[BioC] automatically checking the version of a BioC package

Seth Falcon sfalcon at fhcrc.org
Mon Jul 24 17:09:31 CEST 2006


Hi Burak,

burak kutlu <burak_kutlu at yahoo.com> writes:
> As part of our data pipeline for our database (www.t1dbase.org), our
> code needs to check the version of the most current packages,
> compare them against the already installed ones and attempt to
> download any package that is not the most current.

> How can we do this, without directly using 'update.packages' which
> downloads the packages regardless of their version?

update.packages respects the package versions and should, basically do
what you want.  I'm not sure how well it will work non-interactively.

Here is how I would try running it:

library("Biobase")
update.packages(repos=biocReposList())

As you may know, Bioconductor hosts three main package repositories
for Software, Annotation Data, and Experiment Data.  In turn, many of
these packages depend on packages hosted on CRAN.  I assume you will
want to check for updates in all repositories.

If update.packages doesn't work for you then have a look at

available.packages
installed.packages

Each returns a matrix and one of the columns is version number.

+ seth



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