[Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite

Steve Lianoglou
Mon, 04 Mar 2013 22:15:05 -0000

On Mon, Mar 4, 2013 at 4:28 PM, Aaron Mackey <amackey at virginia.edu>
wrote:
> On Mon, Mar 4, 2013 at 4:13 PM, Cook, Malcolm <MEC at stowers.org>
wrote:
>
>> * where do the dragons lurk
>>
>
> webs of interconnected dynamically loaded libraries, identical versions of
> R compiled with different BLAS/LAPACK options, etc.  Go with the VM if you
> really, truly, want this level of exact reproducibility.

Sounds like the best bet -- maybe tools like vagrant might be useful here:

http://www.vagrantup.com

... or maybe they're overkill?

Haven't really checked it out myself too much, my impression is that
these tools (vagrant, chef, puppet) are built to handle such cases.

I'd imagine you'd probably need a location where you can grab the
precise (versioned) packages for the things you are specifying, but
...

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact