selecting CRAN mirror from remote device

问题

I am running jobs remotely, and the cluster I am running it on does not have the R package I require. I have tried to install it using:

if(!require(hglm)){install.packages("hglm");require(hglm)}

and realise that I am required to select a CRAN mirror. I tried adding:

selectCRANmirror()

to the script, but received the error message, cannot select CRAN mirror non-interactively.

I then tried adding:

selectCRANmirror(ind=72)

as this is what I would use on my local computer to set the CRAN mirror to UK(St. Andrews), but this generates the error message:

Error in chooseCRANmirror(ind = 72) : unused argument(s) (ind = 72)

I was wondering if anyone could explain how to select the CRAN mirror on a remote device?

I amended my script to include the line suggested:

if(!require(hglm)){install.packages("hglm",repos="http://cran.us.r-project.org")

replacing with "http://star-www.st-andrews.ac.uk/cran" (St. Andrews mirror) and received the following message (I have included preceding scripts to help illuminate where the problem lies):

setwd("~/lustre2/s0784669")
load("df1QCMAF.RData")
.libPaths('~/RLibrary')
if(!require(GenABEL)){install.packages("GenABEL");require(GenABEL)}
#Loading required package: GenABEL
#Loading required package: MASS
#GenABEL v. 1.7-6 (May 16, 2013) loaded
if(!require(hglm)){install.packages("hglm",repos="http://star-www.st-andrews.ac.uk/cran");require(hglm)}
#Loading required package: hglm
#Installing package(s) into '/export/users/s0784669/RLibrary'
#(as 'lib' is unspecified)
#Warning: unable to access index for repository http://star-www.st-andrews.ac.uk/cran/src/contrib

I have tried:

library(RCurl)
url.exists("http://star-www.st-andrews.ac.uk/cran")

to ascertain internet access on the cluster and received the following message:

library(RCurl);
#Loading required package: bitops
url.exists("star-www.st-andrews.ac.uk/cran")
#[1] FALSE 

Suggesting no internet access. So would I have to access source code? And is this accessible?

回答1:

Per ?install.packages:

repos character vector, the base URL(s) of the repositories to use, e.g., the URL of a CRAN mirror such as "http://cran.us.r-project.org".

So do something like install.packages("hglm", repos="http://cran.us.r-project.org"). Insert the url to St Andrews instead.

来源：https://stackoverflow.com/questions/17924447/selecting-cran-mirror-from-remote-device