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

Cook, Malcolm MEC at stowers.org
Tue Mar 5 15:36:12 CET 2013

.>>> * 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
 .Right...and this is a bit tricky, because we don't keep old versions
 .around in our BioC software repositories.  They are available through
 .Subversion but with the sometimes additional overhead of setting up
 .build-time dependencies.

So, even if I wanted to go where dragons lurked, it would not be possible to cobble a version of biocLite that installed specific versions of software.

Thus, I might rather consider an approach that at 'publish' time tarzips up a copy of the R package dependencies based on a config file defined from sessionInfo and caches it in the project directory.

Then when/if the project is revisited (and found to produce differnt results under current R enviRonment),  I can "simply" install an old R (oops, I guess I'd have to build it), and then un-tarzip the dependencies into the projects own R/Library which I would put on .libpaths.

Or, or?  

(My virtual machine advocating colleagues are snickering now, I am sure......)

Thanks for all your thoughts and advices....


 .> ...
 .> -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
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