[Bioc-sig-seq] Package affy and its depencies

[Ivan Gregoretti]

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 <sdavis2 at mail.nih.gov> wrote:
>
>
> On Wed, May 11, 2011 at 11:38 AM, Ivan Gregoretti <ivangreg at 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 at 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 at 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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>
>