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I am trying to install the "rpud" package from the bioconductor:

source("http://bioconductor.org/biocLite.R")
biocLite("rpud")

This executed normally, but then lists several old package dependences, and asks me if I want to update them:

Update all/some/none? [a/s/n]:

Since I am submitting this to a cluster, I will not be able to respond to this prompt. Is there any way to write my script so that it responds "a" to this prompt?

Furthermore, if I respond "a" to the above prompt, I recieve ANOTHER prompt:

Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
'lib = "/opt/linux/centos/7.x/x86_64/pkgs/R/3.2.0/lib64/R/library"' is not writable
Would you like to use a personal library instead?  (y/n)

I also want to response "y" to this.

Thanks!

Lewkrr
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  • `?biocLite` loads the help file for `biocLite` – rawr Nov 14 '15 at 22:03
  • @rawr: I am familiar with the "?" function of R. However, my question is more Linux specific, as I need to shape my ".sh" script to respond to a prompt from R while it is being processed on a remote server. Thanks for taking the time, though :) – Lewkrr Nov 16 '15 at 15:33
  • there are parameters of `biocLite` which are directly related to your question, so that I why I assumed you were not familiar, sorry. – rawr Nov 16 '15 at 19:03

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