Issue with installation and updating packages

[mishabalyasin]

I'm not familiar with how process works with Anaconda, so don't have any good advice there. In general, installing R on it's own tends to be fairly uneventful. One thing that you've came across is that current version (3.5.0) changed quite a few things, so not all packages updated yet. I would recommend for now to use 3.4.4 (previous version).

Also, just to make sure we are on the same page, RStudio and R are not the same thing. So, when you say that you've updated RStudio to the latest version you probably mean R. This thread should help:

Differentiating R from RStudio

Aside: goals for this thread

I'm hoping this will help people disambiguate R from RStudio, and also help with getting questions in the right category. This is a bit of a mashup of the times I've tried to explain this in individual threads, so please feel free to add to this topic for further clarification/point out corrections, etc.

Before putting a code-related question in the #rstudio-ide category or using the rstudio tag, it's helpful to ask yourself: Does this work in the regular R GUI, but not when you're in RStudio? If you're using RStudio, you're using R — RStudio is just an IDE (Integrated Development Environment) in which you are using the R language. (On of my favourite fi…

Finally, are you sure that knitr is telling you to install pdflatex? I've checked my installation and I don't have this package and I can assure you that I'm using knitr quite a bit without it.