Wondering how everyone is currently using Rsamtools in the newest version of R. 

Getting the following:

> install.packages("Rsamtools")
Warning in install.packages :
  package ‘Rsamtools’ is not available (for R version 3.4.1)

It's a Bioconductor package so 

source("https://bioconductor.org/biocLite.R")
biocLite("Rsamtools")

as described on the package landing page https://bioconductor.org/packages/Rsamtools

That's not the newest version of R. The current version is R-3.4.3. In addition, that's not how you install Bioconductor packages.