[BioC] SomaticSignatures

Steve Lianoglou lianoglou.steve at gene.com
Mon Mar 24 17:22:39 CET 2014

Hi Huma,

First: please keep all correspondence on-list (by replying with 
"Reply-All") so that other can help as well as benefit from discussion.

Other comments inline:

On 24 Mar 2014, at 6:32, Huma Asif wrote:

> hi,
> i have read that just but i have to get my machine ready first so i 
> can apply the instruction in that 
> i am doing this and got this message
> Warning messages:
> 1: package ‘SomaticSignatures’ is not available (for R version 
> 3.0.3) 

It looks like this package is only available in bioc-devel, which has 
not been released yet.

How would you have known?

It will be released sometime in April (I believe) after R-3.1.x is 
released. In order for you to install SomaticSignatures via biocLite, 
you have to first install the current development version of R-3.1.

> 2: installed directory not writable, cannot update packages 'foreign',
>   'KernSmooth', 'rpart', 'spatial'

It also looks like you are running R as a user who does not have rights 
to install into the default package directory. You can either run R as 
administrator account, or setup a package directory in your home 
directory that R can use "on top of" the default install. To figure out 
how to do that, google "r_libs_user"



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