dear all, The package installation for the R version 2.4 on our Linux server stopped - apparently because of an outdated version of affy (see error message below).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

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 You do not have an outdated version of affy, but rather do have the version you are supposed to have.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' > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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

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 repository). 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 library(Biobase) 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: update.packages(lib.loc=.libPaths()[1], repos=biocReposList(), ask=FALSE) Note that using lib.loc=.libPaths()[1] prevents you from trying to update the system-wide shared packages. Hope this helps... H. > > 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' > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >