[Bioc-devel] Planned changes to biocLite()

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Many questions on the mailing list occur because users have out-of-date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out-of-date packages.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

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

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