[BioC] BrainArray custom CDF repository missing in biocReposList()
Marc Carlson
mcarlson at fhcrc.org
Thu Apr 21 20:59:35 CEST 2011
Hi Diego,
Your requests must have been persuasive since the maintainers at MBNI
have just updated all of their packages again. And so there is now a
version of these packages available for Bioconductor 2.8 (R 2.13).
biocLite() has been updated accordingly and so now you should be able to
get these packages in the very latest release of Bioconductor.
Marc
On 04/20/2011 08:54 PM, Diego Diez wrote:
> Hi Marc
>
> Of course, I understand (and support) the idea behind biocLite() and
> that for the bioconductor installation to properly work it is needed
> to ensure appropriate version of the packages to be installed. The
> problem here is that the custom cdf packages are not - to the best of
> my understanding- official bioconductor packages, but the repository
> is provided in biocReposList() as a convenience. Therefore the lack of
> support for custom cdf packages in this bioconductor version was not
> mentioned in the release announcement. It may have been worth
> mentioning since this may have a big impact on users.
>
> Obviously, removing the repository while not suitable packages exists
> makes all the sense. However, biocReposList() also provides a
> repository for cran, and any package present in cran will be installed
> by biocLite() whether it is compatible with the bioconductor version
> or not. Even there is a recent thread in the list about an old (non
> compatible) version of the graph package present in cran being
> installed because the official one was missing in the repositories.
> Unfortunately I cannot think on a way to overcome this limitation.
> That being said I myself never had a problem using biocLite() on a
> number of year of use.
>
> Two additional comments:
>
> - The help page for biocReposList() might be a bit old since it lists
> two repositories not presently found:
> -----------
> oh : URL for Bioc Omegahat package repository. This repository
> contains the versions of Omegahat packages that were tested
> with the current Bioc release.
>
> li : URL for Bioc Lindsey package repository.
> ------------
>
> whereas the repository "extra" is missing.
>
> - The cran repository is forced to be "http://cran.fhcrc.org".
> Wouldn't be better to try to get the default CRAN repository selected
> by the user in case that option is set?
>
>
> Anyway, to finish this lengthy email just let you know that I
> contacted the custom cdf people and they are working on providing
> packages for bioconductor 2.8 soon!
>
> Diego
>
>
> On Thu, Apr 21, 2011 at 1:55 AM, Marc Carlson<mcarlson at fhcrc.org> wrote:
>> Hi Diego,
>>
>> You can always throw caution to the wind and just forcibly install any
>> tarball (if downloaded manually). Although that would be taking matters
>> into your own hands, and you would obviously have to live with any of the
>> consequences that might result.
>>
>> But you should *not* normally be able to get these package using biocLite()
>> if there is not an appropriate version available. This is because correct
>> version matching is part of what people depend on when using biocLite().
>> And in this case the problem is indeed because of the issue that you
>> mentioned. The .db packages would have been built using sources appropriate
>> for the Bioc 2.7 and so if you installed them with Bioc 2.8, the GO and KEGG
>> terms etc. would be out of sync with the rest of the build.
>>
>> It is also true that the cdf and probe packages might be ok for some things
>> in Bioc 2.8. But without the corresponding .db package you will not really
>> be able to really use them fully. And if you did use them and then tried to
>> use those remapped probe and cdf packages with the wrong (default) .db style
>> packages the result could be quite chaotic. So I can't really recommend
>> that either unless you have some very specialized usage in mind.
>>
>>
>> Marc
>>
>>
>>
>>
>> On 04/19/2011 07:29 PM, Diego Diez wrote:
>>> 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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>>
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