From you original post, it looks like RStudio tries to load from its own mirror version of CRAN:
Warning in install.packages :
unable to access index for repository https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6:
cannot open URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
so maybe there an issue there? I'm not sure, but am glad you discovered a workaround!