[BioC] how to check BioConductor version?

[Jianping Jin]

Many thanks Seth! That script helped a lot.

One more question. After installing a new version of R, for example 2.3.1, 
the command biocLite() should let you install the default subset of 
packages listed in the new release (BC v. 1.8) that are built with the 
newly installed R, shouldn't it?

Thanks again!

Jianping


--On Thursday, August 10, 2006 7:50 AM -0700 Seth Falcon 
<sfalcon at fhcrc.org> wrote:

> 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
>
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##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu