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

Martin Morgan mtmorgan at fhcrc.org
Wed May 11 21:29:01 CEST 2011 

On 05/11/2011 12:19 PM, Ivan Gregoretti wrote:
> Well, if I do annPkgName(annotation(Data)), I get
>
> "mouse4302.db"

My mistake; I think you want cleancdfname(cdfName(Data)). Martin

>
> 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
>>>>>>
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-sig-sequencing mailing list
>>>>> Bioc-sig-sequencing at r-project.org
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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
>>


-- 
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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