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

Wed May 11 20:51:14 CEST 2011

Hello Martin,

When I do annotation(Data) I get the response

"mouse4302"

What would you do now?

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 1:29 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 05/11/2011 08:54 AM, Sean Davis 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
>
> Actually, rma needs the cdf package corresponding to the chip, and calls
> getCdfInfo and eventually cdfFromBioC if it is not installed. This is
> apparently determined by getOption("BioC")$affy$probesloc, but this is not
> well-documented (which is an understatment). A work-around would make sure
> the package (from annotation(Data)) is installed before calling rma(), and
> then you'd at least have more control over what to do if prompted.
>
> just.rma is a (much) more memory efficient approach if the goal is to arrive
> directly at an ExpressionSet without needing the AffyBatch.
>
> Martin
>
>> 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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>>
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>
>
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