[BioC] [Rd] 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....
--Malcolm
.
.
.> ...
.>
.> -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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