I cant be sure since you are not showing the code that produces the error message but it seems you have included install.packages() commands in your Rmd file. You are not supposed to do that, packages only need to be installed once and if you put those commands there, you are going to be installing them every time you knit a document.
Note: Next time please provide a proper REPRoducible EXample (reprex) illustrating your issue.