title: Rmarkdown not outputting results of system command to html file
body: <p>I'm new to using Markdown, and have looked for a similar problem to this on SO without success. I'm using Rmarkdown (with Rstudio and knitr) to write a vignette that describes reading in a datafile which is imported as part of the package.  I can correctly access the datafile using </p>
  
  <pre><code>&gt; system.file("extdata", "Marlin-tag38606.txt", package = "xtractomatic")
  </code></pre>
  
  <p>I want to show the first few lines of this file in the vignette, so my code reads</p>
  
  <pre><code>```{r, results=as.is}
  
  datafile &lt;- system.file("extdata", "Marlin-tag38606.txt", package = "xtractomatic")
  
  system(paste("head -n5 ",datafile))
  
  ```
  </code></pre>
  
  <p>The problem is that the results of this call are output to the Rmarkdown console and NOT to the vignette html file. </p>
  
  <p>The output in the Rmarkdown window of RStudio is (but formatted nicer): </p>
  
  <pre><code> |...................                                              |  29%
  label: unnamed-chunk-8
  date    lon lat lowLon  higLon  lowLat  higLat
  4/23/2003   203.899 19.664  203.899 203.899 19.664  19.664
  4/24/2003   204.151 19.821  203.912597  204.389403  18.78051934 20.86148066
  4/30/2003   203.919 20.351  203.6793669 204.1586331 18.79728188 21.90471812
  5/1/2003    204.229 20.305  203.9943343 204.4636657 18.90440013 21.70559987
    |....................                                             |  31%
  </code></pre>
  
  <p>Which is what I wanted outputted to the vignette text, but it is not there.  Within the resulting vignette all I have is the two lines of R code, but not the output from the system call. 
  Any advice would be appreciated. Thanks. </p>
  
  <p>Cara Wilson</p>