[Bioc-devel] Planned changes to biocLite()

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu May 12 06:33:18 CEST 2011

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


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 Many questions on the mailing list occur because users have out-of-date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 out-of-date packages.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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