Hello Jim, First, thank you for responding.
Indeed, the issue is the request to generate a personal library. I use a wide variety of Bioconductor packages, from the most canonical ones like ShortRead to more obscure ones like cosmo, however, no function ever asked me to create a personal library as a condition for execution. Do you regularly encounter functions that make such demand? I am curious. Thank you, Ivan PS: By the way, cosmo rocks. Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA. Phone: 1-301-496-1016 and 1-301-496-1592 Fax: 1-301-496-9878 On Tue, May 10, 2011 at 7:30 PM, James W. MacDonald <jmac...@med.umich.edu> wrote: > Hi Ivan, > > On 5/10/2011 4:41 PM, Ivan Gregoretti wrote: >> >> There seems to be a dependency error that comes up when running an >> analysis with affy. It only takes three commands. >> >> ################################################################### >> library(affy) >> >> Data<- ReadAffy(file="/home/johndoe/GSM492799.CEL.gz") >> >> eset<- rma(Data) >> >> Warning in install.packages(cdfname, lib = lib, repos = >> Biobase:::biocReposList(), : >> 'lib = "/usr/local/lib64/R/library"' is not writable >> Would you like to create a personal library >> ~/R/x86_64-unknown-linux-gnu-library/2.14 >> to install packages into? (y/n) >> ################################################################### >> >> Is this error reproducible by others? > > I don't see an error here. But perhaps you are referring to the warning? > > I'm not sure how it could be made clearer, however. The gist is that you are > running R as non-root (as you should), and therefore don't have write access > to the /usr/local/lib64/R/library, (which you should not), so R is stating > that fact and asking you if you want it to create a personal library in your > home directory, where in future it will look for any packages that aren't > found in the 'usual' place. > > So, long story short, if you had simply typed a 'y' after that warning, you > would have got the package downloaded and gone about your business. > > Best, > > Jim > > >> >> Thank you >> >> Ivan >> >> >> sessionInfo() >> R version 2.14.0 Under development (unstable) (2011-04-14 r55450) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] affy_1.31.1 Biobase_2.13.1 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.21.0 preprocessCore_1.15.0 tools_2.14.0 >> >> >> Ivan Gregoretti, PhD >> National Institute of Diabetes and Digestive and Kidney Diseases >> National Institutes of Health >> 5 Memorial Dr, Building 5, Room 205. >> Bethesda, MD 20892. USA. >> Phone: 1-301-496-1016 and 1-301-496-1592 >> Fax: 1-301-496-9878 >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> Bioc-sig-sequencing@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing