[BioC] Installing Bioconductor on Linux...

Martin Morgan mtmorgan at fhcrc.org
Mon Oct 4 04:29:44 CEST 2010

Hi James --

On 10/03/2010 06:36 PM, James Carman wrote:
> I've got Bioconductor successfully installed on my linux workstation
> at work, but we need to install it on our server.  I remember it being
> particularly difficult to make sure I had all the right packages
> installed in the O/S.  Is there an easier way?

Others will have different suggestions, but my two cents...

(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.

(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.

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.

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.


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