[Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite
Prof Brian Ripley
ripley at stats.ox.ac.uk
Tue Mar 5 16:19:30 CET 2013
One comment: I have found numerical changes due to updates to the OS's
compilers or runtime at least as often as I have been by changes in R or
packages when trying to reproduce results from a year or two back. That
aspect is rarely mentioned in these discussions.
On 05/03/2013 15:09, Cook, Malcolm wrote:
> .> 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:
> .(which I haven't tested). Best,
> 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
> R-devel at r-project.org mailing list
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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