On Wed, May 11, 2011 at 11:38 AM, Ivan Gregoretti <ivangreg@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
> <jmacdon@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
>
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