[Bioc-devel] A new way to manage side-by-side BioC release and Devel installs

[Hervé Pagès]

Hi Gabe,

Thanks for the heads up, sounds promising.

Note that one major difficulty of switching between BioC release
and devel is that between October and April it also requires to switch
between R release and devel. How is that handled in switchr?

Thanks,
H.


On 07/24/2014 08:42 AM, Gabe Becker wrote:
> Hey all,
>
> One of the things that has come up from the recent Release/Devel
> distinction thread on this list is that people don't consider there to be
> an easy way of handling both at the same time.
>
> I'd like to offer an alternative based on the switchr
> https://github.com/gmbecker/switchr package I'm developing.
>
> switchr is designed to allow seamless switching between distinct sets of
> installed packages. It also has build in support for the BioC release/devel
> distinction, like so:
>
>> * library(switchr)*
>> *switchTo(BiocDevel)*
> trying URL '
> http://www.bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/BiocInstaller_1.15.5.zip
> '
> Content type 'application/zip' length 109769 bytes (107 Kb)
> opened URL
> downloaded 107 Kb
>
> package 'BiocInstaller' successfully unpacked and MD5 sums checked
> Switched to the 'BioC_3.0' computing environment. 31 packages are currently
> available. Packages installed in your site library ARE suppressed.
>   To switch back to your previous environment type switchBack()
>> * BiocInstaller::biocVersion()*
> [1] '3.0'
>> * switchBack()*
> Reverted to the 'original' computing environment. 40 packages are currently
> available. Packages installed in your site library ARE NOT suppressed.
>   To switch back to your previous environment type switchBack()
>> * BiocInstaller::biocVersion()*
> [1] '2.14'
>
> Note that this only works if you have an R version able to install the
> devel version of the BiocInstaller package, but that will be true of any
> solution using BioC Devel. I'm working on making the failure more graceful
> when this is not the case, and on writing/updating the documentation more
> generally.
>
> switchr is more widely useful than this, which I will be talking about
> publicly soon, but since it is so on-topic I figured I'd give this list a
> heads-up on this aspect of it.
>
> Please feel free to try switchr out, any feedback is appreciated.
> ~G
>

-- 
Hervé Pagès

Program in Computational Biology
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