dplyr: "Error in n(): function should not be called directly"

I presume you have dplyr and plyr loaded in the same session. dplyr is not plyr. ddply is not a function in the dplyr package.

Both dplyr and plyr have the functions summarise/summarize.

Look at the results of conflicts() to see masked objects.

As mentioned by the previous answer, you may have a conflict between plyr and dplyr. You can to run this command to unload the plyr package.

detach("package:plyr", unload=TRUE) 

Then you can continue as expected.

library(dplyr) 
...
summarise(n = n()) 

To avoid confusions with masking functions, it is clear to use the "package::function" specification, like example below:

delay <- dplyr::summarise(by_tailnum, 
  count = n(), 
  dist = mean(distance, na.rm = TRUE), 
  delay = mean(arr_delay, na.rm = TRUE))