Large discrepancies in the same object being saved to .RData
Well, I have answered one of my questions below. The hidden environment is attached to the 'terms' component of v1. To see this
lapply(v1, environment)
$coefficients NULL $residuals NULL $effects NULL $rank NULL $fitted.values NULL $assign NULL $qr NULL $df.residual NULL $xlevels NULL $call NULL $terms <environment: 0x021b9e18> $model NULL
rm(junk, envir = with(v1, environment(terms))) usedVcells()
[1] 96532
This is still a bit of a trap for young (and old!) players... I think the main point in my mind is why is it that object.size() excludes enclosing environments in its reckonings? Bill Venables. -----Original Message----- From: Venables, Bill (CMIS, Cleveland) Sent: Sunday, 11 July 2010 11:40 AM To: 'Duncan Murdoch'; 'Paul Johnson' Cc: 'r-devel at r-project.org'; Taylor, Julian (CMIS, Waite Campus) Subject: RE: [Rd] Large discrepancies in the same object being saved to .RData I'm still a bit puzzled by the original question. I don't think it has much to do with .RData files and their sizes. For me the puzzle comes much earlier. Here is an example of what I mean using a little session
usedVcells <- function() gc()["Vcells", "used"] usedVcells() ### the base load
[1] 96345 ### Now look at what happens when a function returns a formula as the ### value, with a big item floating around in the function closure:
f0 <- function() {
+ junk <- rnorm(10000000) + y ~ x + }
v0 <- f0() usedVcells() ### much bigger than base, why?
[1] 10096355
v0 ### no obvious envirnoment
y ~ x
object.size(v0) ### so far, no clue given where
### the extra Vcells are located. 372 bytes ### Does v0 have an enclosing environment?
environment(v0) ### yep.
<environment: 0x021cc538>
ls(envir = environment(v0)) ### as expected, there's the junk
[1] "junk"
rm(junk, envir = environment(v0)) ### this does the trick. usedVcells()
[1] 96355 ### Now consider a second example where the object ### is not a formula, but contains one.
f1 <- function() {
+ junk <- rnorm(10000000) + x <- 1:3 + y <- rnorm(3) + lm(y ~ x) + }
v1 <- f1() usedVcells() ### as might have been expected.
[1] 10096455 ### in this case, though, there is no ### (obvious) enclosing environment
environment(v1)
NULL
object.size(v1) ### so where are the junk Vcells located?
7744 bytes
ls(envir = environment(v1)) ### clearly wil not work
Error in ls(envir = environment(v1)) : invalid 'envir' argument
rm(v1) ### removing the object does clear out the junk. usedVcells()
[1] 96366
And in this second case, as noted by Julian Taylor, if you save() the object the .RData file is also huge. There is an environment attached to the object somewhere, but it appears to be occluded and entirely inaccessible. (I have poked around the object components trying to find the thing but without success.) Have I missed something? Bill Venables. -----Original Message----- From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org] On Behalf Of Duncan Murdoch Sent: Sunday, 11 July 2010 10:36 AM To: Paul Johnson Cc: r-devel at r-project.org Subject: Re: [Rd] Large discrepancies in the same object being saved to .RData
On 10/07/2010 2:33 PM, Paul Johnson wrote:
On Wed, Jul 7, 2010 at 7:12 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
On 06/07/2010 9:04 PM, Julian.Taylor at csiro.au wrote:
Hi developers,
After some investigation I have found there can be large discrepancies in
the same object being saved as an external "xx.RData" file. The immediate
repercussion of this is the possible increased size of your .RData workspace
for no apparent reason.
I haven't worked through your example, but in general the way that local
objects get captured is when part of the return value includes an
environment.
Hi, can I ask a follow up question? Is there a tool to browse *.Rdata files without loading them into R?
I don't know of one. You can load the whole file into an empty environment, but then you lose information about "where did it come from"? Duncan Murdoch
In HDF5 (a data storage format we use sometimes), there is a CLI program "h5dump" that will spit out line-by-line all the contents of a storage entity. It will literally track through all the metadata, all the vectors of scores, etc. I've found that handy to "see what's really in there" in cases like the one that OP asked about. Sometimes, we find that there are things that are "in there" by mistake, as Duncan describes, and then we can try to figure why they are in there. pj
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