On Wed, May 11, 2011 at 11:38 AM, Ivan Gregoretti <ivang...@gmail.com>wrote:
> 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. > > Hi, Ivan. This request is from R, itself, and not from the affy package or any other package. If you haven't seen this before, it was probably because a user Library existed previously (you are asked only the first time it is needed) or because the default system package location was writeable by you. See the R manuals for details on library locations if you want more detail. Sean > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
