
 
@@ -823,56 +985,403 @@ exists (inside the block, or after data written there is observed
 elsewhere). Runnable specs live in
 \textbf{\texttt{new\_bridge\_specs/eval\_r\_async\_spec.rb}}.
 
+\subsection{\texorpdfstring{Background R jobs
+(\texttt{R::Job})}{Background R jobs (R::Job)}}\label{background-r-jobs-rjob}
+
+\texttt{R::Async} / \texttt{R.eval\_r\_async} free the \textbf{Ruby}
+thread while the \textbf{same} bridge R process runs your code. That is
+enough for Rails-style ``don't block the request thread,'' but not
+enough for heavy \texttt{install.packages} or multi-minute model fits:
+the gatekeeper R is still busy, other chunks time out, and abandoning
+the wait can leave compile work burning RAM.
+
+\textbf{\texttt{R::Job}} runs that work in a \textbf{child
+\texttt{Rscript} process}. The bridge stays free. Logs and metadata live
+under \texttt{\textasciitilde{}/.local/share/galaaz/jobs/} (override
+with \texttt{GALAAZ\_JOBS\_DIR}).
+
+\subsubsection{Package installs}\label{package-installs}
+
+\texttt{R.install\_and\_loads} / \texttt{R.install\_rlibs} use
+\texttt{R::Job.install} and \textbf{await until the child finishes}
+(default: no wall-clock limit). Optional limit:
+\texttt{GALAAZ\_INSTALL\_TIMEOUT\_SEC} or
+\texttt{install\_timeout\_sec:}. On timeout the child process group is
+killed so leftover \texttt{make}/\texttt{gcc} cannot OOM the shell.
+Stale \texttt{00LOCK-*} dirs are cleared before the next install. Only
+one install runs at a time (\texttt{install.lock}).
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\CommentTok{\# May take a long time the first time (e.g. caret); the bridge is not}
+\CommentTok{\# used for compile.}
+\ConstantTok{R}\AttributeTok{.install\_and\_loads} \VerbatimStringTok{\textquotesingle{}caret\textquotesingle{}}
+\end{Highlighting}
+\end{Shaded}
+
+\subsubsection{\texorpdfstring{Long arbitrary R (\texttt{eval} /
+\texttt{script})}{Long arbitrary R (eval / script)}}\label{long-arbitrary-r-eval-script}
+
+Prefer the \textbf{block} form (like \texttt{File.open}): await the
+child, yield the job, return the block's value. Without a block, the
+methods still await by default and return the \texttt{Job}.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\ControlFlowTok{begin}
+\NormalTok{  coef }\OperatorTok{=} \ConstantTok{R}\OperatorTok{::}\DataTypeTok{Job}\AttributeTok{.eval}\NormalTok{(}\OperatorTok{\textless{}\textless{}\textasciitilde{}}\ControlFlowTok{R}\DocumentationTok{) \{ |job| job.load\_rds \}}
+\DocumentationTok{    fit \textless{}{-} lm(mpg \textasciitilde{} wt, data = mtcars)}
+\DocumentationTok{    saveRDS(unname(coef(fit)), result\_path)}
+\DocumentationTok{  }\ControlFlowTok{R}
+  \FunctionTok{puts}\NormalTok{ coef}
+\ControlFlowTok{rescue} \OperatorTok{=\textgreater{}}\NormalTok{ e}
+  \FunctionTok{puts}\NormalTok{ e}\AttributeTok{.class.to\_s}
+\NormalTok{  e}\AttributeTok{.message.to\_s.scan}\NormalTok{(}\SpecialStringTok{/.\{1,68\}/}\NormalTok{)}\AttributeTok{.each} \OperatorTok{\{} \OperatorTok{|}\NormalTok{line}\OperatorTok{|} \FunctionTok{puts}\NormalTok{ line }\OperatorTok{\}}
+\ControlFlowTok{end}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## [1] 37.285126 -5.344472
+\end{verbatim}
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\CommentTok{\# Without a block: awaits (wait: true is the default) and returns the}
+\CommentTok{\# Job}
+\NormalTok{job }\OperatorTok{=} \ConstantTok{R}\OperatorTok{::}\DataTypeTok{Job}\AttributeTok{.eval}\NormalTok{(code)}
+\NormalTok{job }\OperatorTok{=} \ConstantTok{R}\OperatorTok{::}\DataTypeTok{Job}\AttributeTok{.eval}\NormalTok{(code, }\WarningTok{wait:} \DecValTok{false}\NormalTok{)  }\CommentTok{\# start only; call job.wait later}
+
+\CommentTok{\# Script file; trailing args → commandArgs(trailingOnly=TRUE) in the}
+\CommentTok{\# child}
+\NormalTok{res }\OperatorTok{=} \ConstantTok{R}\OperatorTok{::}\DataTypeTok{Job}\AttributeTok{.script}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}train.R\textquotesingle{}}\NormalTok{, }\CharTok{\textquotesingle{}5\textquotesingle{}}\NormalTok{) }\OperatorTok{\{} \OperatorTok{|}\NormalTok{job}\OperatorTok{|}\NormalTok{ job}\AttributeTok{.load\_rds} \OperatorTok{\}}
+\end{Highlighting}
+\end{Shaded}
+
+In the child: \texttt{setwd(job.dir)}, \texttt{.libPaths} includes the
+Galaaz user library, \texttt{GALAAZ\_JOB\_DIR} is set, and
+\textbf{\texttt{result\_path}} defaults to
+\texttt{file.path(GALAAZ\_JOB\_DIR,\ "result.rds")}. Persist with
+\texttt{saveRDS(...,\ result\_path)}, then load on the bridge with
+\textbf{\texttt{job.load\_rds}} (short sync \texttt{readRDS} → a normal
+Galaaz R object).
+
+\subsubsection{Choosing async vs Job}\label{choosing-async-vs-job}
+
+{\def\LTcaptype{none} % do not increment counter
+\begin{longtable}[]{@{}
+  >{\raggedright\arraybackslash}p{(\linewidth - 2\tabcolsep) * \real{0.5455}}
+  >{\raggedright\arraybackslash}p{(\linewidth - 2\tabcolsep) * \real{0.4545}}@{}}
+\toprule\noalign{}
+\begin{minipage}[b]{\linewidth}\raggedright
+Need
+\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
+Use
+\end{minipage} \\
+\midrule\noalign{}
+\endhead
+\bottomrule\noalign{}
+\endlastfoot
+Don't freeze a Ruby thread; short/medium R on the bridge is OK &
+\texttt{R::Async} / \texttt{R.eval\_r\_async} \\
+Install CRAN packages, or long R that must not block the bridge &
+\texttt{R::Job} / \texttt{R.install\_and\_loads} \\
+\end{longtable}
+}
+
+\subsection{Galaaz + Rails (R-on-Rails) integration
+baseline}\label{galaaz-rails-r-on-rails-integration-baseline}
+
+This is the practical \textbf{R-on-Rails} starter: an R scientist's
+analysis behind a small Rails app. The baseline we used in WSL aimed at:
+
+\begin{enumerate}
+\def\labelenumi{\arabic{enumi}.}
+\tightlist
+\item
+  Rails boots under \textbf{JRuby or CRuby} (same bridge; see
+  Installation).
+\item
+  Galaaz is loaded from a local checkout (before publishing to
+  RubyGems).
+\item
+  A request path can execute \textbf{\texttt{R.eval(...)}} and return a
+  result.
+\end{enumerate}
+
+\subsubsection{1) Create the app with Ruby-friendly
+options}\label{create-the-app-with-ruby-friendly-options}
+
+Rails defaults can pull gems that are awkward on some setups (for
+example sqlite native extension paths on JRuby, or deployment extras you
+do not need). A minimal app avoids early friction:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\BuiltInTok{cd}\NormalTok{ /home/rbotafogo/desenv\_linux}
+\ExtensionTok{jruby} \AttributeTok{{-}S}\NormalTok{ rails new hedi }\AttributeTok{{-}{-}skip{-}git} \AttributeTok{{-}{-}minimal} \DataTypeTok{\textbackslash{}}
+  \AttributeTok{{-}{-}skip{-}kamal} \AttributeTok{{-}{-}skip{-}solid} \AttributeTok{{-}{-}skip{-}active{-}record}
+\end{Highlighting}
+\end{Shaded}
+
+Then install gems:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\BuiltInTok{cd}\NormalTok{ /home/rbotafogo/desenv\_linux/hedi}
+\ExtensionTok{jruby} \AttributeTok{{-}S}\NormalTok{ bundle install}
+\end{Highlighting}
+\end{Shaded}
+
+\subsubsection{2) Use Galaaz as a local path
+gem}\label{use-galaaz-as-a-local-path-gem}
+
+For local development we keep a stable path:
+
+\begin{itemize}
+\tightlist
+\item
+  \texttt{\textasciitilde{}/gems/galaaz} -\textgreater{} symlink to your
+  Galaaz checkout
+\item
+  optional built gem archive in \texttt{\textasciitilde{}/gems/pkg/}
+\end{itemize}
+
+In Rails \texttt{Gemfile}:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{gem }\StringTok{"galaaz"}\NormalTok{, }\WarningTok{path:} \StringTok{"/home/rbotafogo/gems/galaaz"}\NormalTok{, }\WarningTok{require:} \DecValTok{false}
+\end{Highlighting}
+\end{Shaded}
+
+And load after Rails boot in \texttt{config/application.rb}:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{config}\AttributeTok{.after\_initialize} \OperatorTok{\{} \FunctionTok{require} \StringTok{"galaaz"} \OperatorTok{\}}
+\end{Highlighting}
+\end{Shaded}
+
+Why \texttt{require:\ false} + \texttt{after\_initialize}? In this
+integration, loading Galaaz too early via \texttt{Bundler.require}
+triggered Rails/JRuby initialization failures.
+
+\subsubsection{3) Simple request-path smoke
+test}\label{simple-request-path-smoke-test}
+
+A direct smoke test from Rails runner:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\BuiltInTok{cd}\NormalTok{ /home/rbotafogo/desenv\_linux/hedi}
+\ExtensionTok{jruby} \AttributeTok{{-}S}\NormalTok{ bundle exec rails runner }\DataTypeTok{\textbackslash{}}
+  \StringTok{"puts R.eval(\textquotesingle{}sum(c(1,2,3,4,5))\textquotesingle{}).inspect"}
+\end{Highlighting}
+\end{Shaded}
+
+Expected output:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{15.0}
+\end{Highlighting}
+\end{Shaded}
+
+\subsubsection{4) HTTP endpoint pattern}\label{http-endpoint-pattern}
+
+For this baseline, a small Rack endpoint was the most stable first step
+to prove request-time R evaluation. (A full ActionController stack can
+be enabled later as the app evolves.)
+
+Minimal pattern:
+
+\begin{enumerate}
+\def\labelenumi{\arabic{enumi}.}
+\tightlist
+\item
+  Define a Rack app class under \texttt{lib/} that runs
+  \texttt{R.eval(...)} and returns HTML/JSON.
+\item
+  Point a route to that Rack app (\texttt{root\ to:\ MyRackApp}).
+\item
+  Verify with browser/curl.
+\end{enumerate}
+
+\subsubsection{5) Running from WSL and opening from
+Windows}\label{running-from-wsl-and-opening-from-windows}
+
+Recommended bind:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\ExtensionTok{jruby} \AttributeTok{{-}S}\NormalTok{ bundle exec rails server }\AttributeTok{{-}b}\NormalTok{ 0.0.0.0 }\AttributeTok{{-}p}\NormalTok{ 3000}
+\end{Highlighting}
+\end{Shaded}
+
+Then open from Windows:
+
+\begin{itemize}
+\tightlist
+\item
+  \texttt{http://localhost:3000} (usually works with WSL localhost
+  forwarding), or
+\item
+  \texttt{http://\textless{}wsl-ip\textgreater{}:3000} if needed.
+\end{itemize}
+
+In development, if Host Authorization blocks requests with unexpected
+Host headers, use:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\CommentTok{\# config/environments/development.rb}
+\NormalTok{config}\AttributeTok{.hosts.clear}
+\end{Highlighting}
+\end{Shaded}
+
+\subsubsection{6) Troubleshooting
+checklist}\label{troubleshooting-checklist}
+
+\begin{itemize}
+\tightlist
+\item
+  \texttt{Could\ not\ find\ ...\ in\ locally\ installed\ gems}: run
+  \texttt{jruby\ -S\ bundle\ install} in the Rails app directory.
+\item
+  Stale PID after crash: remove \texttt{tmp/pids/server.pid}.
+\item
+  Local Galaaz path changed: verify \texttt{Gemfile} path target exists
+  and rerun bundler.
+\item
+  R runtime issues: confirm GNU R is installed and on \texttt{PATH} in
+  the same shell where Rails runs.
+\end{itemize}
+
+As new Rails features are added (controllers, jobs, websockets,
+background rendering, plot generation), extend this section with
+concrete, runnable snippets and the associated operational checks.
+
 \section{Accessing R from Ruby}\label{accessing-r-from-ruby}
 
 One of the nice aspects of Galaaz is that variables and functions
 defined in R can be easily accessed from Ruby. For instance, to access
 the \texttt{mtcars} data frame from R in Ruby, we use the symbol
 \texttt{:mtcars} preceded by the \texttt{\textasciitilde{}} operator:
-\texttt{\textasciitilde{}:mtcars} retrieves the value of the
+\texttt{\textasciitilde{}R{[}:mtcars{]}} retrieves the value of the
 \texttt{mtcars} object in R.
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts} \OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}
-\end{Highlighting}
-\end{Shaded}
-
-\begin{verbatim}
-##                      mpg cyl  disp  hp drat    wt  qsec vs am gear carb
-## Mazda RX4           21.0   6 160.0 110 3.90 2.620 16.46  0  1    4    4
-## Mazda RX4 Wag       21.0   6 160.0 110 3.90 2.875 17.02  0  1    4    4
-## Datsun 710          22.8   4 108.0  93 3.85 2.320 18.61  1  1    4    1
-## Hornet 4 Drive      21.4   6 258.0 110 3.08 3.215 19.44  1  0    3    1
-## Hornet Sportabout   18.7   8 360.0 175 3.15 3.440 17.02  0  0    3    2
-## Valiant             18.1   6 225.0 105 2.76 3.460 20.22  1  0    3    1
-## Duster 360          14.3   8 360.0 245 3.21 3.570 15.84  0  0    3    4
-## Merc 240D           24.4   4 146.7  62 3.69 3.190 20.00  1  0    4    2
-## Merc 230            22.8   4 140.8  95 3.92 3.150 22.90  1  0    4    2
-## Merc 280            19.2   6 167.6 123 3.92 3.440 18.30  1  0    4    4
-## Merc 280C           17.8   6 167.6 123 3.92 3.440 18.90  1  0    4    4
-## Merc 450SE          16.4   8 275.8 180 3.07 4.070 17.40  0  0    3    3
-## Merc 450SL          17.3   8 275.8 180 3.07 3.730 17.60  0  0    3    3
-## Merc 450SLC         15.2   8 275.8 180 3.07 3.780 18.00  0  0    3    3
-## Cadillac Fleetwood  10.4   8 472.0 205 2.93 5.250 17.98  0  0    3    4
-## Lincoln Continental 10.4   8 460.0 215 3.00 5.424 17.82  0  0    3    4
-## Chrysler Imperial   14.7   8 440.0 230 3.23 5.345 17.42  0  0    3    4
-## Fiat 128            32.4   4  78.7  66 4.08 2.200 19.47  1  1    4    1
-## Honda Civic         30.4   4  75.7  52 4.93 1.615 18.52  1  1    4    2
-## Toyota Corolla      33.9   4  71.1  65 4.22 1.835 19.90  1  1    4    1
-## Toyota Corona       21.5   4 120.1  97 3.70 2.465 20.01  1  0    3    1
-## Dodge Challenger    15.5   8 318.0 150 2.76 3.520 16.87  0  0    3    2
-## AMC Javelin         15.2   8 304.0 150 3.15 3.435 17.30  0  0    3    2
-## Camaro Z28          13.3   8 350.0 245 3.73 3.840 15.41  0  0    3    4
-## Pontiac Firebird    19.2   8 400.0 175 3.08 3.845 17.05  0  0    3    2
-## Fiat X1-9           27.3   4  79.0  66 4.08 1.935 18.90  1  1    4    1
-## Porsche 914-2       26.0   4 120.3  91 4.43 2.140 16.70  0  1    5    2
-## Lotus Europa        30.4   4  95.1 113 3.77 1.513 16.90  1  1    5    2
-## Ford Pantera L      15.8   8 351.0 264 4.22 3.170 14.50  0  1    5    4
-## Ferrari Dino        19.7   6 145.0 175 3.62 2.770 15.50  0  1    5    6
-## Maserati Bora       15.0   8 301.0 335 3.54 3.570 14.60  0  1    5    8
-## Volvo 142E          21.4   4 121.0 109 4.11 2.780 18.60  1  1    4    2
-\end{verbatim}
+\FunctionTok{puts} \OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+##                      mpg cyl  disp  hp drat    wt  qsec vs am gear
+## Mazda RX4           21.0   6 160.0 110 3.90 2.620 16.46  0  1    4
+## Mazda RX4 Wag       21.0   6 160.0 110 3.90 2.875 17.02  0  1    4
+## Datsun 710          22.8   4 108.0  93 3.85 2.320 18.61  1  1    4
+## Hornet 4 Drive      21.4   6 258.0 110 3.08 3.215 19.44  1  0    3
+## Hornet Sportabout   18.7   8 360.0 175 3.15 3.440 17.02  0  0    3
+## Valiant             18.1   6 225.0 105 2.76 3.460 20.22  1  0    3
+## Duster 360          14.3   8 360.0 245 3.21 3.570 15.84  0  0    3
+## Merc 240D           24.4   4 146.7  62 3.69 3.190 20.00  1  0    4
+## Merc 230            22.8   4 140.8  95 3.92 3.150 22.90  1  0    4
+## Merc 280            19.2   6 167.6 123 3.92 3.440 18.30  1  0    4
+## Merc 280C           17.8   6 167.6 123 3.92 3.440 18.90  1  0    4
+## Merc 450SE          16.4   8 275.8 180 3.07 4.070 17.40  0  0    3
+## Merc 450SL          17.3   8 275.8 180 3.07 3.730 17.60  0  0    3
+## Merc 450SLC         15.2   8 275.8 180 3.07 3.780 18.00  0  0    3
+## Cadillac Fleetwood  10.4   8 472.0 205 2.93 5.250 17.98  0  0    3
+## Lincoln Continental 10.4   8 460.0 215 3.00 5.424 17.82  0  0    3
+## Chrysler Imperial   14.7   8 440.0 230 3.23 5.345 17.42  0  0    3
+## Fiat 128            32.4   4  78.7  66 4.08 2.200 19.47  1  1    4
+## Honda Civic         30.4   4  75.7  52 4.93 1.615 18.52  1  1    4
+## Toyota Corolla      33.9   4  71.1  65 4.22 1.835 19.90  1  1    4
+## Toyota Corona       21.5   4 120.1  97 3.70 2.465 20.01  1  0    3
+## Dodge Challenger    15.5   8 318.0 150 2.76 3.520 16.87  0  0    3
+## AMC Javelin         15.2   8 304.0 150 3.15 3.435 17.30  0  0    3
+## Camaro Z28          13.3   8 350.0 245 3.73 3.840 15.41  0  0    3
+## Pontiac Firebird    19.2   8 400.0 175 3.08 3.845 17.05  0  0    3
+## Fiat X1-9           27.3   4  79.0  66 4.08 1.935 18.90  1  1    4
+## Porsche 914-2       26.0   4 120.3  91 4.43 2.140 16.70  0  1    5
+## Lotus Europa        30.4   4  95.1 113 3.77 1.513 16.90  1  1    5
+## Ford Pantera L      15.8   8 351.0 264 4.22 3.170 14.50  0  1    5
+## Ferrari Dino        19.7   6 145.0 175 3.62 2.770 15.50  0  1    5
+## Maserati Bora       15.0   8 301.0 335 3.54 3.570 14.60  0  1    5
+## Volvo 142E          21.4   4 121.0 109 4.11 2.780 18.60  1  1    4
+##                     carb
+## Mazda RX4              4
+## Mazda RX4 Wag          4
+## Datsun 710             1
+## Hornet 4 Drive         1
+## Hornet Sportabout      2
+## Valiant                1
+## Duster 360             4
+## Merc 240D              2
+## Merc 230               2
+## Merc 280               4
+## Merc 280C              4
+## Merc 450SE             3
+## Merc 450SL             3
+## Merc 450SLC            3
+## Cadillac Fleetwood     4
+## Lincoln Continental    4
+## Chrysler Imperial      4
+## Fiat 128               1
+## Honda Civic            2
+## Toyota Corolla         1
+## Toyota Corona          1
+## Dodge Challenger       2
+## AMC Javelin            2
+## Camaro Z28             4
+## Pontiac Firebird       2
+## Fiat X1-9              1
+## Porsche 914-2          2
+## Lotus Europa           2
+## Ford Pantera L         4
+## Ferrari Dino           6
+## Maserati Bora          8
+## Volvo 142E             2
+\end{verbatim}
+
+\subsection{Scoped symbols and lexical
+scoping}\label{scoped-symbols-and-lexical-scoping}
+
+Galaaz 2.0 uses \textbf{scoped symbols} by default. The canonical style
+is \texttt{R{[}:name{]}}:
+
+\begin{itemize}
+\tightlist
+\item
+  \texttt{\textasciitilde{}R{[}:mtcars{]}} fetches an R object by name.
+\item
+  \texttt{R{[}:a{]}\ +\ R{[}:b{]}} builds an expression.
+\item
+  \texttt{R{[}:year{]}.up\_to(R{[}:day{]})} builds range expressions.
+\end{itemize}
+
+If you prefer the terse \texttt{:x} syntax, you can opt in with lexical
+scoping using a Ruby refinement:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\ControlFlowTok{module} \DataTypeTok{MyScript}
+  \FunctionTok{using} \DataTypeTok{Galaaz}\OperatorTok{::}\DataTypeTok{SymbolDSL}
+
+  \ControlFlowTok{def} \DecValTok{self}\AttributeTok{.run}
+\NormalTok{    expr }\OperatorTok{=} \WarningTok{:a} \OperatorTok{+} \WarningTok{:b}
+    \FunctionTok{puts}\NormalTok{ expr}
+    \FunctionTok{puts} \OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}
+  \ControlFlowTok{end}
+\ControlFlowTok{end}
+\end{Highlighting}
+\end{Shaded}
+
+\texttt{using\ Galaaz::SymbolDSL} is \textbf{lexically scoped}: only
+code in that module/file scope gets \texttt{:x} DSL behavior. Outside
+that scope, plain Ruby \texttt{Symbol} behavior is unchanged.
 
 To access an R function from Ruby, the R function needs to be preceded
 by \texttt{R.} scoping. Below we see an example of creating a R::Vector
@@ -1012,11 +1521,12 @@ element of our previously created vector:
 
 This manual has been formatted using gKnit. gKnit uses knitr and R
 Markdown to knit a document in Ruby or R and output it in any of the
-available formats for R Markdown. gKnit runs with \textbf{JRuby},
-\textbf{GNU R}, and Galaaz. In gKnit, Ruby variables are persisted
-between chunks, making it an ideal solution for literate programming.
-Also, since it is based on Galaaz, Ruby chunks can have access to R
-variables and combining Ruby with R in one document is natural.
+available formats for R Markdown. gKnit runs with \textbf{JRuby or
+CRuby}, \textbf{GNU R}, and Galaaz. In gKnit, Ruby variables are
+persisted between chunks, making it an ideal solution for literate
+programming. Also, since it is based on Galaaz, Ruby chunks can have
+access to R variables and combining Ruby with R in one document is
+natural.
 
 The idea of ``literate programming'' was first introduced by Donald
 Knuth in the 1980's (Knuth 1984). The main intention of this approach
@@ -1150,7 +1660,7 @@ in a single document, text and code.
 In gKnit, Ruby variables are persisted between chunks, making it an
 ideal solution for literate programming in this language. Also, since it
 is based on Galaaz, Ruby chunks can access R variables
-(\texttt{\textasciitilde{}:name}, \texttt{R.*}) through the
+(\texttt{\textasciitilde{}R{[}:name{]}}, \texttt{R.*}) through the
 \textbf{Galaaz bridge} while knitr drives \textbf{GNU R}---no GraalVM
 polyglot runtime is required.
 
@@ -1452,7 +1962,9 @@ linear regression line (method = ``lm'') for every manufacturer.
 \FunctionTok{library}\NormalTok{(ggplot2)}
 \FunctionTok{data}\NormalTok{(mpg, }\AttributeTok{package=}\StringTok{"ggplot2"}\NormalTok{)}
 
-\NormalTok{mpg\_select }\OtherTok{\textless{}{-}}\NormalTok{ mpg[mpg}\SpecialCharTok{$}\NormalTok{manufacturer }\SpecialCharTok{\%in\%} \FunctionTok{c}\NormalTok{(}\StringTok{"audi"}\NormalTok{, }\StringTok{"ford"}\NormalTok{, }\StringTok{"honda"}\NormalTok{, }\StringTok{"hyundai"}\NormalTok{), ]}
+\NormalTok{mpg\_select }\OtherTok{\textless{}{-}}\NormalTok{ mpg[}
+\NormalTok{  mpg}\SpecialCharTok{$}\NormalTok{manufacturer }\SpecialCharTok{\%in\%} \FunctionTok{c}\NormalTok{(}\StringTok{"audi"}\NormalTok{, }\StringTok{"ford"}\NormalTok{, }\StringTok{"honda"}\NormalTok{, }\StringTok{"hyundai"}\NormalTok{),}
+\NormalTok{]}
 
 \CommentTok{\# Scatterplot}
 \FunctionTok{theme\_set}\NormalTok{(}\FunctionTok{theme\_bw}\NormalTok{())  }\CommentTok{\# pre{-}set the bw theme.}
@@ -1469,7 +1981,7 @@ linear regression line (method = ``lm'') for every manufacturer.
 ## `geom_smooth()` using formula = 'y ~ x'
 \end{verbatim}
 
-\pandocbounded{\includegraphics[keepaspectratio]{manual_files/figure-latex/bubble-1.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{manual_files/manual_files/figure-latex/bubble-1.png}}
 
 \subsection{Ruby chunks}\label{ruby-chunks}
 
@@ -1539,7 +2051,8 @@ phrase. gKnit allows adding inline Ruby code with the `rb' engine. The
 following chunk specification will create and inline Ruby text:
 
 \begin{verbatim}
-This is some text with inline Ruby accessing variable 'b' which has value:
+This is some text with inline Ruby accessing
+variable 'b' which has value:
 ```{rb puts b}
 ```
 and is followed by some other text!
@@ -1638,12 +2151,12 @@ library is a great library for creating beautiful tables. Take a look at
 
 In the next chunk, we output the `mtcars' dataframe from R in a nicely
 formatted table. Note that we retrieve the mtcars dataframe by using
-`\textasciitilde:mtcars'.
+`\textasciitilde R{[}:mtcars{]}'.
 
 \begin{Shaded}
 \begin{Highlighting}[]
 \ConstantTok{R}\AttributeTok{.install\_and\_loads}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}kableExtra\textquotesingle{}}\NormalTok{)}
-\NormalTok{outputs (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\AttributeTok{.kable.kable\_styling}
+\NormalTok{outputs (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\AttributeTok{.kable.kable\_styling}
 \end{Highlighting}
 \end{Shaded}
 
@@ -1733,7 +2246,8 @@ is trivial with Galaaz.
 A word of advice: the `caret' package has lots of dependencies and
 installing it in a Linux system is a time consuming operation. Method
 `R.install\_and\_loads' will install the package if it is not already
-installed and can take a while.
+installed (via \textbf{\texttt{R::Job}}: a child \texttt{Rscript}, so
+the bridge stays free) and can take a while.
 
 \begin{verbatim}
 ```{include model}
@@ -1786,7 +2300,7 @@ installed and can take a while.
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{mtcars }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}
+\NormalTok{mtcars }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}
 \NormalTok{model }\OperatorTok{=} \DataTypeTok{Model}\AttributeTok{.new}\NormalTok{(mtcars, }\WarningTok{percent\_train:} \FloatTok{0.8}\NormalTok{)}
 \NormalTok{model}\AttributeTok{.partition}\NormalTok{(}\WarningTok{:mpg}\NormalTok{)}
 \FunctionTok{puts}\NormalTok{ model}\AttributeTok{.train.head}
@@ -2023,15 +2537,17 @@ In order to create a document with one of those templates, use the
 following command:
 
 \begin{verbatim}
-gknit-draft --filename <my_document> --template <template> --package <package>
-            --create_dir
+gknit-draft --filename <my_document> \
+  --template <template> --package <package> \
+  --create_dir
 \end{verbatim}
 
 So, in order to create a template for writing an R Journal, use:
 
 \begin{verbatim}
-gknit-draft --filename my_r_article --template rjournal_article --package rticles
-            --create_dir
+gknit-draft --filename my_r_article \
+  --template rjournal_article --package rticles \
+  --create_dir
 \end{verbatim}
 
 \section{Accessing R variables}\label{accessing-r-variables}
@@ -2046,7 +2562,7 @@ Method \texttt{outputs} is only available when used with gKnit.
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{outputs (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\AttributeTok{.kable.kable\_styling}
+\NormalTok{outputs (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\AttributeTok{.kable.kable\_styling}
 \end{Highlighting}
 \end{Shaded}
 
@@ -2157,7 +2673,10 @@ used to create a data frame is `data.frame', in Galaaz we use
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{df }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.data\_\_frame}\NormalTok{(}\WarningTok{typeof:}\NormalTok{ vec}\AttributeTok{.typeof}\NormalTok{, }\WarningTok{mode:}\NormalTok{ vec}\AttributeTok{.mode}\NormalTok{, }\WarningTok{storage\_\_mode:}\NormalTok{ vec}\AttributeTok{.storage\_\_mode}\NormalTok{)}
+\NormalTok{df }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.data\_\_frame}\NormalTok{(}
+  \WarningTok{typeof:}\NormalTok{ vec}\AttributeTok{.typeof}\NormalTok{,}
+  \WarningTok{mode:}\NormalTok{ vec}\AttributeTok{.mode}\NormalTok{,}
+  \WarningTok{storage\_\_mode:}\NormalTok{ vec}\AttributeTok{.storage\_\_mode}\NormalTok{)}
 \FunctionTok{puts}\NormalTok{ df}
 \end{Highlighting}
 \end{Shaded}
@@ -2186,7 +2705,10 @@ normal Ruby rules and the number 1 is an integer and 1.0 is a float.
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{df }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.data\_\_frame}\NormalTok{(}\WarningTok{typeof:}\NormalTok{ vec}\AttributeTok{.typeof}\NormalTok{, }\WarningTok{mode:}\NormalTok{ vec}\AttributeTok{.mode}\NormalTok{, }\WarningTok{storage\_\_mode:}\NormalTok{ vec}\AttributeTok{.storage\_\_mode}\NormalTok{)}
+\NormalTok{df }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.data\_\_frame}\NormalTok{(}
+  \WarningTok{typeof:}\NormalTok{ vec}\AttributeTok{.typeof}\NormalTok{,}
+  \WarningTok{mode:}\NormalTok{ vec}\AttributeTok{.mode}\NormalTok{,}
+  \WarningTok{storage\_\_mode:}\NormalTok{ vec}\AttributeTok{.storage\_\_mode}\NormalTok{)}
 \NormalTok{outputs df}\AttributeTok{.kable.kable\_styling}
 \end{Highlighting}
 \end{Shaded}
@@ -2207,26 +2729,20 @@ error.
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{vec }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{1}\NormalTok{, hello, }\DecValTok{5}\NormalTok{)}
+\ControlFlowTok{begin}
+\NormalTok{  vec }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{1}\NormalTok{, hello, }\DecValTok{5}\NormalTok{)}
+\ControlFlowTok{rescue} \OperatorTok{=\textgreater{}}\NormalTok{ e}
+  \FunctionTok{puts}\NormalTok{ e}\AttributeTok{.class.to\_s}
+\NormalTok{  e}\AttributeTok{.message.to\_s.scan}\NormalTok{(}\SpecialStringTok{/.\{1,68\}/}\NormalTok{)}\AttributeTok{.each} \OperatorTok{\{} \OperatorTok{|}\NormalTok{line}\OperatorTok{|} \FunctionTok{puts}\NormalTok{ line }\OperatorTok{\}}
+\ControlFlowTok{end}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
+## NameError
 ## undefined local variable or method 'hello' for an instance of RC
 \end{verbatim}
 
-\begin{verbatim}
-## /home/rbotafogo/desenv_linux/galaaz/lib/util/exec_ruby.rb:170:in 'exec_ruby'
-## org/jruby/RubyKernel.java:1268:in 'eval'
-## /home/rbotafogo/desenv_linux/galaaz/lib/util/exec_ruby.rb:169:in 'exec_ruby'
-## /home/rbotafogo/desenv_linux/galaaz/lib/gknit/knitr_engine.rb:777:in 'block in initialize'
-## org/jruby/RubyBasicObject.java:2695:in 'instance_eval'
-## org/jruby/RubyBasicObject.java:2723:in 'instance_eval'
-## /home/rbotafogo/desenv_linux/galaaz/lib/gknit/knitr_engine.rb:748:in 'block in initialize'
-## /home/rbotafogo/desenv_linux/galaaz/lib/R_interface/new_bridge_adapter.rb:358:in 'block in register_callback_proc_stub'
-## /home/rbotafogo/desenv_linux/galaaz/lib/new_bridge/session_client.rb:413:in 'block in handle_call'
-\end{verbatim}
-
 Here is a vector with logical values
 
 \begin{Shaded}
@@ -2659,8 +3175,8 @@ native Ruby type.
 A data frame is a table like structure in which each column has the same
 number of rows. Data frames are the basic structure for storing data for
 data analysis. We have already seen a data frame previously when we
-accessed variable `\textasciitilde:mtcars'. In order to create a data
-frame, function 'data\_\_frame' is used:
+accessed variable `\textasciitilde R{[}:mtcars{]}'. In order to create a
+data frame, function 'data\_\_frame' is used:
 
 \begin{Shaded}
 \begin{Highlighting}[]
@@ -2687,9 +3203,9 @@ the row or column
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\AttributeTok{.head}
-\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\KeywordTok{[}\DecValTok{1}\NormalTok{, }\DecValTok{2}\KeywordTok{]}
-\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\KeywordTok{[}\VerbatimStringTok{\textquotesingle{}Datsun 710\textquotesingle{}}\NormalTok{, }\VerbatimStringTok{\textquotesingle{}mpg\textquotesingle{}}\KeywordTok{]}
+\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\AttributeTok{.head}
+\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\KeywordTok{[}\DecValTok{1}\NormalTok{, }\DecValTok{2}\KeywordTok{]}
+\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\KeywordTok{[}\VerbatimStringTok{\textquotesingle{}Datsun 710\textquotesingle{}}\NormalTok{, }\VerbatimStringTok{\textquotesingle{}mpg\textquotesingle{}}\KeywordTok{]}
 \end{Highlighting}
 \end{Shaded}
 
@@ -2710,14 +3226,14 @@ the double square bracket operator:
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\KeywordTok{[[}\VerbatimStringTok{\textquotesingle{}mpg\textquotesingle{}}\KeywordTok{]]}
+\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\KeywordTok{[[}\VerbatimStringTok{\textquotesingle{}mpg\textquotesingle{}}\KeywordTok{]]}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
-##  [1] 21.0 21.0 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 17.8 16.4 17.3 15.2 10.4
-## [16] 10.4 14.7 32.4 30.4 33.9 21.5 15.5 15.2 13.3 19.2 27.3 26.0 30.4 15.8 19.7
-## [31] 15.0 21.4
+##  [1] 21.0 21.0 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 17.8 16.4 17.3
+## [14] 15.2 10.4 10.4 14.7 32.4 30.4 33.9 21.5 15.5 15.2 13.3 19.2 27.3
+## [27] 26.0 30.4 15.8 19.7 15.0 21.4
 \end{verbatim}
 
 A data frame column can also be accessed as if it were an instance
@@ -2725,14 +3241,14 @@ variable of the data frame:
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\AttributeTok{.mpg}
+\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\AttributeTok{.mpg}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
-##  [1] 21.0 21.0 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 17.8 16.4 17.3 15.2 10.4
-## [16] 10.4 14.7 32.4 30.4 33.9 21.5 15.5 15.2 13.3 19.2 27.3 26.0 30.4 15.8 19.7
-## [31] 15.0 21.4
+##  [1] 21.0 21.0 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 17.8 16.4 17.3
+## [14] 15.2 10.4 10.4 14.7 32.4 30.4 33.9 21.5 15.5 15.2 13.3 19.2 27.3
+## [27] 26.0 30.4 15.8 19.7 15.0 21.4
 \end{verbatim}
 
 Slicing a data frame can be done by indexing it with a vector (we use
@@ -2740,7 +3256,7 @@ Slicing a data frame can be done by indexing it with a vector (we use
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\KeywordTok{[}\ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}mpg\textquotesingle{}}\NormalTok{, }\VerbatimStringTok{\textquotesingle{}hp\textquotesingle{}}\NormalTok{)}\KeywordTok{]}\AttributeTok{.head}
+\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\KeywordTok{[}\ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}mpg\textquotesingle{}}\NormalTok{, }\VerbatimStringTok{\textquotesingle{}hp\textquotesingle{}}\NormalTok{)}\KeywordTok{]}\AttributeTok{.head}
 \end{Highlighting}
 \end{Shaded}
 
@@ -2755,7 +3271,7 @@ keyword for the column:
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\KeywordTok{[}\ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}Datsun 710\textquotesingle{}}\NormalTok{, }\VerbatimStringTok{\textquotesingle{}Camaro Z28\textquotesingle{}}\NormalTok{), }\WarningTok{:all}\KeywordTok{]}
+\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\KeywordTok{[}\ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}Datsun 710\textquotesingle{}}\NormalTok{, }\VerbatimStringTok{\textquotesingle{}Camaro Z28\textquotesingle{}}\NormalTok{), }\WarningTok{:all}\KeywordTok{]}
 \end{Highlighting}
 \end{Shaded}
 
@@ -2768,21 +3284,21 @@ keyword for the column:
 Finally, a data frame can also be indexed with a logical vector. In this
 next example, the `am' column of :mtcars is compared with 0 (with method
 `eq'). When `am' is equal to 0 the car is automatic. So, by doing
-`(\textasciitilde:mtcars).am.eq 0' a logical vector is created with
-`true' whenever `am' is 0 and `false' otherwise.
+`(\textasciitilde R{[}:mtcars{]}).am.eq 0' a logical vector is created
+with `true' whenever `am' is 0 and `false' otherwise.
 
 \begin{Shaded}
 \begin{Highlighting}[]
 \CommentTok{\# obtain a vector with \textquotesingle{}true\textquotesingle{} for cars with automatic transmission}
-\NormalTok{automatic }\OperatorTok{=}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\AttributeTok{.am.eq} \DecValTok{0}
+\NormalTok{automatic }\OperatorTok{=}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\AttributeTok{.am.eq} \DecValTok{0}
 \FunctionTok{puts}\NormalTok{ automatic}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
-##  [1] FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
-## [13]  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE
-## [25]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
+##  [1] FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
+## [12]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE
+## [23]  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
 \end{verbatim}
 
 Using this logical vector, the data frame is indexed, returning a new
@@ -2791,31 +3307,51 @@ data frame in which all cars have automatic transmission.
 \begin{Shaded}
 \begin{Highlighting}[]
 \CommentTok{\# slice the data frame by using this vector}
-\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}\NormalTok{)}\KeywordTok{[}\NormalTok{automatic, }\WarningTok{:all}\KeywordTok{]}
-\end{Highlighting}
-\end{Shaded}
-
-\begin{verbatim}
-##                      mpg cyl  disp  hp drat    wt  qsec vs am gear carb
-## Hornet 4 Drive      21.4   6 258.0 110 3.08 3.215 19.44  1  0    3    1
-## Hornet Sportabout   18.7   8 360.0 175 3.15 3.440 17.02  0  0    3    2
-## Valiant             18.1   6 225.0 105 2.76 3.460 20.22  1  0    3    1
-## Duster 360          14.3   8 360.0 245 3.21 3.570 15.84  0  0    3    4
-## Merc 240D           24.4   4 146.7  62 3.69 3.190 20.00  1  0    4    2
-## Merc 230            22.8   4 140.8  95 3.92 3.150 22.90  1  0    4    2
-## Merc 280            19.2   6 167.6 123 3.92 3.440 18.30  1  0    4    4
-## Merc 280C           17.8   6 167.6 123 3.92 3.440 18.90  1  0    4    4
-## Merc 450SE          16.4   8 275.8 180 3.07 4.070 17.40  0  0    3    3
-## Merc 450SL          17.3   8 275.8 180 3.07 3.730 17.60  0  0    3    3
-## Merc 450SLC         15.2   8 275.8 180 3.07 3.780 18.00  0  0    3    3
-## Cadillac Fleetwood  10.4   8 472.0 205 2.93 5.250 17.98  0  0    3    4
-## Lincoln Continental 10.4   8 460.0 215 3.00 5.424 17.82  0  0    3    4
-## Chrysler Imperial   14.7   8 440.0 230 3.23 5.345 17.42  0  0    3    4
-## Toyota Corona       21.5   4 120.1  97 3.70 2.465 20.01  1  0    3    1
-## Dodge Challenger    15.5   8 318.0 150 2.76 3.520 16.87  0  0    3    2
-## AMC Javelin         15.2   8 304.0 150 3.15 3.435 17.30  0  0    3    2
-## Camaro Z28          13.3   8 350.0 245 3.73 3.840 15.41  0  0    3    4
-## Pontiac Firebird    19.2   8 400.0 175 3.08 3.845 17.05  0  0    3    2
+\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}\KeywordTok{[}\NormalTok{automatic, }\WarningTok{:all}\KeywordTok{]}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+##                      mpg cyl  disp  hp drat    wt  qsec vs am gear
+## Hornet 4 Drive      21.4   6 258.0 110 3.08 3.215 19.44  1  0    3
+## Hornet Sportabout   18.7   8 360.0 175 3.15 3.440 17.02  0  0    3
+## Valiant             18.1   6 225.0 105 2.76 3.460 20.22  1  0    3
+## Duster 360          14.3   8 360.0 245 3.21 3.570 15.84  0  0    3
+## Merc 240D           24.4   4 146.7  62 3.69 3.190 20.00  1  0    4
+## Merc 230            22.8   4 140.8  95 3.92 3.150 22.90  1  0    4
+## Merc 280            19.2   6 167.6 123 3.92 3.440 18.30  1  0    4
+## Merc 280C           17.8   6 167.6 123 3.92 3.440 18.90  1  0    4
+## Merc 450SE          16.4   8 275.8 180 3.07 4.070 17.40  0  0    3
+## Merc 450SL          17.3   8 275.8 180 3.07 3.730 17.60  0  0    3
+## Merc 450SLC         15.2   8 275.8 180 3.07 3.780 18.00  0  0    3
+## Cadillac Fleetwood  10.4   8 472.0 205 2.93 5.250 17.98  0  0    3
+## Lincoln Continental 10.4   8 460.0 215 3.00 5.424 17.82  0  0    3
+## Chrysler Imperial   14.7   8 440.0 230 3.23 5.345 17.42  0  0    3
+## Toyota Corona       21.5   4 120.1  97 3.70 2.465 20.01  1  0    3
+## Dodge Challenger    15.5   8 318.0 150 2.76 3.520 16.87  0  0    3
+## AMC Javelin         15.2   8 304.0 150 3.15 3.435 17.30  0  0    3
+## Camaro Z28          13.3   8 350.0 245 3.73 3.840 15.41  0  0    3
+## Pontiac Firebird    19.2   8 400.0 175 3.08 3.845 17.05  0  0    3
+##                     carb
+## Hornet 4 Drive         1
+## Hornet Sportabout      2
+## Valiant                1
+## Duster 360             4
+## Merc 240D              2
+## Merc 230               2
+## Merc 280               4
+## Merc 280C              4
+## Merc 450SE             3
+## Merc 450SL             3
+## Merc 450SLC            3
+## Cadillac Fleetwood     4
+## Lincoln Continental    4
+## Chrysler Imperial      4
+## Toyota Corona          1
+## Dodge Challenger       2
+## AMC Javelin            2
+## Camaro Z28             4
+## Pontiac Firebird       2
 \end{verbatim}
 
 \section{Writing Expressions in
@@ -2832,7 +3368,7 @@ The code below creates an expression summing two symbols
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp1 }\OperatorTok{=} \WarningTok{:a} \OperatorTok{+} \WarningTok{:b}
+\NormalTok{exp1 }\OperatorTok{=} \ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:b}\KeywordTok{]}
 \FunctionTok{puts}\NormalTok{ exp1}
 \end{Highlighting}
 \end{Shaded}
@@ -2845,7 +3381,7 @@ We can build any complex mathematical expression
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp2 }\OperatorTok{=}\NormalTok{ (}\WarningTok{:a} \OperatorTok{+} \WarningTok{:b}\NormalTok{) }\OperatorTok{*} \FloatTok{2.0} \OperatorTok{+} \WarningTok{:c} \OperatorTok{**} \DecValTok{2} \OperatorTok{/} \WarningTok{:z}
+\NormalTok{exp2 }\OperatorTok{=}\NormalTok{ (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:b}\KeywordTok{]}\NormalTok{) }\OperatorTok{*} \FloatTok{2.0} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:c}\KeywordTok{]} \OperatorTok{**} \DecValTok{2} \OperatorTok{/} \ConstantTok{R}\KeywordTok{[}\WarningTok{:z}\KeywordTok{]}
 \FunctionTok{puts}\NormalTok{ exp2}
 \end{Highlighting}
 \end{Shaded}
@@ -2858,7 +3394,7 @@ It is also possible to use inequality operators in building expressions
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp3 }\OperatorTok{=}\NormalTok{ (}\WarningTok{:a} \OperatorTok{+} \WarningTok{:b}\NormalTok{) }\OperatorTok{\textgreater{}=} \WarningTok{:z}
+\NormalTok{exp3 }\OperatorTok{=}\NormalTok{ (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:b}\KeywordTok{]}\NormalTok{) }\OperatorTok{\textgreater{}=} \WarningTok{:z}
 \FunctionTok{puts}\NormalTok{ exp3}
 \end{Highlighting}
 \end{Shaded}
@@ -2874,7 +3410,7 @@ be written as
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp4 }\OperatorTok{=}\NormalTok{ (}\WarningTok{:a} \OperatorTok{+} \WarningTok{:b}\NormalTok{)}\AttributeTok{.ge} \OperatorTok{:}\NormalTok{z}
+\NormalTok{exp4 }\OperatorTok{=}\NormalTok{ (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:b}\KeywordTok{]}\NormalTok{)}\AttributeTok{.ge} \OperatorTok{:}\NormalTok{z}
 \FunctionTok{puts}\NormalTok{ exp4}
 \end{Highlighting}
 \end{Shaded}
@@ -2890,7 +3426,7 @@ the method `.eq' and for `=' we need the function `.assign'
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp5 }\OperatorTok{=}\NormalTok{ (}\WarningTok{:a} \OperatorTok{+} \WarningTok{:b}\NormalTok{)}\AttributeTok{.eq} \OperatorTok{:}\NormalTok{z}
+\NormalTok{exp5 }\OperatorTok{=}\NormalTok{ (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:b}\KeywordTok{]}\NormalTok{)}\AttributeTok{.eq} \OperatorTok{:}\NormalTok{z}
 \FunctionTok{puts}\NormalTok{ exp5}
 \end{Highlighting}
 \end{Shaded}
@@ -2901,7 +3437,7 @@ the method `.eq' and for `=' we need the function `.assign'
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp6 }\OperatorTok{=} \WarningTok{:y}\AttributeTok{.assign} \OperatorTok{:}\NormalTok{a }\OperatorTok{+} \WarningTok{:b}
+\NormalTok{exp6 }\OperatorTok{=} \ConstantTok{R}\KeywordTok{[}\WarningTok{:y}\KeywordTok{]}\AttributeTok{.assign} \ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:b}\KeywordTok{]}
 \FunctionTok{puts}\NormalTok{ exp6}
 \end{Highlighting}
 \end{Shaded}
@@ -2916,18 +3452,18 @@ expressions such as
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp\_wrong }\OperatorTok{=}\NormalTok{ (}\WarningTok{:a} \OperatorTok{+} \WarningTok{:b}\NormalTok{) }\OperatorTok{==} \WarningTok{:z}
+\NormalTok{exp\_wrong }\OperatorTok{=}\NormalTok{ (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:b}\KeywordTok{]}\NormalTok{) }\OperatorTok{==} \WarningTok{:z}
 \FunctionTok{puts}\NormalTok{ exp\_wrong}
 \end{Highlighting}
 \end{Shaded}
 
 and it might be difficult to understand what is going on here. The
 problem lies with the fact that when using `==' we are comparing
-expression (:a + :b) to expression :z with `=='. When the comparison is
-executed, the system tries to evaluate :a, :b and :z, and those symbols
-at this time are not bound to anything and we get a ``object `a' not
-found'' message. If we only use functional notation, this type of error
-will not occur.
+expression (R{[}:a{]} + R{[}:b{]}) to expression :z with `=='. When the
+comparison is executed, the system tries to evaluate :a, :b and :z, and
+those symbols at this time are not bound to anything and we get a
+``object `a' not found'' message. If we only use functional notation,
+this type of error will not occur.
 
 \subsection{Expressions with R
 methods}\label{expressions-with-r-methods}
@@ -2943,7 +3479,7 @@ such as `E.sin(x)'
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp7 }\OperatorTok{=} \WarningTok{:y}\AttributeTok{.assign} \ConstantTok{E}\AttributeTok{.sin}\NormalTok{(}\WarningTok{:x}\NormalTok{)}
+\NormalTok{exp7 }\OperatorTok{=} \ConstantTok{R}\KeywordTok{[}\WarningTok{:y}\KeywordTok{]}\AttributeTok{.assign} \ConstantTok{E}\AttributeTok{.sin}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:x}\KeywordTok{]}\NormalTok{)}
 \FunctionTok{puts}\NormalTok{ exp7}
 \end{Highlighting}
 \end{Shaded}
@@ -2956,7 +3492,7 @@ Expressions can also be written using `.' notation:
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp8 }\OperatorTok{=} \WarningTok{:y}\AttributeTok{.assign} \OperatorTok{:}\NormalTok{x}\AttributeTok{.sin}
+\NormalTok{exp8 }\OperatorTok{=} \ConstantTok{R}\KeywordTok{[}\WarningTok{:y}\KeywordTok{]}\AttributeTok{.assign} \ConstantTok{R}\KeywordTok{[}\WarningTok{:x}\KeywordTok{]}\AttributeTok{.sin}
 \FunctionTok{puts}\NormalTok{ exp8}
 \end{Highlighting}
 \end{Shaded}
@@ -2970,7 +3506,7 @@ the `.':
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp9 }\OperatorTok{=} \WarningTok{:x}\AttributeTok{.c}\NormalTok{(}\WarningTok{:y}\NormalTok{)}
+\NormalTok{exp9 }\OperatorTok{=} \ConstantTok{R}\KeywordTok{[}\WarningTok{:x}\KeywordTok{]}\AttributeTok{.c}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:y}\KeywordTok{]}\NormalTok{)}
 \FunctionTok{puts}\NormalTok{ exp9}
 \end{Highlighting}
 \end{Shaded}
@@ -2986,7 +3522,7 @@ A binding can be provided with a list:
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{exp }\OperatorTok{=}\NormalTok{ (}\WarningTok{:a} \OperatorTok{+} \WarningTok{:b}\NormalTok{) }\OperatorTok{*} \FloatTok{2.0} \OperatorTok{+} \WarningTok{:c} \OperatorTok{**} \DecValTok{2} \OperatorTok{/} \WarningTok{:z}
+\NormalTok{exp }\OperatorTok{=}\NormalTok{ (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:b}\KeywordTok{]}\NormalTok{) }\OperatorTok{*} \FloatTok{2.0} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:c}\KeywordTok{]} \OperatorTok{**} \DecValTok{2} \OperatorTok{/} \ConstantTok{R}\KeywordTok{[}\WarningTok{:z}\KeywordTok{]}
 \FunctionTok{puts}\NormalTok{ exp}\AttributeTok{.eval}\NormalTok{(}\ConstantTok{R}\AttributeTok{.list}\NormalTok{(}\WarningTok{a:} \DecValTok{10}\NormalTok{, }\WarningTok{b:} \DecValTok{20}\NormalTok{, }\WarningTok{c:} \DecValTok{30}\NormalTok{, }\WarningTok{z:} \DecValTok{40}\NormalTok{))}
 \end{Highlighting}
 \end{Shaded}
@@ -3043,51 +3579,53 @@ use \texttt{head} / \texttt{str} in R via \texttt{R} calls).
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{flights }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\WarningTok{:flights}
+\NormalTok{flights }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:flights}\KeywordTok{]}
 \FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.head}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
 ## # A tibble: 6 x 19
-##    year month   day dep_time sched_dep_time dep_delay arr_time sched_arr_time
-##   <int> <int> <int>    <int>          <int>     <dbl>    <int>          <int>
-## 1  2013     1     1      517            515         2      830            819
-## 2  2013     1     1      533            529         4      850            830
-## 3  2013     1     1      542            540         2      923            850
-## 4  2013     1     1      544            545        -1     1004           1022
-## 5  2013     1     1      554            600        -6      812            837
-## 6  2013     1     1      554            558        -4      740            728
-## # i 11 more variables: arr_delay <dbl>, carrier <chr>, flight <int>,
-## #   tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>,
-## #   hour <dbl>, minute <dbl>, time_hour <dttm>
+##    year month   day dep_time sched_dep_time dep_delay arr_time
+##   <int> <int> <int>    <int>          <int>     <dbl>    <int>
+## 1  2013     1     1      517            515         2      830
+## 2  2013     1     1      533            529         4      850
+## 3  2013     1     1      542            540         2      923
+## 4  2013     1     1      544            545        -1     1004
+## 5  2013     1     1      554            600        -6      812
+## 6  2013     1     1      554            558        -4      740
+## # i 12 more variables: sched_arr_time <int>, arr_delay <dbl>,
+## #   carrier <chr>, flight <int>, tailnum <chr>, origin <chr>,
+## #   dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
+## #   minute <dbl>, time_hour <dttm>
 \end{verbatim}
 
 \subsection{Filtering rows with
 Filter}\label{filtering-rows-with-filter}
 
 In this example we filter the flights data set by giving to the filter
-function two expressions: the first :month.eq 1
+function two expressions: the first R{[}:month{]}.eq 1
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.filter}\NormalTok{((}\WarningTok{:month}\AttributeTok{.eq} \DecValTok{1}\NormalTok{), (}\WarningTok{:day}\AttributeTok{.eq} \DecValTok{1}\NormalTok{))}\AttributeTok{.head}
+\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.filter}\NormalTok{((}\ConstantTok{R}\KeywordTok{[}\WarningTok{:month}\KeywordTok{]}\AttributeTok{.eq} \DecValTok{1}\NormalTok{), (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:day}\KeywordTok{]}\AttributeTok{.eq} \DecValTok{1}\NormalTok{))}\AttributeTok{.head}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
 ## # A tibble: 6 x 19
-##    year month   day dep_time sched_dep_time dep_delay arr_time sched_arr_time
-##   <int> <int> <int>    <int>          <int>     <dbl>    <int>          <int>
-## 1  2013     1     1      517            515         2      830            819
-## 2  2013     1     1      533            529         4      850            830
-## 3  2013     1     1      542            540         2      923            850
-## 4  2013     1     1      544            545        -1     1004           1022
-## 5  2013     1     1      554            600        -6      812            837
-## 6  2013     1     1      554            558        -4      740            728
-## # i 11 more variables: arr_delay <dbl>, carrier <chr>, flight <int>,
-## #   tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>,
-## #   hour <dbl>, minute <dbl>, time_hour <dttm>
+##    year month   day dep_time sched_dep_time dep_delay arr_time
+##   <int> <int> <int>    <int>          <int>     <dbl>    <int>
+## 1  2013     1     1      517            515         2      830
+## 2  2013     1     1      533            529         4      850
+## 3  2013     1     1      542            540         2      923
+## 4  2013     1     1      544            545        -1     1004
+## 5  2013     1     1      554            600        -6      812
+## 6  2013     1     1      554            558        -4      740
+## # i 12 more variables: sched_arr_time <int>, arr_delay <dbl>,
+## #   carrier <chr>, flight <int>, tailnum <chr>, origin <chr>,
+## #   dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
+## #   minute <dbl>, time_hour <dttm>
 \end{verbatim}
 
 \subsection{Logical Operators}\label{logical-operators}
@@ -3096,23 +3634,24 @@ All flights that departed in November of December
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.filter}\NormalTok{((}\WarningTok{:month}\AttributeTok{.eq} \DecValTok{11}\NormalTok{) }\OperatorTok{|}\NormalTok{ (}\WarningTok{:month}\AttributeTok{.eq} \DecValTok{12}\NormalTok{))}\AttributeTok{.head}
+\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.filter}\NormalTok{((}\ConstantTok{R}\KeywordTok{[}\WarningTok{:month}\KeywordTok{]}\AttributeTok{.eq} \DecValTok{11}\NormalTok{) }\OperatorTok{|}\NormalTok{ (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:month}\KeywordTok{]}\AttributeTok{.eq} \DecValTok{12}\NormalTok{))}\AttributeTok{.head}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
 ## # A tibble: 6 x 19
-##    year month   day dep_time sched_dep_time dep_delay arr_time sched_arr_time
-##   <int> <int> <int>    <int>          <int>     <dbl>    <int>          <int>
-## 1  2013    11     1        5           2359         6      352            345
-## 2  2013    11     1       35           2250       105      123           2356
-## 3  2013    11     1      455            500        -5      641            651
-## 4  2013    11     1      539            545        -6      856            827
-## 5  2013    11     1      542            545        -3      831            855
-## 6  2013    11     1      549            600       -11      912            923
-## # i 11 more variables: arr_delay <dbl>, carrier <chr>, flight <int>,
-## #   tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>,
-## #   hour <dbl>, minute <dbl>, time_hour <dttm>
+##    year month   day dep_time sched_dep_time dep_delay arr_time
+##   <int> <int> <int>    <int>          <int>     <dbl>    <int>
+## 1  2013    11     1        5           2359         6      352
+## 2  2013    11     1       35           2250       105      123
+## 3  2013    11     1      455            500        -5      641
+## 4  2013    11     1      539            545        -6      856
+## 5  2013    11     1      542            545        -3      831
+## 6  2013    11     1      549            600       -11      912
+## # i 12 more variables: sched_arr_time <int>, arr_delay <dbl>,
+## #   carrier <chr>, flight <int>, tailnum <chr>, origin <chr>,
+## #   dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
+## #   minute <dbl>, time_hour <dttm>
 \end{verbatim}
 
 The same as above, but using the `in' operator. In R, it is possible to
@@ -3123,23 +3662,24 @@ in this case `:in' and the second argument is the vector:
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.filter}\NormalTok{(}\WarningTok{:month}\AttributeTok{.\_} \OperatorTok{:}\ControlFlowTok{in}\NormalTok{, }\ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{11}\NormalTok{, }\DecValTok{12}\NormalTok{))}\AttributeTok{.head}
+\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.filter}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:month}\KeywordTok{]}\AttributeTok{.\_} \OperatorTok{:}\ControlFlowTok{in}\NormalTok{, }\ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{11}\NormalTok{, }\DecValTok{12}\NormalTok{))}\AttributeTok{.head}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
 ## # A tibble: 6 x 19
-##    year month   day dep_time sched_dep_time dep_delay arr_time sched_arr_time
-##   <int> <int> <int>    <int>          <int>     <dbl>    <int>          <int>
-## 1  2013    11     1        5           2359         6      352            345
-## 2  2013    11     1       35           2250       105      123           2356
-## 3  2013    11     1      455            500        -5      641            651
-## 4  2013    11     1      539            545        -6      856            827
-## 5  2013    11     1      542            545        -3      831            855
-## 6  2013    11     1      549            600       -11      912            923
-## # i 11 more variables: arr_delay <dbl>, carrier <chr>, flight <int>,
-## #   tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>,
-## #   hour <dbl>, minute <dbl>, time_hour <dttm>
+##    year month   day dep_time sched_dep_time dep_delay arr_time
+##   <int> <int> <int>    <int>          <int>     <dbl>    <int>
+## 1  2013    11     1        5           2359         6      352
+## 2  2013    11     1       35           2250       105      123
+## 3  2013    11     1      455            500        -5      641
+## 4  2013    11     1      539            545        -6      856
+## 5  2013    11     1      542            545        -3      831
+## 6  2013    11     1      549            600       -11      912
+## # i 12 more variables: sched_arr_time <int>, arr_delay <dbl>,
+## #   carrier <chr>, flight <int>, tailnum <chr>, origin <chr>,
+## #   dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
+## #   minute <dbl>, time_hour <dttm>
 \end{verbatim}
 
 \subsection{Filtering with NA (Not
@@ -3172,7 +3712,7 @@ condition, where the row with R:NA does not.
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ df}\AttributeTok{.filter}\NormalTok{(}\WarningTok{:x} \OperatorTok{\textgreater{}} \DecValTok{1}\NormalTok{)}
+\FunctionTok{puts}\NormalTok{ df}\AttributeTok{.filter}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:x}\KeywordTok{]} \OperatorTok{\textgreater{}} \DecValTok{1}\NormalTok{)}
 \end{Highlighting}
 \end{Shaded}
 
@@ -3187,7 +3727,7 @@ To match an NA use method 'is\_\_na'
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ df}\AttributeTok{.filter}\NormalTok{((}\WarningTok{:x}\AttributeTok{.is\_\_na}\NormalTok{) }\OperatorTok{|}\NormalTok{ (}\WarningTok{:x} \OperatorTok{\textgreater{}} \DecValTok{1}\NormalTok{))}
+\FunctionTok{puts}\NormalTok{ df}\AttributeTok{.filter}\NormalTok{((}\ConstantTok{R}\KeywordTok{[}\WarningTok{:x}\KeywordTok{]}\AttributeTok{.is\_\_na}\NormalTok{) }\OperatorTok{|}\NormalTok{ (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:x}\KeywordTok{]} \OperatorTok{\textgreater{}} \DecValTok{1}\NormalTok{))}
 \end{Highlighting}
 \end{Shaded}
 
@@ -3211,40 +3751,42 @@ Arrange reorders the rows of a data frame by the given arguments.
 
 \begin{verbatim}
 ## # A tibble: 6 x 19
-##    year month   day dep_time sched_dep_time dep_delay arr_time sched_arr_time
-##   <int> <int> <int>    <int>          <int>     <dbl>    <int>          <int>
-## 1  2013     1     1      517            515         2      830            819
-## 2  2013     1     1      533            529         4      850            830
-## 3  2013     1     1      542            540         2      923            850
-## 4  2013     1     1      544            545        -1     1004           1022
-## 5  2013     1     1      554            600        -6      812            837
-## 6  2013     1     1      554            558        -4      740            728
-## # i 11 more variables: arr_delay <dbl>, carrier <chr>, flight <int>,
-## #   tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>,
-## #   hour <dbl>, minute <dbl>, time_hour <dttm>
+##    year month   day dep_time sched_dep_time dep_delay arr_time
+##   <int> <int> <int>    <int>          <int>     <dbl>    <int>
+## 1  2013     1     1      517            515         2      830
+## 2  2013     1     1      533            529         4      850
+## 3  2013     1     1      542            540         2      923
+## 4  2013     1     1      544            545        -1     1004
+## 5  2013     1     1      554            600        -6      812
+## 6  2013     1     1      554            558        -4      740
+## # i 12 more variables: sched_arr_time <int>, arr_delay <dbl>,
+## #   carrier <chr>, flight <int>, tailnum <chr>, origin <chr>,
+## #   dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
+## #   minute <dbl>, time_hour <dttm>
 \end{verbatim}
 
 To arrange in descending order, use function `desc'
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.arrange}\NormalTok{(}\WarningTok{:dep\_delay}\AttributeTok{.desc}\NormalTok{)}\AttributeTok{.head}
+\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.arrange}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:dep\_delay}\KeywordTok{]}\AttributeTok{.desc}\NormalTok{)}\AttributeTok{.head}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
 ## # A tibble: 6 x 19
-##    year month   day dep_time sched_dep_time dep_delay arr_time sched_arr_time
-##   <int> <int> <int>    <int>          <int>     <dbl>    <int>          <int>
-## 1  2013     1     9      641            900      1301     1242           1530
-## 2  2013     6    15     1432           1935      1137     1607           2120
-## 3  2013     1    10     1121           1635      1126     1239           1810
-## 4  2013     9    20     1139           1845      1014     1457           2210
-## 5  2013     7    22      845           1600      1005     1044           1815
-## 6  2013     4    10     1100           1900       960     1342           2211
-## # i 11 more variables: arr_delay <dbl>, carrier <chr>, flight <int>,
-## #   tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>,
-## #   hour <dbl>, minute <dbl>, time_hour <dttm>
+##    year month   day dep_time sched_dep_time dep_delay arr_time
+##   <int> <int> <int>    <int>          <int>     <dbl>    <int>
+## 1  2013     1     9      641            900      1301     1242
+## 2  2013     6    15     1432           1935      1137     1607
+## 3  2013     1    10     1121           1635      1126     1239
+## 4  2013     9    20     1139           1845      1014     1457
+## 5  2013     7    22      845           1600      1005     1044
+## 6  2013     4    10     1100           1900       960     1342
+## # i 12 more variables: sched_arr_time <int>, arr_delay <dbl>,
+## #   carrier <chr>, flight <int>, tailnum <chr>, origin <chr>,
+## #   dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
+## #   minute <dbl>, time_hour <dttm>
 \end{verbatim}
 
 \subsection{Selecting columns}\label{selecting-columns}
@@ -3273,7 +3815,7 @@ It is also possible to select column in a given range
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.select}\NormalTok{(}\WarningTok{:year}\AttributeTok{.up\_to} \OperatorTok{:}\NormalTok{day)}\AttributeTok{.head}
+\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.select}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:year}\KeywordTok{]}\AttributeTok{.up\_to}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:day}\KeywordTok{]}\NormalTok{))}\AttributeTok{.head}
 \end{Highlighting}
 \end{Shaded}
 
@@ -3335,17 +3877,18 @@ column order is `Everything':
 
 \begin{verbatim}
 ## # A tibble: 6 x 19
-##    year month   day dep_time sched_dep_time dep_delay arr_time sched_arr_time
-##   <int> <int> <int>    <int>          <int>     <dbl>    <int>          <int>
-## 1  2013     1     1      517            515         2      830            819
-## 2  2013     1     1      533            529         4      850            830
-## 3  2013     1     1      542            540         2      923            850
-## 4  2013     1     1      544            545        -1     1004           1022
-## 5  2013     1     1      554            600        -6      812            837
-## 6  2013     1     1      554            558        -4      740            728
-## # i 11 more variables: arr_delay <dbl>, carrier <chr>, flight <int>,
-## #   tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>,
-## #   hour <dbl>, minute <dbl>, time_hour <dttm>
+##    year month   day dep_time sched_dep_time dep_delay arr_time
+##   <int> <int> <int>    <int>          <int>     <dbl>    <int>
+## 1  2013     1     1      517            515         2      830
+## 2  2013     1     1      533            529         4      850
+## 3  2013     1     1      542            540         2      923
+## 4  2013     1     1      544            545        -1     1004
+## 5  2013     1     1      554            600        -6      812
+## 6  2013     1     1      554            558        -4      740
+## # i 12 more variables: sched_arr_time <int>, arr_delay <dbl>,
+## #   carrier <chr>, flight <int>, tailnum <chr>, origin <chr>,
+## #   dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
+## #   minute <dbl>, time_hour <dttm>
 \end{verbatim}
 
 \subsection{Add variables to a dataframe with
@@ -3354,7 +3897,7 @@ column order is `Everything':
 \begin{Shaded}
 \begin{Highlighting}[]
 \NormalTok{flights\_sm }\OperatorTok{=}\NormalTok{ flights}\AttributeTok{.}
-               \AttributeTok{select}\NormalTok{((}\WarningTok{:year}\AttributeTok{.up\_to} \OperatorTok{:}\NormalTok{day),}
+               \AttributeTok{select}\NormalTok{((}\ConstantTok{R}\KeywordTok{[}\WarningTok{:year}\KeywordTok{]}\AttributeTok{.up\_to}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:day}\KeywordTok{]}\NormalTok{)),}
                       \ConstantTok{E}\AttributeTok{.ends\_with}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}delay\textquotesingle{}}\NormalTok{),}
                       \WarningTok{:distance}\NormalTok{,}
                       \WarningTok{:air\_time}\NormalTok{)}
@@ -3378,8 +3921,8 @@ column order is `Everything':
 \begin{Shaded}
 \begin{Highlighting}[]
 \NormalTok{flights\_sm }\OperatorTok{=}\NormalTok{ flights\_sm}\AttributeTok{.}
-               \AttributeTok{mutate}\NormalTok{(}\WarningTok{gain:} \WarningTok{:dep\_delay} \OperatorTok{{-}} \WarningTok{:arr\_delay}\NormalTok{,}
-                      \WarningTok{speed:} \WarningTok{:distance} \OperatorTok{/} \WarningTok{:air\_time} \OperatorTok{*} \DecValTok{60}\NormalTok{)}
+               \AttributeTok{mutate}\NormalTok{(}\WarningTok{gain:} \ConstantTok{R}\KeywordTok{[}\WarningTok{:dep\_delay}\KeywordTok{]} \OperatorTok{{-}} \ConstantTok{R}\KeywordTok{[}\WarningTok{:arr\_delay}\KeywordTok{]}\NormalTok{,}
+                      \WarningTok{speed:} \ConstantTok{R}\KeywordTok{[}\WarningTok{:distance}\KeywordTok{]} \OperatorTok{/} \ConstantTok{R}\KeywordTok{[}\WarningTok{:air\_time}\KeywordTok{]} \OperatorTok{*} \DecValTok{60}\NormalTok{)}
 \FunctionTok{puts}\NormalTok{ flights\_sm}\AttributeTok{.head}
 \end{Highlighting}
 \end{Shaded}
@@ -3420,7 +3963,7 @@ given group:
 \begin{Shaded}
 \begin{Highlighting}[]
 \NormalTok{by\_day }\OperatorTok{=}\NormalTok{ flights}\AttributeTok{.group\_by}\NormalTok{(}\WarningTok{:year}\NormalTok{, }\WarningTok{:month}\NormalTok{, }\WarningTok{:day}\NormalTok{)}
-\FunctionTok{puts}\NormalTok{ by\_day}\AttributeTok{.summarise}\NormalTok{(}\WarningTok{delay:} \WarningTok{:dep\_delay}\AttributeTok{.mean}\NormalTok{(}\WarningTok{na\_\_rm:} \DecValTok{true}\NormalTok{))}\AttributeTok{.head}
+\FunctionTok{puts}\NormalTok{ by\_day}\AttributeTok{.summarise}\NormalTok{(}\WarningTok{delay:} \ConstantTok{R}\KeywordTok{[}\WarningTok{:dep\_delay}\KeywordTok{]}\AttributeTok{.mean}\NormalTok{(}\WarningTok{na\_\_rm:} \DecValTok{true}\NormalTok{))}\AttributeTok{.head}
 \end{Highlighting}
 \end{Shaded}
 
@@ -3446,9 +3989,9 @@ other:
            \AttributeTok{group\_by}\NormalTok{(}\WarningTok{:dest}\NormalTok{)}\AttributeTok{.}
            \AttributeTok{summarise}\NormalTok{(}
              \WarningTok{count:} \ConstantTok{E}\AttributeTok{.n}\NormalTok{,}
-             \WarningTok{dist:} \WarningTok{:distance}\AttributeTok{.mean}\NormalTok{(}\WarningTok{na\_\_rm:} \DecValTok{true}\NormalTok{),}
-             \WarningTok{delay:} \WarningTok{:arr\_delay}\AttributeTok{.mean}\NormalTok{(}\WarningTok{na\_\_rm:} \DecValTok{true}\NormalTok{))}\AttributeTok{.}
-           \AttributeTok{filter}\NormalTok{(}\WarningTok{:count} \OperatorTok{\textgreater{}} \DecValTok{20}\NormalTok{, }\WarningTok{:dest} \OperatorTok{!=} \StringTok{"NHL"}\NormalTok{)}
+             \WarningTok{dist:} \ConstantTok{R}\KeywordTok{[}\WarningTok{:distance}\KeywordTok{]}\AttributeTok{.mean}\NormalTok{(}\WarningTok{na\_\_rm:} \DecValTok{true}\NormalTok{),}
+             \WarningTok{delay:} \ConstantTok{R}\KeywordTok{[}\WarningTok{:arr\_delay}\KeywordTok{]}\AttributeTok{.mean}\NormalTok{(}\WarningTok{na\_\_rm:} \DecValTok{true}\NormalTok{))}\AttributeTok{.}
+           \AttributeTok{filter}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:count}\KeywordTok{]} \OperatorTok{\textgreater{}} \DecValTok{20}\NormalTok{, }\ConstantTok{R}\KeywordTok{[}\WarningTok{:dest}\KeywordTok{]} \OperatorTok{!=} \StringTok{"NHL"}\NormalTok{)}
 
 \FunctionTok{puts}\NormalTok{ delays}\AttributeTok{.head}
 \end{Highlighting}
@@ -3468,77 +4011,66 @@ other:
 
 \section{Using Data Table}\label{using-data-table}
 
-The next chunk reads the \textbf{flights14} sample (same file as the
-data.table vignette). Prefer \textbf{downloading in Ruby} and
-\textbf{\texttt{R.fread} on a local path}:
-\texttt{data.table::fread("https://…")} runs the HTTP transfer
-\textbf{inside R} while the Galaaz bridge waits on a \textbf{single}
-eval; if the remote server stalls, that looks like an intermittent
-``hang'' and eventually hits the \textbf{per-eval} bridge timeout.
-Ruby's \textbf{\texttt{Net::HTTP}} \texttt{open\_timeout} /
-\texttt{read\_timeout} fail fast with a clear error instead. The chunk
-passes \textbf{\texttt{nrows:}} to \textbf{\texttt{fread}} so a single
-bridge eval does not have to materialize the full
-\textasciitilde1.2M-row table during a gknit run.
+The next chunk converts the \textbf{nycflights13} \texttt{flights}
+tibble already loaded above into a \textbf{\texttt{data.table}}. That
+keeps the manual offline and avoids downloading a remote CSV during
+gknit (network stalls look like bridge hangs when the transfer runs
+inside a single R eval).
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{require} \VerbatimStringTok{\textquotesingle{}net/http\textquotesingle{}}
-\FunctionTok{require} \VerbatimStringTok{\textquotesingle{}uri\textquotesingle{}}
-\FunctionTok{require} \VerbatimStringTok{\textquotesingle{}tmpdir\textquotesingle{}}
-
 \ConstantTok{R}\AttributeTok{.library}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}data.table\textquotesingle{}}\NormalTok{)}
 
-\NormalTok{url }\OperatorTok{=} \ConstantTok{URI}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}https://raw.githubusercontent.com/Rdatatable/data.table/master/vignettes/flights14.csv\textquotesingle{}}\NormalTok{)}
-\NormalTok{csv }\OperatorTok{=} \DataTypeTok{File}\AttributeTok{.join}\NormalTok{(}\DataTypeTok{Dir}\AttributeTok{.tmpdir}\NormalTok{, }\StringTok{"galaaz\_manual\_flights14\_}\SpecialCharTok{\#\{}\DataTypeTok{Process}\AttributeTok{.pid}\SpecialCharTok{\}}\StringTok{.csv"}\NormalTok{)}
-\ControlFlowTok{begin}
-  \DataTypeTok{Net}\OperatorTok{::}\ConstantTok{HTTP}\AttributeTok{.start}\NormalTok{(url}\AttributeTok{.host}\NormalTok{, url}\AttributeTok{.port}\NormalTok{, }\WarningTok{use\_ssl:} \DecValTok{true}\NormalTok{, }\WarningTok{open\_timeout:} \DecValTok{25}\NormalTok{, }\WarningTok{read\_timeout:} \DecValTok{120}\NormalTok{) }\ControlFlowTok{do} \OperatorTok{|}\NormalTok{http}\OperatorTok{|}
-\NormalTok{    resp }\OperatorTok{=}\NormalTok{ http}\AttributeTok{.request\_get}\NormalTok{(url}\AttributeTok{.request\_uri}\NormalTok{)}
-    \FunctionTok{raise} \StringTok{"HTTP }\SpecialCharTok{\#\{}\NormalTok{resp}\AttributeTok{.code}\SpecialCharTok{\}}\StringTok{"} \ControlFlowTok{unless}\NormalTok{ resp}\AttributeTok{.is\_a?}\NormalTok{(}\DataTypeTok{Net}\OperatorTok{::}\DataTypeTok{HTTPSuccess}\NormalTok{)}
-
-    \DataTypeTok{File}\AttributeTok{.binwrite}\NormalTok{(csv, resp}\AttributeTok{.body}\NormalTok{)}
-  \ControlFlowTok{end}
-
-  \CommentTok{\# Cap rows so one bridge eval stays short on slow disks (full file is \textasciitilde{}1.2M rows).}
-\NormalTok{  flights }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.fread}\NormalTok{(csv, }\WarningTok{nrows:} \DecValTok{120\_000}\NormalTok{)}
-  \FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.dim}
-  \FunctionTok{puts} \ConstantTok{R}\AttributeTok{.head}\NormalTok{(flights, }\DecValTok{12}\NormalTok{)}
-\ControlFlowTok{ensure}
-  \DataTypeTok{File}\AttributeTok{.unlink}\NormalTok{(csv) }\ControlFlowTok{if}\NormalTok{ csv }\OperatorTok{\&\&} \DataTypeTok{File}\AttributeTok{.exist?}\NormalTok{(csv)}
-\ControlFlowTok{end}
-\end{Highlighting}
-\end{Shaded}
-
-\begin{verbatim}
-## [1] 120000     11
-##      year month   day dep_delay arr_delay carrier origin   dest air_time
-##     <int> <int> <int>     <int>     <int>  <char> <char> <char>    <int>
-##  1:  2014     1     1        14        13      AA    JFK    LAX      359
-##  2:  2014     1     1        -3        13      AA    JFK    LAX      363
-##  3:  2014     1     1         2         9      AA    JFK    LAX      351
-##  4:  2014     1     1        -8       -26      AA    LGA    PBI      157
-##  5:  2014     1     1         2         1      AA    JFK    LAX      350
-##  6:  2014     1     1         4         0      AA    EWR    LAX      339
-##  7:  2014     1     1        -2       -18      AA    JFK    LAX      338
-##  8:  2014     1     1        -3       -14      AA    JFK    LAX      356
-##  9:  2014     1     1        -1       -17      AA    JFK    MIA      161
-## 10:  2014     1     1        -2       -14      AA    JFK    SEA      349
-## 11:  2014     1     1        -5       -17      AA    EWR    MIA      161
-## 12:  2014     1     1         7        -5      AA    JFK    SFO      365
-##     distance  hour
-##        <int> <int>
-##  1:     2475     9
-##  2:     2475    11
-##  3:     2475    19
-##  4:     1035     7
-##  5:     2475    13
-##  6:     2454    18
-##  7:     2475    21
-##  8:     2475    15
-##  9:     1089    15
-## 10:     2422    18
-## 11:     1085    16
-## 12:     2586    17
+\NormalTok{flights }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.as\_\_data\_\_table}\NormalTok{(}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:flights}\KeywordTok{]}\NormalTok{)}
+\FunctionTok{puts}\NormalTok{ flights}\AttributeTok{.dim}
+\FunctionTok{puts} \ConstantTok{R}\AttributeTok{.head}\NormalTok{(flights, }\DecValTok{12}\NormalTok{)}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## [1] 336776     19
+##      year month   day dep_time sched_dep_time dep_delay arr_time
+##     <int> <int> <int>    <int>          <int>     <num>    <int>
+##  1:  2013     1     1      517            515         2      830
+##  2:  2013     1     1      533            529         4      850
+##  3:  2013     1     1      542            540         2      923
+##  4:  2013     1     1      544            545        -1     1004
+##  5:  2013     1     1      554            600        -6      812
+##  6:  2013     1     1      554            558        -4      740
+##  7:  2013     1     1      555            600        -5      913
+##  8:  2013     1     1      557            600        -3      709
+##  9:  2013     1     1      557            600        -3      838
+## 10:  2013     1     1      558            600        -2      753
+## 11:  2013     1     1      558            600        -2      849
+## 12:  2013     1     1      558            600        -2      853
+##     sched_arr_time arr_delay carrier flight tailnum origin   dest
+##              <int>     <num>  <char>  <int>  <char> <char> <char>
+##  1:            819        11      UA   1545  N14228    EWR    IAH
+##  2:            830        20      UA   1714  N24211    LGA    IAH
+##  3:            850        33      AA   1141  N619AA    JFK    MIA
+##  4:           1022       -18      B6    725  N804JB    JFK    BQN
+##  5:            837       -25      DL    461  N668DN    LGA    ATL
+##  6:            728        12      UA   1696  N39463    EWR    ORD
+##  7:            854        19      B6    507  N516JB    EWR    FLL
+##  8:            723       -14      EV   5708  N829AS    LGA    IAD
+##  9:            846        -8      B6     79  N593JB    JFK    MCO
+## 10:            745         8      AA    301  N3ALAA    LGA    ORD
+## 11:            851        -2      B6     49  N793JB    JFK    PBI
+## 12:            856        -3      B6     71  N657JB    JFK    TPA
+##     air_time distance  hour minute           time_hour
+##        <num>    <num> <num>  <num>              <POSc>
+##  1:      227     1400     5     15 2013-01-01 05:00:00
+##  2:      227     1416     5     29 2013-01-01 05:00:00
+##  3:      160     1089     5     40 2013-01-01 05:00:00
+##  4:      183     1576     5     45 2013-01-01 05:00:00
+##  5:      116      762     6      0 2013-01-01 06:00:00
+##  6:      150      719     5     58 2013-01-01 05:00:00
+##  7:      158     1065     6      0 2013-01-01 06:00:00
+##  8:       53      229     6      0 2013-01-01 06:00:00
+##  9:      140      944     6      0 2013-01-01 06:00:00
+## 10:      138      733     6      0 2013-01-01 06:00:00
+## 11:      149     1028     6      0 2013-01-01 06:00:00
+## 12:      158     1005     6      0 2013-01-01 06:00:00
 \end{verbatim}
 
 \begin{Shaded}
@@ -3570,7 +4102,7 @@ bridge eval does not have to materialize the full
 \begin{Shaded}
 \begin{Highlighting}[]
 \CommentTok{\# subset rows in i}
-\NormalTok{ans }\OperatorTok{=}\NormalTok{ flights}\KeywordTok{[}\NormalTok{(}\WarningTok{:origin}\AttributeTok{.eq} \StringTok{"JFK"}\NormalTok{) }\OperatorTok{\&}\NormalTok{ (}\WarningTok{:month}\AttributeTok{.eq} \DecValTok{6}\NormalTok{)}\KeywordTok{]}
+\NormalTok{ans }\OperatorTok{=}\NormalTok{ flights}\KeywordTok{[}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:origin}\KeywordTok{]}\AttributeTok{.eq} \StringTok{"JFK"}\NormalTok{) }\OperatorTok{\&}\NormalTok{ (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:month}\KeywordTok{]}\AttributeTok{.eq} \DecValTok{6}\NormalTok{)}\KeywordTok{]}
 \FunctionTok{puts}\NormalTok{ ans}\AttributeTok{.head}
 
 \CommentTok{\# Get the first two rows from flights.}
@@ -3585,15 +4117,42 @@ bridge eval does not have to materialize the full
 \end{Shaded}
 
 \begin{verbatim}
-## Empty data.table (0 rows and 11 cols): year,month,day,dep_delay,arr_delay,carrier...
-##     year month   day dep_delay arr_delay carrier origin   dest air_time
-##    <int> <int> <int>     <int>     <int>  <char> <char> <char>    <int>
-## 1:  2014     1     1        14        13      AA    JFK    LAX      359
-## 2:  2014     1     1        -3        13      AA    JFK    LAX      363
-##    distance  hour
-##       <int> <int>
-## 1:     2475     9
-## 2:     2475    11
+##     year month   day dep_time sched_dep_time dep_delay arr_time
+##    <int> <int> <int>    <int>          <int>     <num>    <int>
+## 1:  2013     6     1        2           2359         3      341
+## 2:  2013     6     1      538            545        -7      925
+## 3:  2013     6     1      539            540        -1      832
+## 4:  2013     6     1      553            600        -7      700
+## 5:  2013     6     1      554            600        -6      851
+## 6:  2013     6     1      557            600        -3      934
+##    sched_arr_time arr_delay carrier flight tailnum origin   dest
+##             <int>     <num>  <char>  <int>  <char> <char> <char>
+## 1:            350        -9      B6    739  N618JB    JFK    PSE
+## 2:            922         3      B6    725  N806JB    JFK    BQN
+## 3:            840        -8      AA    701  N5EAAA    JFK    MIA
+## 4:            711       -11      EV   5716  N835AS    JFK    IAD
+## 5:            908       -17      UA   1159  N33132    JFK    LAX
+## 6:            942        -8      B6    715  N766JB    JFK    SJU
+##    air_time distance  hour minute           time_hour
+##       <num>    <num> <num>  <num>              <POSc>
+## 1:      200     1617    23     59 2013-06-01 23:00:00
+## 2:      203     1576     5     45 2013-06-01 05:00:00
+## 3:      140     1089     5     40 2013-06-01 05:00:00
+## 4:       42      228     6      0 2013-06-01 06:00:00
+## 5:      330     2475     6      0 2013-06-01 06:00:00
+## 6:      198     1598     6      0 2013-06-01 06:00:00
+##     year month   day dep_time sched_dep_time dep_delay arr_time
+##    <int> <int> <int>    <int>          <int>     <num>    <int>
+## 1:  2013     1     1      517            515         2      830
+## 2:  2013     1     1      533            529         4      850
+##    sched_arr_time arr_delay carrier flight tailnum origin   dest
+##             <int>     <num>  <char>  <int>  <char> <char> <char>
+## 1:            819        11      UA   1545  N14228    EWR    IAH
+## 2:            830        20      UA   1714  N24211    LGA    IAH
+##    air_time distance  hour minute           time_hour
+##       <num>    <num> <num>  <num>              <POSc>
+## 1:      227     1400     5     15 2013-01-01 05:00:00
+## 2:      227     1416     5     29 2013-01-01 05:00:00
 \end{verbatim}
 
 \begin{Shaded}
@@ -3606,23 +4165,23 @@ bridge eval does not have to materialize the full
 
 \CommentTok{\# arr\_delay as data.table (not plain vector).}
 
-\NormalTok{ans }\OperatorTok{=}\NormalTok{ flights}\KeywordTok{[}\WarningTok{:all}\NormalTok{, }\WarningTok{:arr\_delay}\AttributeTok{.list}\KeywordTok{]}
+\NormalTok{ans }\OperatorTok{=}\NormalTok{ flights}\KeywordTok{[}\WarningTok{:all}\NormalTok{, }\ConstantTok{R}\KeywordTok{[}\WarningTok{:arr\_delay}\KeywordTok{]}\AttributeTok{.list}\KeywordTok{]}
 \FunctionTok{puts}\NormalTok{ ans}\AttributeTok{.head}
 
-\NormalTok{ans }\OperatorTok{=}\NormalTok{ flights}\KeywordTok{[}\WarningTok{:all}\NormalTok{, }\ConstantTok{E}\AttributeTok{.list}\NormalTok{(}\WarningTok{:arr\_delay}\NormalTok{, }\WarningTok{:dep\_delay}\NormalTok{)}\KeywordTok{]}
+\NormalTok{ans }\OperatorTok{=}\NormalTok{ flights}\KeywordTok{[}\WarningTok{:all}\NormalTok{, }\ConstantTok{E}\AttributeTok{.list}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:arr\_delay}\KeywordTok{]}\NormalTok{, }\ConstantTok{R}\KeywordTok{[}\WarningTok{:dep\_delay}\KeywordTok{]}\NormalTok{)}\KeywordTok{]}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
-## [1]  13  13   9 -26   1   0
+## [1]  11  20  33 -18 -25  12
 ##    arr_delay
-##        <int>
-## 1:        13
-## 2:        13
-## 3:         9
-## 4:       -26
-## 5:         1
-## 6:         0
+##        <num>
+## 1:        11
+## 2:        20
+## 3:        33
+## 4:       -18
+## 5:       -25
+## 6:        12
 \end{verbatim}
 
 \section{Apache Arrow}\label{apache-arrow}
@@ -3639,10 +4198,10 @@ ordinary Ruby structures (arrays of row hashes), and
 \textbf{\texttt{collect()}} to materialize a tibble when you need
 in-memory R rows.
 
-That pattern matches production use: \textbf{JRuby threads} (or
-sequential code) assemble many rows in Ruby; you pay \textbf{one}
-bridge-heavy handoff to R; \textbf{dplyr} runs vectorised work on the
-Arrow table in R.
+That pattern matches production use: \textbf{JRuby threads} or a
+\textbf{multi-process CRuby} app (or sequential code) assemble many rows
+in Ruby; you pay \textbf{one} bridge-heavy handoff to R; \textbf{dplyr}
+runs vectorised work on the Arrow table in R.
 
 \textbf{Prerequisites:} install R packages \textbf{\texttt{arrow}} and
 \textbf{\texttt{dplyr}}. Run scripts with
@@ -3681,8 +4240,12 @@ can knit quickly; increase \texttt{thread\_count} and
 \begin{Shaded}
 \begin{Highlighting}[]
 \CommentTok{\# Scaled{-}down version of slow{-}specs/arrow\_large\_pipeline\_spec.rb.}
-\ControlFlowTok{unless} \ConstantTok{R}\OperatorTok{::}\DataTypeTok{Support}\AttributeTok{.eval}\NormalTok{(}\StringTok{"requireNamespace(\textquotesingle{}arrow\textquotesingle{}, quietly=TRUE) \&\& requireNamespace(\textquotesingle{}dplyr\textquotesingle{}, quietly=TRUE)"}\NormalTok{) }\OperatorTok{==} \DecValTok{true}
-  \FunctionTok{puts} \VerbatimStringTok{\textquotesingle{}(Skip: need arrow + dplyr in R; use bin/galaaz{-}jruby outside gKnit.)\textquotesingle{}}
+\NormalTok{arrow\_ok }\OperatorTok{=} \ConstantTok{R}\OperatorTok{::}\DataTypeTok{Support}\AttributeTok{.eval}\NormalTok{(}
+  \StringTok{"requireNamespace(\textquotesingle{}arrow\textquotesingle{}, quietly=TRUE) \&\& "} \OperatorTok{+}
+  \StringTok{"requireNamespace(\textquotesingle{}dplyr\textquotesingle{}, quietly=TRUE)"}\NormalTok{)}
+\ControlFlowTok{unless}\NormalTok{ arrow\_ok }\OperatorTok{==} \DecValTok{true}
+  \FunctionTok{puts} \VerbatimStringTok{\textquotesingle{}(Skip: need arrow + dplyr in R; \textquotesingle{}} \OperatorTok{+}
+       \VerbatimStringTok{\textquotesingle{}use bin/galaaz{-}jruby outside gKnit.)\textquotesingle{}}
 \ControlFlowTok{else}
 \NormalTok{  thread\_count }\OperatorTok{=} \DecValTok{4}
 \NormalTok{  rows\_per\_thread }\OperatorTok{=} \DecValTok{500}
@@ -3716,7 +4279,7 @@ can knit quickly; increase \texttt{thread\_count} and
 \NormalTok{    grouped,}
     \WarningTok{n:} \ConstantTok{E}\AttributeTok{.n}\NormalTok{(),}
     \WarningTok{total:} \ConstantTok{E}\AttributeTok{.sum}\NormalTok{(}\WarningTok{:value}\NormalTok{),}
-    \WarningTok{wsum:} \ConstantTok{E}\AttributeTok{.sum}\NormalTok{(}\WarningTok{:value} \OperatorTok{*} \WarningTok{:weight}\NormalTok{)}
+    \WarningTok{wsum:} \ConstantTok{E}\AttributeTok{.sum}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:value}\KeywordTok{]} \OperatorTok{*} \ConstantTok{R}\KeywordTok{[}\WarningTok{:weight}\KeywordTok{]}\NormalTok{)}
 \NormalTok{  )}
 \NormalTok{  out }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.dplyr\_\_\_collect}\NormalTok{(summarised)}
 
@@ -3725,7 +4288,9 @@ can knit quickly; increase \texttt{thread\_count} and
 
 \NormalTok{  total\_n }\OperatorTok{=} \DecValTok{0}
 \NormalTok{  (}\DecValTok{1}\OperatorTok{..}\NormalTok{(out}\AttributeTok{.nrow} \OperatorTok{\textgreater{}\textgreater{}} \DecValTok{0}\NormalTok{))}\AttributeTok{.each} \OperatorTok{\{} \OperatorTok{|}\NormalTok{i}\OperatorTok{|}\NormalTok{ total\_n }\OperatorTok{+=}\NormalTok{ (out}\KeywordTok{[[}\CharTok{\textquotesingle{}n\textquotesingle{}}\KeywordTok{]][}\NormalTok{i}\KeywordTok{]} \OperatorTok{\textgreater{}\textgreater{}} \DecValTok{0}\NormalTok{) }\OperatorTok{\}}
-  \FunctionTok{puts} \StringTok{"Sum of group counts n (should equal }\SpecialCharTok{\#\{}\NormalTok{thread\_count }\OperatorTok{*}\NormalTok{ rows\_per\_thread}\SpecialCharTok{\}}\StringTok{): }\SpecialCharTok{\#\{}\NormalTok{total\_n}\SpecialCharTok{\}}\StringTok{"}
+  \FunctionTok{puts} \StringTok{"Sum of group counts n "} \OperatorTok{+}
+       \StringTok{"(should equal }\SpecialCharTok{\#\{}\NormalTok{thread\_count }\OperatorTok{*}\NormalTok{ rows\_per\_thread}\SpecialCharTok{\}}\StringTok{): "} \OperatorTok{+}
+       \StringTok{"}\SpecialCharTok{\#\{}\NormalTok{total\_n}\SpecialCharTok{\}}\StringTok{"}
 \ControlFlowTok{end}
 \end{Highlighting}
 \end{Shaded}
@@ -3788,11 +4353,14 @@ dataset}\label{example-deseq2-on-the-airway-dataset}
 The script
 \textbf{\texttt{examples/bioconductor\_deseq2\_airway/deseq2\_airway\_galaaz.rb}}
 is the canonical version in the repository. Run it from the
-\textbf{Galaaz repository root} with JRuby, for example:
+\textbf{Galaaz repository root} with either engine, for example:
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{bin/galaaz{-}jruby examples/bioconductor\_deseq2\_airway/deseq2\_airway\_galaaz.rb}
+\NormalTok{bin/galaaz{-}ruby \textbackslash{}}
+\NormalTok{  examples/bioconductor\_deseq2\_airway/deseq2\_airway\_galaaz.rb}
+\NormalTok{\# or: bin/galaaz{-}jruby \textbackslash{}}
+\NormalTok{\#   examples/bioconductor\_deseq2\_airway/deseq2\_airway\_galaaz.rb}
 \end{Highlighting}
 \end{Shaded}
 
@@ -3809,14 +4377,14 @@ The workflow in Ruby mirrors a standard DESeq2 vignette:
   \textbf{\texttt{R.data(\textquotesingle{}airway\textquotesingle{})}}
   so the object exists in R's global environment.
 \item
-  \textbf{\texttt{airway\ =\ \textasciitilde{}:airway}} pulls the
+  \textbf{\texttt{airway\ =\ \textasciitilde{}R{[}:airway{]}}} pulls the
   experiment into a Galaaz wrapper so you can pass it to R functions as
   a Ruby value.
 \item
-  \textbf{\texttt{R.DESeqDataSet(...,\ design:\ (:all.til\ :cell\ +\ :dex))}}
+  \textbf{\texttt{R.DESeqDataSet(...,\ design:\ (R{[}:all{]}.til\ R{[}:cell{]}\ +\ R{[}:dex{]}))}}
   builds the \textbf{\texttt{DESeqDataSet}}. The
-  \textbf{\texttt{(:all.til\ :cell\ +\ :dex)}} form is Galaaz's way of
-  passing the one-sided formula
+  \textbf{\texttt{(R{[}:all{]}.til\ R{[}:cell{]}\ +\ R{[}:dex{]})}} form
+  is Galaaz's way of passing the one-sided formula
   \textbf{\texttt{\textasciitilde{}\ cell\ +\ dex}} (adjust for the
   design you need).
 \item
@@ -3848,8 +4416,9 @@ Below is the full listing (same as the file in the repository). It is
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\CommentTok{\# Canonical script: examples/bioconductor\_deseq2\_airway/deseq2\_airway\_galaaz.rb}
-\CommentTok{\# Run: bin/galaaz{-}jruby examples/.../deseq2\_airway\_galaaz.rb (repo root).}
+\CommentTok{\# Canonical script:}
+\CommentTok{\# examples/bioconductor\_deseq2\_airway/deseq2\_airway\_galaaz.rb}
+\CommentTok{\# Run: bin/galaaz{-}ruby examples/.../deseq2\_airway\_galaaz.rb (repo root).}
 
 \FunctionTok{require} \VerbatimStringTok{\textquotesingle{}galaaz\textquotesingle{}}
 
@@ -3857,10 +4426,10 @@ Below is the full listing (same as the file in the repository). It is
 \ConstantTok{R}\AttributeTok{.library}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}airway\textquotesingle{}}\NormalTok{)}
 \ConstantTok{R}\AttributeTok{.data}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}airway\textquotesingle{}}\NormalTok{)}
 
-\NormalTok{airway }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\WarningTok{:airway}
+\NormalTok{airway }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:airway}\KeywordTok{]}
 
 \CommentTok{\# Build DESeq2 dataset with one{-}sided formula: \textasciitilde{} cell + dex.}
-\NormalTok{dds }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.}\DataTypeTok{DESeqDataSet}\NormalTok{(airway, }\WarningTok{design:}\NormalTok{ (}\WarningTok{:all}\AttributeTok{.til} \OperatorTok{:}\NormalTok{cell }\OperatorTok{+} \WarningTok{:dex}\NormalTok{))}
+\NormalTok{dds }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.}\DataTypeTok{DESeqDataSet}\NormalTok{(airway, }\WarningTok{design:}\NormalTok{ (}\ConstantTok{R}\KeywordTok{[}\WarningTok{:all}\KeywordTok{]}\AttributeTok{.til} \ConstantTok{R}\KeywordTok{[}\WarningTok{:cell}\KeywordTok{]} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:dex}\KeywordTok{]}\NormalTok{))}
 
 \CommentTok{\# Prefilter genes with almost no counts.}
 \NormalTok{keep }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.rowSums}\NormalTok{(}\ConstantTok{R}\AttributeTok{.counts}\NormalTok{(dds)) }\OperatorTok{\textgreater{}=} \DecValTok{10}
@@ -3875,7 +4444,8 @@ Below is the full listing (same as the file in the repository). It is
 \FunctionTok{puts} \StringTok{"Genes after prefilter: }\SpecialCharTok{\#\{}\ConstantTok{R}\AttributeTok{.nrow}\NormalTok{(dds)}\SpecialCharTok{\}}\StringTok{"}
 \FunctionTok{puts} \StringTok{"Result rows: }\SpecialCharTok{\#\{}\ConstantTok{R}\AttributeTok{.nrow}\NormalTok{(res)}\SpecialCharTok{\}}\StringTok{"}
 \FunctionTok{puts} \StringTok{"Result columns: }\SpecialCharTok{\#\{}\ConstantTok{R}\AttributeTok{.colnames}\NormalTok{(res)}\SpecialCharTok{\}}\StringTok{"}
-\FunctionTok{puts} \StringTok{"Significant genes (padj \textless{} 0.05): }\SpecialCharTok{\#\{}\ConstantTok{R}\AttributeTok{.sum}\NormalTok{(res}\AttributeTok{.padj} \OperatorTok{\textless{}} \FloatTok{0.05}\NormalTok{, }\WarningTok{na\_\_rm:} \DecValTok{true}\NormalTok{)}\SpecialCharTok{\}}\StringTok{"}
+\FunctionTok{puts} \StringTok{"Significant genes (padj \textless{} 0.05): "} \OperatorTok{+}
+     \StringTok{"}\SpecialCharTok{\#\{}\ConstantTok{R}\AttributeTok{.sum}\NormalTok{(res}\AttributeTok{.padj} \OperatorTok{\textless{}} \FloatTok{0.05}\NormalTok{, }\WarningTok{na\_\_rm:} \DecValTok{true}\NormalTok{)}\SpecialCharTok{\}}\StringTok{"}
 
 \NormalTok{res\_ordered }\OperatorTok{=}\NormalTok{ res}\KeywordTok{[}\ConstantTok{R}\AttributeTok{.order}\NormalTok{(res}\AttributeTok{.padj}\NormalTok{), }\WarningTok{:all}\KeywordTok{]}
 \FunctionTok{puts} \ConstantTok{R}\AttributeTok{.head}\NormalTok{(}\ConstantTok{R}\AttributeTok{.as\_\_data\_\_frame}\NormalTok{(res\_ordered), }\DecValTok{10}\NormalTok{)}
@@ -3893,13 +4463,17 @@ loads the data and prints a short preview (it does \textbf{not} run
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\ControlFlowTok{unless} \ConstantTok{R}\OperatorTok{::}\DataTypeTok{Support}\AttributeTok{.eval}\NormalTok{(}\StringTok{"requireNamespace(\textquotesingle{}DESeq2\textquotesingle{}, quietly=TRUE) \&\& requireNamespace(\textquotesingle{}airway\textquotesingle{}, quietly=TRUE)"}\NormalTok{)}
-  \FunctionTok{puts} \VerbatimStringTok{\textquotesingle{}(Skip: install DESeq2 and airway via BiocManager in R to run the full example.)\textquotesingle{}}
+\NormalTok{deseq\_ok }\OperatorTok{=} \ConstantTok{R}\OperatorTok{::}\DataTypeTok{Support}\AttributeTok{.eval}\NormalTok{(}
+  \StringTok{"requireNamespace(\textquotesingle{}DESeq2\textquotesingle{}, quietly=TRUE) \&\& "} \OperatorTok{+}
+  \StringTok{"requireNamespace(\textquotesingle{}airway\textquotesingle{}, quietly=TRUE)"}\NormalTok{)}
+\ControlFlowTok{unless}\NormalTok{ deseq\_ok}
+  \FunctionTok{puts} \VerbatimStringTok{\textquotesingle{}(Skip: install DESeq2 and airway via \textquotesingle{}} \OperatorTok{+}
+       \VerbatimStringTok{\textquotesingle{}BiocManager in R for the full example.)\textquotesingle{}}
 \ControlFlowTok{else}
   \ConstantTok{R}\AttributeTok{.library}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}DESeq2\textquotesingle{}}\NormalTok{)}
   \ConstantTok{R}\AttributeTok{.library}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}airway\textquotesingle{}}\NormalTok{)}
   \ConstantTok{R}\AttributeTok{.data}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}airway\textquotesingle{}}\NormalTok{)}
-\NormalTok{  airway }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\WarningTok{:airway}
+\NormalTok{  airway }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:airway}\KeywordTok{]}
   \FunctionTok{puts} \VerbatimStringTok{\textquotesingle{}airway object (head of assay / dims via R):\textquotesingle{}}
   \FunctionTok{puts} \StringTok{"ncol(samples): }\SpecialCharTok{\#\{}\ConstantTok{R}\AttributeTok{.ncol}\NormalTok{(airway)}\SpecialCharTok{\}}\StringTok{"}
   \FunctionTok{puts} \ConstantTok{R}\AttributeTok{.head}\NormalTok{(}\ConstantTok{R}\AttributeTok{.assay}\NormalTok{(airway), }\DecValTok{3}\NormalTok{)}
@@ -3910,14 +4484,14 @@ loads the data and prints a short preview (it does \textbf{not} run
 \begin{verbatim}
 ## airway object (head of assay / dims via R):
 ## ncol(samples): [1] 8
-##                 SRR1039508 SRR1039509 SRR1039512 SRR1039513 SRR1039516
-## ENSG00000000003        679        448        873        408       1138
-## ENSG00000000005          0          0          0          0          0
-## ENSG00000000419        467        515        621        365        587
-##                 SRR1039517 SRR1039520 SRR1039521
-## ENSG00000000003       1047        770        572
-## ENSG00000000005          0          0          0
-## ENSG00000000419        799        417        508
+##                 SRR1039508 SRR1039509 SRR1039512 SRR1039513
+## ENSG00000000003        679        448        873        408
+## ENSG00000000005          0          0          0          0
+## ENSG00000000419        467        515        621        365
+##                 SRR1039516 SRR1039517 SRR1039520 SRR1039521
+## ENSG00000000003       1138       1047        770        572
+## ENSG00000000005          0          0          0          0
+## ENSG00000000419        587        799        417        508
 \end{verbatim}
 
 \section{Performance}\label{performance}
@@ -3962,10 +4536,10 @@ first prepare the data frame with the necessary data:
 \begin{Shaded}
 \begin{Highlighting}[]
 \CommentTok{\# :mtcars {-}\textgreater{} Ruby handle}
-\NormalTok{mtcars }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\WarningTok{:mtcars}
+\NormalTok{mtcars }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}
 
 \CommentTok{\# Row labels are not a plot column; copy them to car\_name.}
-\NormalTok{mtcars}\AttributeTok{.car\_name} \OperatorTok{=} \ConstantTok{R}\AttributeTok{.rownames}\NormalTok{(}\WarningTok{:mtcars}\NormalTok{)}
+\NormalTok{mtcars}\AttributeTok{.car\_name} \OperatorTok{=} \ConstantTok{R}\AttributeTok{.rownames}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mtcars}\KeywordTok{]}\NormalTok{)}
 
 \CommentTok{\# Z{-}score mpg (mean/sd on mtcars.mpg); round to 2 decimals.}
 \NormalTok{mtcars}\AttributeTok{.mpg\_z} \OperatorTok{=}\NormalTok{ ((mtcars}\AttributeTok{.mpg} \OperatorTok{{-}}\NormalTok{ mtcars}\AttributeTok{.mpg.mean}\NormalTok{)}\OperatorTok{/}\NormalTok{mtcars}\AttributeTok{.mpg.sd}\NormalTok{)}\AttributeTok{.round} \DecValTok{2}
@@ -3984,20 +4558,20 @@ first prepare the data frame with the necessary data:
 \end{Shaded}
 
 \begin{verbatim}
-##                      mpg cyl disp  hp drat    wt  qsec vs am gear carb
-## Cadillac Fleetwood  10.4   8  472 205 2.93 5.250 17.98  0  0    3    4
-## Lincoln Continental 10.4   8  460 215 3.00 5.424 17.82  0  0    3    4
-## Camaro Z28          13.3   8  350 245 3.73 3.840 15.41  0  0    3    4
-## Duster 360          14.3   8  360 245 3.21 3.570 15.84  0  0    3    4
-## Chrysler Imperial   14.7   8  440 230 3.23 5.345 17.42  0  0    3    4
-## Maserati Bora       15.0   8  301 335 3.54 3.570 14.60  0  1    5    8
-##                                car_name mpg_z mpg_type
-## Cadillac Fleetwood   Cadillac Fleetwood -1.61    below
-## Lincoln Continental Lincoln Continental -1.61    below
-## Camaro Z28                   Camaro Z28 -1.13    below
-## Duster 360                   Duster 360 -0.96    below
-## Chrysler Imperial     Chrysler Imperial -0.89    below
-## Maserati Bora             Maserati Bora -0.84    below
+##                      mpg cyl disp  hp drat    wt  qsec vs am gear
+## Cadillac Fleetwood  10.4   8  472 205 2.93 5.250 17.98  0  0    3
+## Lincoln Continental 10.4   8  460 215 3.00 5.424 17.82  0  0    3
+## Camaro Z28          13.3   8  350 245 3.73 3.840 15.41  0  0    3
+## Duster 360          14.3   8  360 245 3.21 3.570 15.84  0  0    3
+## Chrysler Imperial   14.7   8  440 230 3.23 5.345 17.42  0  0    3
+## Maserati Bora       15.0   8  301 335 3.54 3.570 14.60  0  1    5
+##                     carb            car_name mpg_z mpg_type
+## Cadillac Fleetwood     4  Cadillac Fleetwood -1.61    below
+## Lincoln Continental    4 Lincoln Continental -1.61    below
+## Camaro Z28             4          Camaro Z28 -1.13    below
+## Duster 360             4          Duster 360 -0.96    below
+## Chrysler Imperial      4   Chrysler Imperial -0.89    below
+## Maserati Bora          8       Maserati Bora -0.84    below
 \end{verbatim}
 
 Now, let's plot the diverging bar plot. When using gKnit, you normally
@@ -4024,18 +4598,22 @@ we add `coord\_flip'.
 \begin{Highlighting}[]
 \FunctionTok{require} \VerbatimStringTok{\textquotesingle{}ggplot\textquotesingle{}}
 
-\FunctionTok{puts}\NormalTok{ mtcars}\AttributeTok{.ggplot}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{x:} \WarningTok{:car\_name}\NormalTok{, }\WarningTok{y:} \WarningTok{:mpg\_z}\NormalTok{, }\WarningTok{label:} \WarningTok{:mpg\_z}\NormalTok{)) }\OperatorTok{+}
-     \ConstantTok{R}\AttributeTok{.geom\_bar}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{fill:} \WarningTok{:mpg\_type}\NormalTok{), }\WarningTok{stat:} \VerbatimStringTok{\textquotesingle{}identity\textquotesingle{}}\NormalTok{, }\WarningTok{width:} \FloatTok{0.5}\NormalTok{) }\OperatorTok{+}
-     \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}\WarningTok{name:} \VerbatimStringTok{\textquotesingle{}Mileage\textquotesingle{}}\NormalTok{,}
-                         \WarningTok{labels:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}Above Average\textquotesingle{}}\NormalTok{, }\VerbatimStringTok{\textquotesingle{}Below Average\textquotesingle{}}\NormalTok{),}
-                         \WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}above\textquotesingle{}}\WarningTok{:} \VerbatimStringTok{\textquotesingle{}\#00ba38\textquotesingle{}}\NormalTok{, }\VerbatimStringTok{\textquotesingle{}below\textquotesingle{}}\WarningTok{:} \VerbatimStringTok{\textquotesingle{}\#f8766d\textquotesingle{}}\NormalTok{)) }\OperatorTok{+}
+\FunctionTok{puts}\NormalTok{ mtcars}\AttributeTok{.ggplot}\NormalTok{(}
+       \ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{x:} \WarningTok{:car\_name}\NormalTok{, }\WarningTok{y:} \WarningTok{:mpg\_z}\NormalTok{, }\WarningTok{label:} \WarningTok{:mpg\_z}\NormalTok{)) }\OperatorTok{+}
+     \ConstantTok{R}\AttributeTok{.geom\_bar}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{fill:} \WarningTok{:mpg\_type}\NormalTok{),}
+                \WarningTok{stat:} \VerbatimStringTok{\textquotesingle{}identity\textquotesingle{}}\NormalTok{, }\WarningTok{width:} \FloatTok{0.5}\NormalTok{) }\OperatorTok{+}
+     \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}
+       \WarningTok{name:} \VerbatimStringTok{\textquotesingle{}Mileage\textquotesingle{}}\NormalTok{,}
+       \WarningTok{labels:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}Above Average\textquotesingle{}}\NormalTok{, }\VerbatimStringTok{\textquotesingle{}Below Average\textquotesingle{}}\NormalTok{),}
+       \WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\VerbatimStringTok{\textquotesingle{}above\textquotesingle{}}\WarningTok{:} \VerbatimStringTok{\textquotesingle{}\#00ba38\textquotesingle{}}\NormalTok{,}
+                   \VerbatimStringTok{\textquotesingle{}below\textquotesingle{}}\WarningTok{:} \VerbatimStringTok{\textquotesingle{}\#f8766d\textquotesingle{}}\NormalTok{)) }\OperatorTok{+}
      \ConstantTok{R}\AttributeTok{.labs}\NormalTok{(}\WarningTok{subtitle:} \StringTok{"Normalised mileage from \textquotesingle{}mtcars\textquotesingle{}"}\NormalTok{,}
-            \WarningTok{title:} \StringTok{"Diverging Bars"}\NormalTok{) }\OperatorTok{+} 
+            \WarningTok{title:} \StringTok{"Diverging Bars"}\NormalTok{) }\OperatorTok{+}
      \ConstantTok{R}\AttributeTok{.coord\_flip}
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{manual_files/figure-latex/diverging_bar.pdf}}
+\pandocbounded{\includegraphics[keepaspectratio]{manual_files/manual_files/figure-latex/diverging_bar.pdf}}
 
 \section{Coding with Tidyverse}\label{coding-with-tidyverse}
 
@@ -4070,15 +4648,15 @@ and now, let's look at this code:
 It generates the following error: ``object `x' not found.
 
 However, in Galaaz, arguments are referentially transparent as can be
-seen by the code below. Note initially that `my\_var = :x' will not give
-the error ``object `x' not found'' since `:x' is treated as an
+seen by the code below. Note initially that `my\_var = R{[}:x{]}' will
+not give the error ``object `x' not found'' since `:x' is treated as an
 expression and assigned to my\_var. Then when doing (my\_var.eq 1),
 my\_var is a variable that resolves to `:x' and it becomes equivalent to
-(:x.eq 1) which is what we want.
+(R{[}:x{]}.eq 1) which is what we want.
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{my\_var }\OperatorTok{=} \WarningTok{:x}
+\NormalTok{my\_var }\OperatorTok{=} \ConstantTok{R}\KeywordTok{[}\WarningTok{:x}\KeywordTok{]}
 \FunctionTok{puts}\NormalTok{ df}\AttributeTok{.filter}\NormalTok{(my\_var}\AttributeTok{.eq} \DecValTok{1}\NormalTok{)}
 \end{Highlighting}
 \end{Shaded}
@@ -4104,11 +4682,11 @@ df[x == y, ]
 
 In galaaz this ambiguity does not exist, filter(df, x.eq y) is not a
 valid expression as expressions are build with symbols. In doing
-filter(df, :x.eq y) we are looking for elements of the `x' column that
-are equal to a previously defined y variable. Finally in filter(df,
-:x.eq :y) we are looking for elements in which the `x' column value is
-equal to the `y' column value. This can be seen in the following two
-chunks of code:
+filter(df, R{[}:x{]}.eq y) we are looking for elements of the `x' column
+that are equal to a previously defined y variable. Finally in filter(df,
+R{[}:x{]}.eq R{[}:y{]}) we are looking for elements in which the `x'
+column value is equal to the `y' column value. This can be seen in the
+following two chunks of code:
 
 \begin{Shaded}
 \begin{Highlighting}[]
@@ -4116,7 +4694,7 @@ chunks of code:
 \NormalTok{x }\OperatorTok{=} \DecValTok{2}
 
 \CommentTok{\# looking for values where the \textquotesingle{}x\textquotesingle{} column is equal to the \textquotesingle{}y\textquotesingle{} column}
-\FunctionTok{puts}\NormalTok{ df}\AttributeTok{.filter}\NormalTok{(}\WarningTok{:x}\AttributeTok{.eq} \OperatorTok{:}\NormalTok{y)}
+\FunctionTok{puts}\NormalTok{ df}\AttributeTok{.filter}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:x}\KeywordTok{]}\AttributeTok{.eq} \ConstantTok{R}\KeywordTok{[}\WarningTok{:y}\KeywordTok{]}\NormalTok{)}
 \end{Highlighting}
 \end{Shaded}
 
@@ -4129,7 +4707,7 @@ chunks of code:
 \begin{Highlighting}[]
 \CommentTok{\# looking for values where the \textquotesingle{}x\textquotesingle{} column is equal to the \textquotesingle{}y\textquotesingle{} variable}
 \CommentTok{\# in this case, the number 1}
-\FunctionTok{puts}\NormalTok{ df}\AttributeTok{.filter}\NormalTok{(}\WarningTok{:x}\AttributeTok{.eq}\NormalTok{ y)}
+\FunctionTok{puts}\NormalTok{ df}\AttributeTok{.filter}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:x}\KeywordTok{]}\AttributeTok{.eq}\NormalTok{ y)}
 \end{Highlighting}
 \end{Shaded}
 
@@ -4173,7 +4751,9 @@ silently.
 \begin{Shaded}
 \begin{Highlighting}[]
 \ControlFlowTok{def}\NormalTok{ mutate\_y(df)}
-\NormalTok{  df}\AttributeTok{.mutate}\NormalTok{(}\WarningTok{:y}\AttributeTok{.assign} \OperatorTok{:}\NormalTok{a }\OperatorTok{+} \WarningTok{:x}\NormalTok{)}
+  \CommentTok{\# Column names are Ruby kwargs (y: …).}
+  \CommentTok{\# Use .assign only for R \textasciigrave{}\textless{}{-}\textasciigrave{} expressions.}
+\NormalTok{  df}\AttributeTok{.mutate}\NormalTok{(}\WarningTok{y:} \ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]} \OperatorTok{+} \ConstantTok{R}\KeywordTok{[}\WarningTok{:x}\KeywordTok{]}\NormalTok{)}
 \ControlFlowTok{end}
 \end{Highlighting}
 \end{Shaded}
@@ -4196,19 +4776,26 @@ Here we create a data frame that has only one column named `x':
 
 Note that method mutate\_y will fail independently from the fact that
 variable `a' is defined and in the scope of the method. Variable `a' has
-no relationship with the symbol `:a' used in the definition of
-`mutate\_y' above:
+no relationship with the symbol \texttt{R{[}:a{]}} used in the
+definition of `mutate\_y' above:
 
 \begin{Shaded}
 \begin{Highlighting}[]
 \NormalTok{a }\OperatorTok{=} \DecValTok{10}
-\NormalTok{mutate\_y(df1)}
+\ControlFlowTok{begin}
+\NormalTok{  mutate\_y(df1)}
+\ControlFlowTok{rescue} \OperatorTok{=\textgreater{}}\NormalTok{ e}
+  \FunctionTok{puts}\NormalTok{ e}\AttributeTok{.class.to\_s}
+\NormalTok{  e}\AttributeTok{.message.to\_s.scan}\NormalTok{(}\SpecialStringTok{/.\{1,68\}/}\NormalTok{)}\AttributeTok{.each} \OperatorTok{\{} \OperatorTok{|}\NormalTok{line}\OperatorTok{|} \FunctionTok{puts}\NormalTok{ line }\OperatorTok{\}}
+\ControlFlowTok{end}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
-## Error in strsplit(path, "/") : non-character argument
-## Calls: mutate ... .rlang_purrr_map_mold -> vapply -> FUN -> path_trim_prefix -> strsplit
+## NewBridge::SessionClient::RProcessError
+## Error: i In argument: `y = a + x`.
+## Caused by error:
+## ! object 'a' not found
 \end{verbatim}
 
 \subsection{Different expressions}\label{different-expressions}
@@ -4304,7 +4891,7 @@ e.g.~\texttt{:df}).
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts} \OperatorTok{\textasciitilde{}}\WarningTok{:df}
+\FunctionTok{puts} \OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:df}\KeywordTok{]}
 \end{Highlighting}
 \end{Shaded}
 
@@ -4318,16 +4905,16 @@ e.g.~\texttt{:df}).
 \end{verbatim}
 
 We then create the `my\_summarize' method and call it passing the R data
-frame and the group by variable `:g1':
+frame and the group by variable `R{[}:g1{]}':
 
 \begin{Shaded}
 \begin{Highlighting}[]
 \ControlFlowTok{def}\NormalTok{ my\_summarize(df, group\_var)}
 \NormalTok{  df}\AttributeTok{.group\_by}\NormalTok{(group\_var)}\AttributeTok{.}
-    \AttributeTok{summarize}\NormalTok{(}\WarningTok{a:} \WarningTok{:a}\AttributeTok{.mean}\NormalTok{)}
+    \AttributeTok{summarize}\NormalTok{(}\WarningTok{a:} \ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]}\AttributeTok{.mean}\NormalTok{)}
 \ControlFlowTok{end}
 
-\FunctionTok{puts}\NormalTok{ my\_summarize(}\WarningTok{:df}\NormalTok{, }\WarningTok{:g1}\NormalTok{)}
+\FunctionTok{puts}\NormalTok{ my\_summarize(}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:df}\KeywordTok{]}\NormalTok{, }\ConstantTok{R}\KeywordTok{[}\WarningTok{:g1}\KeywordTok{]}\NormalTok{)}
 \end{Highlighting}
 \end{Shaded}
 
@@ -4343,7 +4930,7 @@ It works!!! Well, let's make sure this was not just some coincidence
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ my\_summarize(}\WarningTok{:df}\NormalTok{, }\WarningTok{:g2}\NormalTok{)}
+\FunctionTok{puts}\NormalTok{ my\_summarize(}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:df}\KeywordTok{]}\NormalTok{, }\ConstantTok{R}\KeywordTok{[}\WarningTok{:g2}\KeywordTok{]}\NormalTok{)}
 \end{Highlighting}
 \end{Shaded}
 
@@ -4396,10 +4983,10 @@ Let's try it in galaaz:
 \NormalTok{  )}
 \ControlFlowTok{end}
 
-\FunctionTok{puts}\NormalTok{ my\_summarise2((}\OperatorTok{\textasciitilde{}}\WarningTok{:df}\NormalTok{), }\WarningTok{:a}\NormalTok{)}
+\FunctionTok{puts}\NormalTok{ my\_summarise2((}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:df}\KeywordTok{]}\NormalTok{), }\WarningTok{:a}\NormalTok{)}
 \FunctionTok{puts} \StringTok{"}
 \StringTok{"}
-\FunctionTok{puts}\NormalTok{ my\_summarise2((}\OperatorTok{\textasciitilde{}}\WarningTok{:df}\NormalTok{), }\WarningTok{:a} \OperatorTok{*} \WarningTok{:b}\NormalTok{)}
+\FunctionTok{puts}\NormalTok{ my\_summarise2((}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:df}\KeywordTok{]}\NormalTok{), }\ConstantTok{R}\KeywordTok{[}\WarningTok{:a}\KeywordTok{]} \OperatorTok{*} \ConstantTok{R}\KeywordTok{[}\WarningTok{:b}\KeywordTok{]}\NormalTok{)}
 \end{Highlighting}
 \end{Shaded}
 
@@ -4462,10 +5049,10 @@ Here is our Ruby code:
 \NormalTok{            sum\_name }\OperatorTok{=\textgreater{}} \ConstantTok{E}\AttributeTok{.sum}\NormalTok{(expr))}
 \ControlFlowTok{end}
 
-\FunctionTok{puts}\NormalTok{ my\_mutate((}\OperatorTok{\textasciitilde{}}\WarningTok{:df}\NormalTok{), }\WarningTok{:a}\NormalTok{)}
+\FunctionTok{puts}\NormalTok{ my\_mutate((}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:df}\KeywordTok{]}\NormalTok{), }\WarningTok{:a}\NormalTok{)}
 \FunctionTok{puts} \StringTok{"}
 \StringTok{"}
-\FunctionTok{puts}\NormalTok{ my\_mutate((}\OperatorTok{\textasciitilde{}}\WarningTok{:df}\NormalTok{), }\WarningTok{:b}\NormalTok{)}
+\FunctionTok{puts}\NormalTok{ my\_mutate((}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:df}\KeywordTok{]}\NormalTok{), }\WarningTok{:b}\NormalTok{)}
 \end{Highlighting}
 \end{Shaded}
 
@@ -4513,7 +5100,7 @@ number of paramenters the paramenter is preceded by '*':
     \AttributeTok{summarise}\NormalTok{(}\WarningTok{a:} \ConstantTok{E}\AttributeTok{.mean}\NormalTok{(}\WarningTok{:a}\NormalTok{))}
 \ControlFlowTok{end}
 
-\FunctionTok{puts}\NormalTok{ my\_summarise3((}\OperatorTok{\textasciitilde{}}\WarningTok{:df}\NormalTok{), }\WarningTok{:g1}\NormalTok{, }\WarningTok{:g2}\NormalTok{)}
+\FunctionTok{puts}\NormalTok{ my\_summarise3((}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:df}\KeywordTok{]}\NormalTok{), }\ConstantTok{R}\KeywordTok{[}\WarningTok{:g1}\KeywordTok{]}\NormalTok{, }\ConstantTok{R}\KeywordTok{[}\WarningTok{:g2}\KeywordTok{]}\NormalTok{)}
 \end{Highlighting}
 \end{Shaded}
 
@@ -4548,10 +5135,10 @@ used, so `x = a' is immediately evaluate and variable `x' will receive
 the value of variable `a' as soon as the Ruby statement is executed.
 Ruby also provides the notion of a symbol; `:a' is a symbol and does not
 evaluate to anything. Galaaz uses Ruby symbols to build expressions that
-are not bound to anything: `:a.eq :b' is clearly an expression and has
-no relationship whatsoever with the statment `a = b'. By using symbols,
-variables and expressions all the possible ambiguities that are found in
-R are eliminated in Galaaz.
+are not bound to anything: `R{[}:a{]}.eq R{[}:b{]}' is clearly an
+expression and has no relationship whatsoever with the statment `a = b'.
+By using symbols, variables and expressions all the possible ambiguities
+that are found in R are eliminated in Galaaz.
 
 The main problem that remains, is that in R, functions are not clearly
 documented as what type of input they are expecting, they might be
@@ -4560,7 +5147,7 @@ the R function will know how to deal with an input of the form `a = b',
 now for the Ruby developer it might not be immediately clear if it
 should call the function passing the value `true' if variable `a' is
 equal to variable `b' or if it should call the function passing the
-expression `:a.eq :b'.
+expression `R{[}:a{]}.eq R{[}:b{]}'.
 
 \subsection{Advanced dplyr features}\label{advanced-dplyr-features}
 
@@ -4589,22 +5176,22 @@ the Starwars movies:
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\WarningTok{:starwars}\NormalTok{)}\AttributeTok{.head}
+\FunctionTok{puts}\NormalTok{ (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:starwars}\KeywordTok{]}\NormalTok{)}\AttributeTok{.head}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
 ## # A tibble: 6 x 14
-##   name      height  mass hair_color skin_color eye_color birth_year sex   gender
-##   <chr>      <int> <dbl> <chr>      <chr>      <chr>          <dbl> <chr> <chr> 
-## 1 Luke Sky~    172    77 blond      fair       blue            19   male  mascu~
-## 2 C-3PO        167    75 <NA>       gold       yellow         112   none  mascu~
-## 3 R2-D2         96    32 <NA>       white, bl~ red             33   none  mascu~
-## 4 Darth Va~    202   136 none       white      yellow          41.9 male  mascu~
-## 5 Leia Org~    150    49 brown      light      brown           19   fema~ femin~
-## 6 Owen Lars    178   120 brown, gr~ light      blue            52   male  mascu~
-## # i 5 more variables: homeworld <chr>, species <chr>, films <list>,
-## #   vehicles <list>, starships <list>
+##   name   height  mass hair_color skin_color eye_color birth_year sex  
+##   <chr>   <int> <dbl> <chr>      <chr>      <chr>          <dbl> <chr>
+## 1 Luke ~    172    77 blond      fair       blue            19   male 
+## 2 C-3PO     167    75 <NA>       gold       yellow         112   none 
+## 3 R2-D2      96    32 <NA>       white, bl~ red             33   none 
+## 4 Darth~    202   136 none       white      yellow          41.9 male 
+## 5 Leia ~    150    49 brown      light      brown           19   fema~
+## 6 Owen ~    178   120 brown, gr~ light      blue            52   male 
+## # i 6 more variables: gender <chr>, homeworld <chr>, species <chr>,
+## #   films <list>, vehicles <list>, starships <list>
 \end{verbatim}
 
 The grouped\_mean function below will receive a grouping variable and
@@ -4635,8 +5222,8 @@ calculate summaries for the value\_variables given:
 ## # Auto named with `tibble::lst()`: tibble::lst(mean, median)
 ## 
 ## # Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
-## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
-## generated.
+## Call `lifecycle::last_lifecycle_warnings()` to see where this warning
+## was generated.
 \end{verbatim}
 
 \begin{Shaded}
@@ -4672,11 +5259,19 @@ The same code with Galaaz, becomes:
 \NormalTok{  data}\AttributeTok{.}
     \AttributeTok{group\_by\_at}\NormalTok{(grouping\_variables)}\AttributeTok{.}
     \AttributeTok{mutate}\NormalTok{(}\WarningTok{count:} \ConstantTok{E}\AttributeTok{.n}\NormalTok{)}\AttributeTok{.}
-    \AttributeTok{summarise\_at}\NormalTok{(}\ConstantTok{E}\AttributeTok{.c}\NormalTok{(value\_variables, }\StringTok{"count"}\NormalTok{), }\OperatorTok{\textasciitilde{}}\WarningTok{:mean}\NormalTok{, }\WarningTok{na\_\_rm:} \DecValTok{true}\NormalTok{)}\AttributeTok{.}
-    \AttributeTok{rename\_at}\NormalTok{(value\_variables, }\ConstantTok{E}\AttributeTok{.funs}\NormalTok{(}\ConstantTok{E}\AttributeTok{.paste0}\NormalTok{(}\StringTok{"mean\_"}\NormalTok{, value\_variables)))}
+    \AttributeTok{summarise\_at}\NormalTok{(}
+      \ConstantTok{E}\AttributeTok{.c}\NormalTok{(value\_variables, }\StringTok{"count"}\NormalTok{),}
+      \OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:mean}\KeywordTok{]}\NormalTok{,}
+      \WarningTok{na\_\_rm:} \DecValTok{true}\NormalTok{)}\AttributeTok{.}
+    \AttributeTok{rename\_at}\NormalTok{(}
+\NormalTok{      value\_variables,}
+      \ConstantTok{E}\AttributeTok{.funs}\NormalTok{(}\ConstantTok{E}\AttributeTok{.paste0}\NormalTok{(}\StringTok{"mean\_"}\NormalTok{, value\_variables)))}
 \ControlFlowTok{end}
 
-\FunctionTok{puts}\NormalTok{ grouped\_mean((}\OperatorTok{\textasciitilde{}}\WarningTok{:starwars}\NormalTok{), }\StringTok{"eye\_color"}\NormalTok{, }\ConstantTok{E}\AttributeTok{.c}\NormalTok{(}\StringTok{"mass"}\NormalTok{, }\StringTok{"birth\_year"}\NormalTok{))}
+\FunctionTok{puts}\NormalTok{ grouped\_mean(}
+\NormalTok{  (}\OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:starwars}\KeywordTok{]}\NormalTok{),}
+  \StringTok{"eye\_color"}\NormalTok{,}
+  \ConstantTok{E}\AttributeTok{.c}\NormalTok{(}\StringTok{"mass"}\NormalTok{, }\StringTok{"birth\_year"}\NormalTok{))}
 \end{Highlighting}
 \end{Shaded}
 
@@ -4718,8 +5313,9 @@ function-specific arguments.
   (\texttt{git\ checkout\ -b\ my-new-feature})
 \item
   Write tests --- use \textbf{\texttt{bin/run\_rspec}} or
-  \textbf{\texttt{bin/run\_all\_rspec}} with \textbf{JRuby} so JVM flags
-  and the load path match \textbf{\texttt{docs/testing.md}}
+  \textbf{\texttt{bin/run\_all\_rspec}} (JRuby or CRuby via
+  \textbf{\texttt{GALAAZ\_RUBY}}) so the load path matches
+  \textbf{\texttt{docs/testing.md}}
 \item
   Commit your changes
   (\texttt{git\ commit\ -am\ \textquotesingle{}Add\ some\ feature\textquotesingle{}})