From MEC at stowers.org  Tue Mar  5 16:09:15 2013
From: MEC at stowers.org (Cook, Malcolm)
Date: Tue, 5 Mar 2013 15:09:15 +0000
Subject: [Rd] [BioC] enabling reproducible research & R package
 management & install.package.version & BiocLite
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Message-ID: <D4772401B9D976478C0895769BE3E792073403@MBSRV02.sgc.loc>

.> 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.
 .
 .Sounds a little like this:
 .
 .http://cran.r-project.org/web/packages/rbundler/index.html
 .
 .(which I haven't tested). Best,
 .
 .Greg.

Looks interesting - thanks for the suggestion.

But, but.... my use case is one in which an analyst at my site depends upon the local library installation and only retrospectively, at some publishable event (like handing the results over the in-house customer/scientist), seeks to ensure the ability to return to that exact R library environment  later.  This tool, on the other hand, commits the user to keep a project specific "bundle" from the outset.  Another set of trade-offs.  I will have to synthesize the options I am learning.....

~ Malcolm 



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