[BioC] affylmGUI/biocReposList() Problem

[Dan Tenenbaum]

It looks like affylmGUI (maintainer CC'd) still has a lot of calls to
Biobase:::biocReposList() which is indeed a defunct function. It
should use BiocInstaller biocinstallRepos() instead.

Dan


On Thu, Jul 5, 2012 at 2:47 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
> Hi Burkhard,
>
> Well, that all looks OK. So the next likely culprit is affylmGUI itself.
> Since you are not getting the gene symbols, it would be reasonable to assume
> that affylmGUI is trying to download and install the correct annotation
> package.
>
> You don't say what chip data you are analyzing, so I can't give much more
> than a generalized pointer. If it is an old-school 3'-biased chip (like the
> HG-U133 plus 2 chip), then you can usually get really close to the right
> name by just reducing to lower case and removing all punctuation, then
> adding a .db, so e.g, hgu133plus2.db is the annotation package. If you are
> using a Gene ST package, then you want to do the same, but add
> transcriptcluster.db. So e.g., the HuGene 1.0 ST chip annotation package is
> the hugene10sttranscriptcluster.db.
>
> So try installing the correct annotation package first, then do your
> analysis. See if that helps.
>
> Best,
>
> Jim
>
>
>
> On 7/5/2012 4:54 PM, Burkhard Heil wrote:
>>
>> Hi Jim,
>>
>> Thanks for your quick reply. Here is the Output of sessionInfo:
>>
>>
>> sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] tcltk     stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] affylmGUI_1.30.0   affyio_1.24.0      affy_1.34.0
>> Biobase_2.16.0
>> [5] BiocGenerics_0.2.0 limma_3.12.1       stringr_0.6
>>
>> loaded via a namespace (and not attached):
>> [1] BiocInstaller_1.4.7   plyr_1.7.1            preprocessCore_1.18.0
>> [4] zlibbioc_1.2.0
>> Cheers
>> Burkhard
>>
>>
>> On 05.07.2012, at 21:05, "James W. MacDonald"<jmacdon at uw.edu>  wrote:
>>
>>
>>> HI Burkhard,
>>>
>>> On 7/5/2012 9:24 AM, Burkhard Heil wrote:
>>>>
>>>> Hi everybody,
>>>>
>>>> when trying to calculate the Toptable in affylmGUI there pops the
>>>> following error message up:
>>>>
>>>> Error: The biocReposList() function is defunct. Please use biocLite() to
>>>> install packages source("http://bioconductor.org/biocLite.R")
>>>> biocLite("<pkgname>") if you really need to get the list of Bioconductor
>>>> package repositories (like biocReposList() does), then do:
>>>> source("http://bioconductor.org/biocLite.R") biocinstallRepos()
>>>>
>>>> The Toptable ist still calculated but without the Gene Symbols. When I
>>>> call biocLite() from R, it tries to install the packages 'Biobase' 'IRanges'
>>>> and 'AnnotationDbi'. Sounds to me that the last one is causing the problem.
>>>> Also, biocLite complains that it can't access
>>>> "http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15".
>>>> I read the post about that problem and changed the mirror via
>>>> chooseBioCmirror(). biocLite still looks for the brainarray adress but then
>>>> install from another mirror. But everytime I call biocLite it installs those
>>>> 3 packges.
>>>>
>>>> I'm running R 2.15.1 on OS X Lion. AffylmGUI and all the relevant
>>>> packages should have the most recent version.
>>>
>>> Should have? That's not very reassuring. Why don't you load affylmGUI,
>>> run sessionInfo() and then post the output.
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>> Any help would be greatly appreciated! Thanks
>>>>
>>>> Burkhard
>>>>
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>>>
>>> --
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> University of Washington
>>> Environmental and Occupational Health Sciences
>>> 4225 Roosevelt Way NE, # 100
>>> Seattle WA 98105-6099
>>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
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