[BioC] make check with Biobase 2.18.0
dtenenba at fhcrc.org
Fri Mar 8 21:52:46 CET 2013
On Fri, Mar 8, 2013 at 12:46 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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>
>>> 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
>>> 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):
>> 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
> Piecing things together a bit, an R session
> 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.
describes how to rsync the entire BioC 2.10 repository to your local machine.
Also, maybe your institution already has an internal BioC mirror.
NCI/NIH has one but I don't know if it is available internally. You
could ask the maintainer of that mirror whose contact information is
>>>> Also the recommended route to installing packages, without worrying
>>>> dependencies, is just
>>> Unfortunately that won't work in our set-up because we run a CM system,
>>> so software is pushed out from a central server.
>>> Nigel Horne (NIH, Bethesda, MD, USA)
>>> [[alternative HTML version deleted]]
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> Search the archives:
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> Search the archives:
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
More information about the Bioconductor