I see. Thank you. Ivan
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 Wed, May 11, 2011 at 11:54 AM, Sean Davis <sdav...@mail.nih.gov> wrote: > > > 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 > > _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
