[BioC] BrainArray custom CDF repository missing in biocReposList()

[Diego Diez]

Hi Marc

On Wed, Apr 20, 2011 at 1:10 AM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> Hi Diego,
>
> The brainarray CDFs are only missing from the 2.8 build of Bioconductor
> because there is not yet a brainarray build that matches that.  There is a
> recent brainarray build that matches Bioconductor 2.7 though, so we have of
> course provided access to that for the older 2.7 branch.

Do you mean that the recent brainarray build was not generated using
the latest versions of the framework in Bioconductor 2.8 (like GO.db,
KEGG.db, etc.)? Because other than that I can install those packages
without problem in R2.13/Bioc2.8. I imagine this may create some
problems with unmatched entries...

> If you are interested in access to a set of brainarray packages that match
> Bioconductor 2.8, then I would recommend that you contact them and let them
> know how much you appreciate their hard work.   ;)

I will, since I really appreciate their hard work!

> We will of course make such packages available as soon as it is possible to
> do so.

Thank you for the clarification.

Diego

>
>  Marc
>
>
> On 04/18/2011 11:20 PM, Diego Diez wrote:
>>
>> Hi all,
>>
>> I noticed that the mirror for the custom CDFs available at the
>> BrainArray Microarray laboratory is missing in BioC 2.8, and wonder
>> whether this is intentional and permanent.
>>
>> Thank you,
>>
>> --
>> Diego Diez, PhD
>> Bioinformatics center,
>> Institute for Chemical Research,
>> Kyoto University.
>> Gokasho, Uji, Kyoto 611-0011 JAPAN
>> diez at kuicr.kyoto-u.ac.jp
>>
>>
>>> library(Biobase)
>>
>> Welcome to Bioconductor
>>
>>  Vignettes contain introductory material. To view, type
>>  'browseVignettes()'. To cite Bioconductor, see
>>  'citation("Biobase")' and for packages 'citation("pkgname")'.
>>
>>> biocReposList()
>>
>>                                                  bioc
>>           "http://bioconductor.org/packages/2.8/bioc"
>>                                                 aData
>> "http://bioconductor.org/packages/2.8/data/annotation"
>>                                                 eData
>> "http://bioconductor.org/packages/2.8/data/experiment"
>>                                                 extra
>>          "http://bioconductor.org/packages/2.8/extra"
>>                                                  cran
>>                               "http://cran.fhcrc.org"
>>>
>>> sessionInfo()
>>
>> R version 2.13.0 Patched (2011-04-13 r55441)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C/UTF-8/C/C/C/C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] Biobase_2.12.1
>>
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>
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