First of all, please show what packages are you using in your code (dplyr, scales).

There's a boost module for highcharts. sadly rCharts dont include that module by default so you need to add manually.

By other hand. There is a new wrapper for highcharts called highcharter which have an implementation of this module. Using it dont take more than 1 second to chart the 3900 columns.

highchart2() %>% 
  hc_title(text = "Not so slow chart ;)") %>% 
  hc_subtitle(text = "Thanks boost module") %>% 
  hc_chart(zoomType = "x", animation = FALSE, type = "column") %>% 
  hc_plotOptions(series = list(turboThreshold = 4000)) %>% 
  hc_add_serie(data = input)

Check the speed/here:

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