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!)

Setup in your .bash_profile file:

export PATH=/share/apps/R/R-3.2.3/:$PATH  #note that this may already be defined in .bash_profile, check first

export R_LIBS=/home/pcook/R/x86_64-unknown-linux-gnu-library/3.2

Then on chead

[...]# R

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