testing.Rnw

\section{Package unit testing}

\begin{frame}
  \begin{block}{How to test the code in your package?}
    Or how to make sure that changes in your code do not break existing functionality?
    \begin{itemize}
      \item Implicitely, documentation examples and a vignette do some tests.
      \item Using \R's built-in testing, that runs some code and compares the output to a saved template.
      \item Specific packages for unit testing: 
        \Rpackage{RUnit}\footnote{\url{http://cran.r-project.org/web/packages/RUnit/index.html}} or 
        \Rpackage{testthat}\footnote{\url{http://cran.r-project.org/web/packages/testthat/index.html}}.
    \end{itemize}
  \end{block}
\end{frame}

\begin{frame}{Using an \texttt{.Rout.save} file}
  \begin{block}{In \texttt{package/tests/}}
    Create
    \begin{itemize}
      \item \texttt{mytest.R} with code to be tested
      \item \texttt{mytest.Rout.save} with the reference output
    \end{itemize}
    When \texttt{check}ing your package \R will
    \begin{enumerate}
      \item execute the code in \texttt{mytest.R}
      \item save the output to \texttt{mytest.Rout}
      \item compare \texttt{mytest.Rout} to \texttt{mytest.Rout.save}
      \item report any differences
    \end{enumerate}
  \end{block}
\end{frame}

\begin{frame}{Using \Rpackage{testthat}}
  \begin{block}{Test individual expression}
    \texttt{expect\_that(object\_or\_expression, condition)} with conditions 
    \begin{description}
    \item[equals] \texttt{expect\_that(1+2,equals(3))} or \texttt{expect\_equal(1+2,3)}
    \item[gives\_warning] \texttt{expect\_that(warning("a"), gives\_warning())}
    \item[is\_a] \texttt{expect\_that(1, is\_a("numeric"))} or \texttt{expect\_is(1,"numeric")}
    \item[is\_true] \texttt{expect\_that(2 == 2, is\_true())} or \texttt{expect\_true(2==2)} 
    \item[matches] \texttt{expect\_that("Testing is fun", matches("fun"))} or 
      \texttt{expect\_match("Testing is fun", "f.n")}
    \item[takes\_less\_than] \texttt{expect\_that(Sys.sleep(1),takes\_less\_than(3))}
    \item[...]
    \end{description}
  \end{block}
\end{frame}


\begin{frame}[fragile]{Using \Rpackage{testthat}}
  \begin{example}
<<testthat1,echo=TRUE,tidy=FALSE>>=
library(sequences)
library(testthat)
a <- new("DnaSeq",sequence="ACGTaa")
test_that("ok test", { 
  expect_equal(length(a),6)
  expect_true(seq(a)=="ACGTAA")
  expect_is(a,"DnaSeq")
})
expect_true(seq(a)=="ACGTaa")
@ 
  \end{example}
\end{frame}