[BioC] DEseq version and R version compatibility

Steve Lianoglou mailinglist.honeypot at gmail.com
Thu Oct 4 16:40:20 CEST 2012


On Thu, Oct 4, 2012 at 9:41 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Thu, Oct 4, 2012 at 9:30 AM, José Luis Lavín <jluis.lavin at unavarra.es> wrote:
>> Hello Sean,
>> The main problem with updating the R version of the servers is that I'm not
>> the SysAdmin, and he told me that they couldn't update it at the moment
>> because they have some processes and pipelines that need the old R version
>> (2.13), so he can't update it (weird, isn't it?). That's why I was looking
>> for such strange compatibility...
>> Anyway, due to my current low level on R scripting, when I come across a
>> command that isn't functional I don't really know what to do but trying to
>> use another manual version hoping the code there will fix it...but I've had
>> no luck with that at the moment. That's why I asked about this.
>> I'll keep trying to make DEseq work, but I begin to feel stupid, reading
>> everybody seems to be able to run it except myself.
> If you have a good relationship with your sysadmin, ask him/her to
> help you to install R in your home directory.  This is not hard to do
> (hopefully, for a sysadmin) and will allow you to run a different
> version of R than that already installed on the system.  Really, doing
> this will be much better than copying code from various versions of
> packages to "just make it work".

In fact, I bet you can do it w/o a sysadmin. Let's assume your
username is `jose`

(1) Log into your compute server
(2) cd ~ ## you're likely already there

Create directories to put the source code in as well as the compiled R
(3) mkdir tmp
(4) mkdir -p R/R-2.15 ## R will be installed here

Let's get the source code and put it into `tmp`
(5) cd tmp

Get the code with `curl` or `wget` (whichever your system has)
(6a) curl -O http://cran.r-project.org/src/base/R-2/R-2.15.1.tar.gz
## or ##
(6b) wget http://cran.r-project.org/src/base/R-2/R-2.15.1.tar.gz

Open it up, configure, compile, install
(7) tar xvfz R-2.15.1.tar.gz
(8) cd R-2.15.1

## This is where you tell it where to install the new version of R
## Since it is in your home directory, your sysadmin doesn't need to be there
## and it won't affect anybody else's stuff
(9) ./configure --prefix=/home/jose/R/R-2.15
(10) make && make install

... now you wait a while until it's all done ...

Start R:
(11) ~/R/R-2.15/bin/R

biocLite() your packages and have fun.

You may want to add /home/R/R-2.15/bin to your PATH -- you can ask
your sysadmin how to do that, if you like ;-)


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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