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

Ivan Gregoretti ivangreg at gmail.com
Wed May 11 21:19:44 CEST 2011


Well, if I do annPkgName(annotation(Data)), I get

"mouse4302.db"

Now, even though I do library(mouse4302.db), I still get the same
cdfname warning.

This behaviour seems not to be new:
https://stat.ethz.ch/pipermail/bioconductor/2009-January/025787.html

In case anybody is interested, here is the link to the CEL file:
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM492nnn/GSM492799/GSM492799%2ECEL%2Egz

So, I am not quite there yet.

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 2:59 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 05/11/2011 11:51 AM, Ivan Gregoretti wrote:
>>
>> Hello Martin,
>>
>> When I do annotation(Data) I get the response
>>
>> "mouse4302"
>>
>> What would you do now?
>
> maybe
>
> library(annotate)
>
> pkg <- annPkgName(annotation(Data))
> ok <- require(pkg, character.only=TRUE)
> if (!ok)
>    stop(pkg, " not found; install using biocLite?")
>
>> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-sig-sequencing mailing list
>>>>> Bioc-sig-sequencing at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>>
>>>>
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>>>>
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>>>
>>>
>>> --
>>> Computational Biology
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>>
>>> Location: M1-B861
>>> Telephone: 206 667-2793
>>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>



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