[BioC] SomaticSignatures

Steve Lianoglou lianoglou.steve at gene.com
Mon Mar 24 17:33:58 CET 2014

Woops, meant to expand on the "how would you have known" (that this
package is only available in bioc-devel) bit before hitting send.

There are two things that would have clued you into that fact:

First, on the package page, under the "Details" section, there is a
row that says "In Bioconductor since", with a value of "BioC 2.14

btw, the current version of bioconductor is bioc 2.13 (which is tied
to R-3.0.x (the "announcement" message you get when  you load the
"BiocInstaller" package should tell you the version of bioconductor it
thinks you are using)).

Also, the URL for the package only works with "devel" in it, instead
of "release".

This works:


This doesn't:




On Mon, Mar 24, 2014 at 9:22 AM, Steve Lianoglou
<lianoglou.steve at gene.com> wrote:
> 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"
> HTH,
> -steve
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Steve Lianoglou
Computational Biologist

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