[BioC] make check with Biobase 2.18.0

Dan Tenenbaum dtenenba at fhcrc.org
Fri Mar 8 21:55:18 CET 2013

On Fri, Mar 8, 2013 at 12:53 PM, Nigel Horne <nigel_horne at hotmail.com> wrote:
> Martin/Dan,
>> > 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.
> I appreciate what you're saying, however that doesn't map into the model that we have where we use a CM system to push things out from a central server: no software is installed directly on the development or production machines, so like it or not I can't go down that route.

I think what Martin is saying is that the above code could be used to
populate your central server which then would push the resulting files
out to the machines that will use them.


> Regards,
> -Nigel
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list