[BioC] how to check BioConductor version?

[Seth Falcon]

Hi Jianping,

Jianping Jin <jjin at email.unc.edu> writes:
> We are running R-2.3.1/BioConductor on a Sun machine. I am wondering how I 
> can check which version of BioConductor, 1.8 or 1.7 for example, was 
> installed? Do I need to check package(s) of my  interest by 
> packageDescription() and see what version of R this package was
> built with?

Packages in a Bioconductor release do not share a common version
number.  As a result, you will want to verify installed package
versions against the version number that is part of a given release.

You can use packageDescription to find the installed package version.

You can browse the package version number in a particular release
here:

http://www.bioconductor.org/packages/bioc/1.7/src/contrib/html/
http://www.bioconductor.org/packages/1.8/bioc/

You can also pull the package information from the online repositories
using available.packages and then do comparisons in R.

[below, untested outline of how to go about this]

bioc18 = available.packages(contrib.url("http://www.bioconductor.org/packages/1.8/bioc/"))
instPkgs = installed.packages()
commonPkgs = intersect(rownames(bioc18), rownames(instPkgs))
mapply(function(x, y) compareVersion(x, y), 
       instPkgs[commonPkgs, "Version"], 
       bioc18[commonPkgs, "Version"])

+ seth