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

Aaron Mackey
Mon, 04 Mar 2013 21:28:48 -0000

On Mon, Mar 4, 2013 at 4:13 PM, Cook, Malcolm <MEC@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.

An alternative (and arguably more useful) strategy would be to cache
results of each computational step, and report when results differ upon
re-execution with identical inputs; if you cache sessionInfo along with
each result, you can identify which package(s) changed, and begin to hunt
down why the change occurred (possibly for the better); couple this with
the concept of keeping both code *and* results in version control, then you
can move forward with a (re)analysis without being crippled by out-of-date
software.

-Aaron

--
Aaron J. Mackey, PhD
Assistant Professor
Center for Public Health Genomics
University of Virginia
amackey@virginia.edu
http://www.cphg.virginia.edu/mackey

	[[alternative HTML version deleted]]