[Bioc-sig-seq] Package affy and its depencies
Martin Morgan
mtmorgan at fhcrc.org
Wed May 11 19:29:36 CEST 2011
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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