[BioC] outdated version of 'affy' in biocLite ?

hpages at fhcrc.org hpages at fhcrc.org
Tue Jan 16 01:53:02 CET 2007

Quoting "Talloen, Willem [PRDBE]" <WTALLOEN at PRDBE.JNJ.COM>:

> dear all,
> The package installation for the R version 2.4 on our Linux server stopped -
> apparently because of an outdated version of affy (see error message below).

Hi Willem,

The version of affy you have (probably 1.12.*) is the expected
version for BioC-1.9/R-2.4 users but you seem to have the devel
version of affydata (1.11.1) which itself requires the devel version
of affy.
You didn't do anything wrong: biocLite() is catching the wrong version
of affydata for BioC-1.9/R-2.4 users. I've just fixed the problem (last
week I inadvertendly dropped affydata devel in the 1.9/data/experiment
Please re-install affydata with biocLite(): you should now catch
the correct version (1.10.0).
Thanks for reporting this and sorry for the inconvenience.

> A more general question - has anybody an helpful suggestion how to maintain
> R and its BioC packages on a server? Our informaticians are getting annoyed
> with our frequent questions about adding or updating packages, and also with
> the dependencies between versions of the different packages. I thought to
> apply BiocLite more routinely now that we are switching to 2.4, but this
> -again- doesn't work out as smoothly as we hoped it to be.

If R is installed at the system level, I can suggest this (not really tested):

  1. Install and update a group of system-wide shared packages (as root):

    - run biocLite() (with no argument) or biocLite(groupName='all')
      only once (after a fresh install of R)

    - run
        update.packages(repos=biocReposList(), ask=FALSE)
      on a regular basis (e.g. 1/week).

  2. Each user can administrate its own group of extra packages:

    - define your personal R library folder with (from the shell):
        mkdir ~/Rlibs
        export R_LIBS=~/Rlibs

    - use biocLite() to install packages that are not found system-wide
      (by default, biocLite will install them in your ~/Rlibs)

    - update packages in your ~/Rlibs on a regular basis:
      Note that using lib.loc=.libPaths()[1] prevents you from
      trying to update the system-wide shared packages.

Hope this helps...


> thanks in advance,
> Willem 
> error message;
> Loading required package: affy
> Loading required package: Biobase
> Loading required package: tools
> Loading required package: affyio
> Loading required package: affydata
> Error: package 'affy' 1.12.2 is loaded, but >= 1.13.9 is required by
> 'affydata'
> Execution halted
> cat: write error: Broken pipe
> ERROR: execution of package source for 'affyPLM' failed
> ** Removing
> '/dvl/bix/pkgs/r-project.org/R/2.4.1_64/bioconductor/lib64/affyPLM'
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