[Bioc-devel] Planned changes to biocLite()

[Dan Tenenbaum]

Hi Kasper,

On Wed, May 11, 2011 at 9:33 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> Have you guys considered to implement something like
>
> biocLite(checkInstall = TRUE)
>
> This should check whether all packages a user has corresponds to the
> correct Bioconductor release.  Specifically, it should check whether
> the user has _newer_ (or older, but that is easier I guess) packages
> installed.  I think the functionality of newer packages could be very
> useful
>

This is an intriguing idea. We will consider it.

Thanks
Dan


> Kasper
>
> On Wed, May 11, 2011 at 7:09 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> Bioconductors!
>>
>> We're planning to change how the biocLite script works in R-2.14 and later.
>> These changes should not disrupt day-to-day use.
>>
>> Currently, calling biocLite() with no arguments installs an unusual mixture
>> of packages:
>>
>> affy, affydata, affyPLM, affyQCReport, annaffy, annotate, Biobase, biomaRt,
>> Biostrings, DynDoc, gcrma, genefilter, geneplotter, GenomicRanges,
>> hgu95av2.db, limma, marray, multtest, vsn, xtable, globaltest, makecdfenv,
>> pamr, siggenes, sma, statmod, tkWidgets, widgetTools
>>
>> We plan to change this, so that only Biobase, IRanges, and AnnotationDbi are
>> installed, representing building blocks for microarray, sequence, and
>> annotation work flows.
>>
>> Many questions on the mailing list occur because users have out-of-date
>> packages installed. The new biocLite will, by default, ask to update any
>> out-of-date packages. Users can specify packages not to update (using
>> regular expressions), or to update packages without asking.
>>
>> Finally, biocLite functionality will be in a new package, 'Bioconductor'.
>> This means that help will be available through standard mechanisms
>> (?biocLite), and that changes in repositories and other 'housekeeping' items
>> are handled automatically.
>>
>> We hope these changes make Bioconductor software more accessible, and
>> welcome any feedback you have.
>>
>> Best wishes, and see you at BioC2011 in Seattle, July 28 & 29 (July 27 for
>> developer day).
>>
>> Martin
>> --
>> 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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>>
>
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