[BioC] Installing Bioconductor on Linux...

[James Carman]

Replies in-line:

On Sun, Oct 3, 2010 at 10:29 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>
> (1) Probably the way to proceed is to install R and biocLite() packages
> as 'root' or similarly privileged account. Base and commonly used
> packages will be stored in a system-wide location. Individual users
> requiring additional packages will say biocLite("OtherPackage") and
> these will be installed in their own user directory as described in
> ?install.packages (which is what biocLite uses to install packages):
>
>     If 'lib' is omitted or is of length
>     one and is not a (group) writable directory, the code offers to
>     create a personal library tree (the first element of
>     'Sys.getenv("R_LIBS_USER")') and install there.
>

R is quite easy to install on my Redhat linux machine (I run Fedora,
but our servers are RHEL4).  I just did "yum install R" I believe.

> (2) 'Third party' dependencies need to be satisfied in a rational way,
> remembering (a) that R packages have complex dependencies with other R
> packages, and (b) R compiles C (and other) source code and so requires
> header files associated with third party libraries. Combining these, one
> can imagine biocLite("biomaRt") failing because XML fails because RCurl
> fails because the *devel* libcurl (devel required for the curl headers)
> is not installed. This will be indicated in the output of biocLite, but
> will require patient inspection of the output to see this. Part of the
> third party installation process may mean evaluating standard Linux
> commands (e.g., /sbin/ldconfig), setting environment variables
> (LD_LIBRARY_PATH ?), and under worst-case scenarios (Rmpi comes to mind)
> inspecting the R package configure.in / configure.ac script (by
> downloading the source package from CRAN or Bioconductor) to understand
> what the requirements are and how they are supposed to be satisfied.
>

This is my main concern, the libraries that Bioconductor needs to be
installed in the operating system.  So, there's no one-shot method of
getting this done, eh?  I basically need to see what it complains
about and then figure out how to satisfy the dependency?

> A final comment is that the next version of R is about to be released
> (scheduled October 15 for R, Oct 18 for Bioconductor), so if you're only
> going to get one opportunity to sit down with your system administrator
> you might want to delay for a couple of weeks. On the other hand it's a
> learning experience and much easier the second time.
>

Very cool!  Updating R isn't really that tough.  It should happen with
a "yum update".  Hopefully the Bioconductor dependencies won't change
much so that the upgrade path for it is easy too.

> The Bioconductor team is interested in developing, over the next year or
> so, a more fool-proof way of distributing Bioconductor, so I encourage
> others to contribute their solutions and experiences.
>

This would be a great for us linux geeks! :)  It installed just fine
on my windoze box at home.  No worries there.

Thank you for your insights!  I'll keep plugging away at it.