On 10/07/2010 10:10 PM, bill.venab...@csiro.au wrote:
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>
$model
NULL
rm(junk, envir = with(v1, environment(terms)))
usedVcells()
[1] 96532
This is still a bit of a trap for young (and old!) players...
I think the main point in my mind is why is it that object.size()
excludes enclosing environments in its reckonings?
I think the idea is that the environment is not part of the object, it
is just referenced by the object. In fact, there are at least two
references to the environment in your second example:
environment(v1$terms)
and
attr(v1$terms, ".Environment")
both refer to it. So you can't just add the size of an environment every
time you come across it, you would need to keep track of whether it had
already been counted or not. So as ?object.size says,
"Associated space (e.g. the environment of a function and what the
pointer in a ‘EXTPTRSXP’ points to) is not included in the
calculation."
If you really want to know how much space an object will take when saved,
probably the only reliable way is to save the object and look at how much space
the file takes.
Duncan Murdoch
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@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-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On
Behalf Of Duncan Murdoch
Sent: Sunday, 11 July 2010 10:36 AM
To: Paul Johnson
Cc: r-devel@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.dun...@gmail.com> wrote:
On 06/07/2010 9:04 PM, julian.tay...@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
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
