From dtenenba at fhcrc.org  Mon Mar  4 23:28:40 2013
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Mon, 4 Mar 2013 14:28:40 -0800
Subject: [Rd] [BioC] enabling reproducible research & R package
 management & install.package.version & BiocLite
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On Mon, Mar 4, 2013 at 2:15 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> On Mon, Mar 4, 2013 at 4:28 PM, Aaron Mackey <amackey at virginia.edu> wrote:
>> On Mon, Mar 4, 2013 at 4:13 PM, Cook, Malcolm <MEC at 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.
>
> 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.

Dan



> ...
>
> -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
>
> ______________________________________________
> R-devel at r-project.org mailing list
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[Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite
Dan Tenenbaum