[R] Question about citing R packages in an academic paper

[Dr. Mehdi Dadkhah]

Hi,
I hope you are doing well!

I have a question. I and my colleagues wrote a paper by using R language and its packages. We also used some tutorials. We have words count limitation for our paper. In early version of paper, I cited all packages in the reference list of paper (my paper will be published in an academic journal). After that, we had to keep references to tutorials in the reference list and remove reference to R and its packages (I strictly should fit paper to 2000 words). We created an online appendix and listed all packages which we used. Some packages are related to paper. For example, when i used command 'citation()'  in R console for package "tidytext", R informed me that i should cite such package as this:


Silge, J., & Robinson, D. (2016). tidytext: Text Mining and Analysis Using Tidy Data Principles in R. JOSS, 1(3). https://doi.org/10.21105/joss.00037

Now, all packages and their related papers are not in the reference list of paper, but they will be available in an online appendix in the journal website. Is such practice OK or should I cite all packages in the reference list?
I attached online appendix. We will submit our paper to a journal soon.
Should I cite papers which are related to packages in the reference list? if I do not cite, i will face with permission problem regard to usage of package?

Many thanks!
With best regards,


Dr. Mehdi Dadkhah