[BioC] SomaticSignatures

Thu Mar 27 23:10:15 CET 2014

So, to wrap this all up for the OP.

To identify the packages needed for installation of SomaticSignatures,
 you will need to be running R-3.1-alpha on an internet connected
machine and enter these commands:

library(tools)
library(utils)
library(BiocInstaller)
pdb <- available.packages(contrib.url(biocinstallRepos()))
pkgs <- unlist(unname(package_dependencies("SomaticSignatures", db=pdb)))

Then to download the packages into the *current working directory*
that R is executing in, he would then do:

download.packages(pkgs, '.', repos=biocinstallRepos(), type="source")

These copies could then be copied to the cluster and will have to be
installed individually (ensuring that the cluster already has
R-3.1-alpha already installed!).

The OP will have to be careful to install them in the correct order,
which might require some trial and error, but at least all of the
packages will be available on the filesystem to do so.

OP: let us know how that goes.

On a side note: that's pretty cool! Perhaps parts of this would make
handy utility functions in the BiocInstaller package ... I could
imagine a function to "identify dependent packages" being useful.

-steve

On Thu, Mar 27, 2014 at 2:01 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
>
> ----- Original Message -----
>> From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
>> To: "Steve Lianoglou" <lianoglou.steve at gene.com>
>> Cc: "Huma Asif" <humaasif79 at yahoo.com>, "bioconductor at r-project.org list" <bioconductor at r-project.org>
>> Sent: Thursday, March 27, 2014 1:59:27 PM
>> Subject: Re: [BioC] SomaticSignatures
>>
>>
>>
>> ----- Original Message -----
>> > From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
>> > To: "Steve Lianoglou" <lianoglou.steve at gene.com>
>> > Cc: "Huma Asif" <humaasif79 at yahoo.com>, "bioconductor at r-project.org
>> > list" <bioconductor at r-project.org>
>> > Sent: Thursday, March 27, 2014 1:49:13 PM
>> > Subject: Re: [BioC] SomaticSignatures
>> >
>> >
>> >
>> > ----- Original Message -----
>> > > From: "Steve Lianoglou" <lianoglou.steve at gene.com>
>> > > To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
>> > > Cc: "Huma Asif" <humaasif79 at yahoo.com>,
>> > > "bioconductor at r-project.org
>> > > list" <bioconductor at r-project.org>
>> > > Sent: Thursday, March 27, 2014 1:45:18 PM
>> > > Subject: Re: [BioC] SomaticSignatures
>> > >
>> > > 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.
>> > >
>> >
>> > A trick I learned from Martin yesterday may help with this step
>> > (eliminating the need to know URLs):
>> >
>> > library(BiocInstaller)
>> > download.packages(c("SomaticSignatures", "gridBase", "NMF",
>> > "pcaMethods"),
>> > repos=biocinstallRepos(), type="source")
>> >
>> > This will download all the source package tarballs to your current
>> > directory.
>> >
>> > As Steve and Vince point out, your actual list of packages that
>> > you'd
>> > need to download would be longer.
>> >
>> > I think there is another trick to tell you the recursive
>> > dependencies
>> > of a package, but I don't know if off the top of my head.
>>
>> Here it is:
>>
>> library(BiocInstaller)
> #oops, you need to do this here:
> library(tools)
> library(utils)
>
> Dan
>
>> pdb <- available.packages(contrib.url(biocinstallRepos()))
>> pkgs <- unlist(unname(package_dependencies("SomaticSignatures",
>> db=pdb)))
>>
>> Then use pkgs as the first argument to download.packages() above.
>> Dan
>>
>>
>> >
>> > Dan
>> >
>> >
>> > > 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
>> > >
>> >
>> > _______________________________________________
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>> >
>>
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>>
>
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-- 
Steve Lianoglou
Computational Biologist
Genentech