Hi
Is there any other way to install Somatic signature if not via biocLite
Do you  means i have to wait till April to use this Package.
Though i have downloaded and unzip the package but dont know how to proceed next.
in document it says
The starting point of the analysis is a VRanges object which describes the somatic variants in terms of their genomic locations as well as reference and alternative alleles



so do i need to install VariantAnnotation  also 
Sorry if it sounds stupid 
Huma



>________________________________
> From: Steve Lianoglou <lianoglou.steve@gene.com>
>To: Huma Asif <humaasif79@yahoo.com> 
>Cc: "bioconductor@r-project.org list" <bioconductor@r-project.org> 
>Sent: Monday, March 24, 2014 1:33 PM
>Subject: Re: [BioC] SomaticSignatures
> 
>
>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
>(R-3.1)"
>
>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:
>
>http://www.bioconductor.org/packages/devel/bioc/html/SomaticSignatures.html
>
>This doesn't:
>
>http://www.bioconductor.org/packages/release/bioc/html/SomaticSignatures.html
>
>
>HTH,
>
>-steve
>
>
>
>On Mon, Mar 24, 2014 at 9:22 AM, Steve Lianoglou
><lianoglou.steve@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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>> Search the archives:
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>
>
>
>-- 
>Steve Lianoglou
>Computational Biologist
>Genentech
>
>
>
>
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