[BioC] Installing Bioconductor on Linux...

James Carman james at carmanconsulting.com
Mon Oct 4 13:59:28 CEST 2010

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.

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