I have been using Knitr via R-Studio, and think it is pretty neat. I have a minor issue though. When I source a file in an R-Chunk, the knitr output includes external comments as follows:

+ FALSE Loading required package: ggplot2
+ FALSE Loading required package: gridExtra
+ FALSE Loading required package: grid
+ FALSE Loading required package: VGAM
+ FALSE Loading required package: splines
+ FALSE Loading required package: stats4
+ FALSE Attaching package: 'VGAM'
+ FALSE The following object(s) are masked from 'package:stats4':

I have tried to set R-chunk options in various ways but still didn't seem to avoid the problem:

```{r echo=FALSE, cache=FALSE, results=FALSE, warning=FALSE, comment=FALSE, warning=FALSE} 
source("C:/Rscripts/source.R");

```

My best solution on R Markdown was to create a code chunk only to load libraries and exclude everything in the chunk.

{r results='asis', echo=FALSE, include=FALSE,}
knitr::opts_chunk$set(echo = TRUE, warning=FALSE)
#formating tables
library(xtable)

#data wrangling
library(dplyr)

#text processing
library(stringi)

```{r results='hide', message=FALSE, warning=FALSE}
library(RJSONIO)
library(AnotherPackage)
```