Nobody cites every package they use, it's not feasible. I use a lot of packages, and some journals have a limit on the number of citations you can have. I only cite packages when it provides specialized statistical functionality.

For example, I do a lot of work with data from complex surveys, and I always cite Lumley's survey package because without it I wouldn't be able to do the work. On the flip side, I use Hadley's readr package extensively because I think his I/O functions are more sane than the defaults. I'm not going to cite readr in every paper I write just because I'm too lazy to type stringsAsFactors = FALSE when I read a csv file.

Our genomics workflows use dozens of packages even before I get the data and start really doing analysis, statistics, and plots. It's just not feasible to cite every bit of code we use (though we certainly point people to the higher level routines, which they can use to see what was run/how to reproduce the results).