[Bioc-sig-seq] Package affy and its depencies
Martin Morgan
mtmorgan at fhcrc.org
Wed May 11 20:59:53 CEST 2011
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
>>>>
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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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