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

[Ivan Gregoretti]

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
<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