Hello,

I am trying to download VIPER. I downloaded the most up to date version of R. I inputed this:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

and received this:

Bioconductor version 3.9 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installation path not writeable, unable to update packages: boot, foreign,
  KernSmooth, mgcv, nlme

I am on a computer that has adminstrative access and abilities. Please let me know if you know how to fix this bug so I can keep going forward.

Thank you!!!

The message you are getting (presumably you are on Windows?) is simply telling you that you don't have privileges to update the packages that come by default with R. Which, generally speaking, isn't an issue for most people because those packages are pretty stable, having been around since like the late 1990's, and more to the point, most people who use Bioconductor probably don't ever use boot or foreign, or KernSmooth, etc.

Anyway, you haven't actually tried to install viper, which is all lower caps (and given that R is case-sensitive, that matters). You need to do

BiocManager::install("viper")
library(viper)

To use that package.