title: GitHub displays all code chunks from README.rmd (despite include=FALSE)
body: <p>I am currently writing a documentation for an <a href="https://github.com/environmentalinformatics-marburg/GSODTools" rel="nofollow noreferrer">R package hosted on GitHub</a>. I use <code>knitr</code> along with R Markdown to write the README file. Hitting the 'Knit HTML' button in RStudio produces an HTML like I would expect it.</p>
  <p>However, pushing README.rmd to GitHub results in what you see in the lower page section when following the above link. For example, the topmost code chunk is declared as follows in the README.rmd file:</p>
  <pre><code>```{r global_options, include = FALSE}
  library(knitr)
  options(width = 120)
  opts_chunk$set(fig.width = 12, fig.height = 8, fig.path = 'Figs/',
                 include = TRUE, warning = FALSE, message = FALSE)
  ```
  </code></pre>
  <p>However, the <code>include = FALSE</code> statement in the first line of code is simply ignored in this case, and the piece of code that was supposed to be hidden is displayed on the referring GitHub page. In addition, results (e.g. from <code>plot()</code>, <code>head()</code>) are not visualized although <code>opts_chunk$set(..., include = TRUE)</code>.</p>
  <p>Did anyone encounter a similar problem and can me help me get my README document displayed correct, i.e. in the way RStudio would handle it, on GitHub?</p>