[Bioc-devel] Planned changes to biocLite()

Martin Morgan mtmorgan at fhcrc.org
Thu May 12 01:09:03 CEST 2011


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Many questions on the mailing list occur because users have out-of-date 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out-of-date packages.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

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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