[BioC] SomaticSignatures

[Steve Lianoglou]

On Thu, Mar 27, 2014 at 1:39 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
[snip]
>>
>> Why is installing it via `biocLite('SomaticSignatures')` out of the
>> question here? You obviously have access to an internet connection --
>> you are sending email and downloading the dependent packages by hand
>> --
>> so, why don't you just install it that way?
>
> I think the machine in question (a cluster?) has no direct access to the internet, so packages
> must be downloaded to some other machine and then copied there.

I see.

>
> Though usually we direct people in the opposite direction, this StackOverflow post may help:
>
> https://stackoverflow.com/questions/19268515/installing-bioconductor-without-internet/19269962#19269962
>
> If the machine that has internet and the machine that doesn't are similar enough and have the same libraries installed, this could work. You could also create your own internal CRAN and BioC mirrors though this may be overkill, but our mirror page will provide more info:
>
> http://www.bioconductor.org/about/mirrors/mirror-how-to/

An altertnative would be to "cheat" and follow along with what Vincent did.

You could start on your own machine w/ a brand new empty R-3.1-alpha install.

Then do:

R> source('http://bioconductor.org/biocLite.R')
R> biocLite('SomaticSignatures')

You will then see all of the packages that were downloaded to satisfy
the dependency tree required for the installation (here are just three
of them that Vincent required):

"""
trying URL 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz'
Content type 'application/x-gzip' length 153373 bytes (149 Kb)
opened URL
==================================================
downloaded 149 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz'
Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb)
opened URL
==================================================
downloaded 1.7 Mb

trying URL '
http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMethods_1.53.4.tar.gz
'
"""

Now you have the packages required (here he needed gridBase, NMF and
pcaMethods) *as well as* the URLs required to download them.

Go back and pull out all of the URLs

Download the packages.

Move them over to your cluster.

Then install by the command line as you like *into R-3.1-alpha*

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech