[BioC] make check with Biobase 2.18.0

[Martin Morgan]

On 03/08/2013 12:23 PM, Dan Tenenbaum wrote:
> On Fri, Mar 8, 2013 at 12:13 PM, Nigel Horne <nigel_horne at hotmail.com> wrote:
>> Dan,
>> Thanks for getting back to me.
>>>> Can you send your sessionInfo()?
>>>>
>>>> My guess is your version of R is too old--Biobase 2.18.0 requires R 2.15.
>> Ah, OK, this is R2.14.  I was wondering if I needed something more recent.  Updating here would be a large undertaking so before I start could I get a 'yes you definitely need R2.15'?
>>
>
> There is a version of Biobase that works with R 2.14.
> You should probably get that version. This page links to the package
> pages for that release (which contain version numbers at the bottom):
>
> http://www.bioconductor.org/packages/2.10/BiocViews.html#___Software
>
> But as Martin says, it's really not recommended to install packages in
> this way.
> You want to make sure that all your packages are from the same
> Bioconductor release so they will work with each other. Mixing and
> matching packages from different releases is a sure recipe for
> problems.

Piecing things together a bit, an R session

   source("http://bioconductor.org/biocLite.R")

gets enough information, specific to the version of R you're in, to proceed to 
find the packages that are available to your installation of R, and then to 
identify the dependencies of the package(s) you're interested in.

   urls = contrib.url(biocinstallRepos())
   avail = available.packages(urls)
   need = utils:::getDependencies("Biobase", TRUE, avail)

(the first argument to getDependencies can be a vector of packages). The 
packages can be downloaded to a local directory

   dest = tempdir()
   download.packages(need, dest, repos=biocinstallRepos())

and then managed as needed.

Martin

>
> Dan
>
>
>
>
>>> Also the recommended route to installing packages, without worrying about
>>> dependencies, is just
>>>
>>>     source("http://bioconductor.org/biocLite.R")
>>>     biocLite("Biobase")
>> Unfortunately that won't work in our set-up because we run a CM system, so software is pushed out from a central server.
>> Regards,
>> -Nigel
>>
>> --
>> Nigel Horne (NIH, Bethesda, MD, USA)
>> http://www.ncbi.nlm.nih.gov/
>>
>>          [[alternative HTML version deleted]]
>>
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