Computing

When installing a package using an https URL, you may see this:

> install.packages("mclust", repos="https://cran.cnr.berkeley.edu/")
Installing package into ‘/share/apps/ANTsR/20140930-R3.1.1-lib’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository https://cran.cnr.berkeley.edu/src/contrib:
  unsupported URL scheme

This seems to be an R issue relating to SSL/HTTPS connections. Here's a workaround:

options(download.file.method = "wget")

This will tell R to use the wget command for downloads.

(Thanks to Phil Cook! Updated 4/2017)

Setup in your .bash_profile file:

export PATH=/share/apps/R/<R version>/:$PATH  #note that this may already be defined in .bash_profile, check first

Then on chead

[...]# R

> install.packages("devtools", repos="http://cran.cnr.berkeley.edu/")
> library(devtools)
> install_github("stnava/ITKR")
> install_github("stnava/ANTsRCore")
> install_github("stnava/ANTsR")

NOTE about R_LIBS environment variable:

As of R 3.2, R should create a default location for local libraries (i.e. that you install on your own). Check using the .libPaths() command. It should be something like /home/pcook/R/x86_64-pc-linux-gnu-library/3.2. If you want to install packages somewhere other than the default, you can set R_LIBS.