-discuss...@listserv.stowers.org .Subject: RE: [Rd] [BioC] enabling .
.reproducible research R package management . install.package.version
BiocLite . . .I hate to ask what go this . thread started
.but it sounds like someone was counting on .exact . numeric reproducibility
PM
.To: Cook, Malcolm
.Cc: 'r-devel@r-project.org'; 'bioconduc...@r-project.org';
'r-discuss...@listserv.stowers.org'
.Subject: Re: [Rd] [BioC] enabling reproducible research R package
management install.package.version BiocLite .
.(More on the original question further below.) .
.On 13
-project.org'; '
r-discuss...@listserv.stowers.org'
. .Subject: Re: [Rd] [BioC] enabling reproducible research R package
management install.package.version BiocLite .
. .(More on the original question further below.) .
. .On 13-03-05 09:48 AM, Cook, Malcolm wrote:
. . All,
. .
. . What
On Mon, Mar 4, 2013 at 4:13 PM, Cook, Malcolm m...@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
-project.org;
r-discuss...@listserv.stowers.org
Subject: Re: [Rd] [BioC] enabling reproducible research R package
management install.package.version BiocLite
On Mon, Mar 4, 2013 at 4:13 PM, Cook, Malcolm m...@stowers.org wrote:
* where do the dragons lurk
webs of interconnected
. * 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
On 5 Mar 2013, at 14:36, 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
-project.org;
r-discuss...@listserv.stowers.org
.Subject: RE: [Rd] [BioC] enabling reproducible research R package
management install.package.version BiocLite
.
.
.I hate to ask what go this thread started but it sounds like someone was
counting on
.exact numeric reproducibility or was there a bug
On Tue, 5 Mar 2013, Cook, Malcolm wrote:
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.
If you had a separate environment for every
. 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
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,
;
bioconduc...@r-project.org; r-discuss...@listserv.stowers.org .
Subject: Re: [Rd] [BioC] enabling reproducible research R package
management install.package.version BiocLite . . On Mon, Mar 4,
2013 at 4:13 PM, Cook, Malcolm m...@stowers.org wrote: . . *
where do the dragons lurk . . . webs
Hi Paul,
You outline some great suggestions!
I just wanted to point that in this case:
On Tue, Mar 5, 2013 at 5:34 PM, Paul Gilbert pgilbert...@gmail.com wrote:
[snip]
Regarding NFS mounts, it is relatively robust. There can be occasional
problems, especially for users that have a habit of
.To: Cook, Malcolm
.Cc: 'r-devel@r-project.org'; 'bioconduc...@r-project.org';
'r-discuss...@listserv.stowers.org'
.Subject: Re: [Rd] [BioC] enabling reproducible research R package
management install.package.version BiocLite
.
.(More on the original question further below.)
.
.On 13-03
On Mon, Mar 4, 2013 at 4:28 PM, Aaron Mackey amac...@virginia.edu wrote:
On Mon, Mar 4, 2013 at 4:13 PM, Cook, Malcolm m...@stowers.org wrote:
* where do the dragons lurk
webs of interconnected dynamically loaded libraries, identical versions of
R compiled with different BLAS/LAPACK
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