Going from an old version of to a new version R

My old mac had a breakdown and I had to download a new version of R. Everytime I try to install packages I keep getting error messages. Additionally, when I open rmd. files it won't allow me to knit anymore. I'm not sure if it's because I worked on those files in an older version of R.

For instance:

The message after library(dplyr) is not an error message. It is informing you that dplyr has some functions that have the same name as other functions. For example, there is a filter() function in both dplyr and stats. The dplyr function will be run if you call filter(), because dplyr was loaded after stats. If you want to use the function is stats, run stats::filter(). This is all normal.

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