[BioC] outdated version of 'affy' in biocLite ?

[Robert Gentleman]

Hi Willem,
   biocLite should be dealing with this in a sensible way. I wonder if 
you could give us a little more information (as requested in the posting 
guide) and in particular the output of sessionInfo().
   Please also note that R 2.4.0 (you leave out this information as 
well) is *not* the current release (www.r-project.org will inform you 
and your system folks that it is R 2.4.1). R releases relatively major 
changes on a six month cycle, with patches (generally worth applying in 
between). Bioconductor's release version tracks R's release version.

You do not have an outdated version of affy, but rather do have the 
version you are supposed to have. The affydata package seems to be the 
one that is in error as it looks to be a version for the devel version 
of Bioconductor. From the download page,
http://bioconductor.org/packages/1.9/bioc/html/affydata.html
you will see that the release version of this package is 1.10.0. Is that 
the version you have? If not, then someone has decided to install an 
updated version of this, without using biocLite (or by one of the 
several ways you can "trick" biocLite).  If your folks revert to the 
correct version of affydata for your system, then I believe that things 
will work.

These packages do have rather intricate dependencies, you cannot simply 
mix and match between bioc release and devel. People that choose to do 
that, must bear all of the burden of finding and fixing these sorts of 
problems.

Please note that today is a holiday in this part of the US, so there is 
no one in, and responses will be a bit slow.

best wishes
   Robert


Talloen, Willem [PRDBE] wrote:
> 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 apparently because of an outdated version of affy (see error message below).
> 
> 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.
> 
> 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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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org