[BioC] make check with Biobase 2.18.0

[Dan Tenenbaum]

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>
>> 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.
>

Other options:
http://www.bioconductor.org/about/mirrors/mirror-how-to/
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
listed here:

http://www.bioconductor.org/about/mirrors/

Dan


> 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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>>
>>
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>>
>
>
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