From Bill.Venables at csiro.au  Sun Jul 11 04:10:05 2010
From: Bill.Venables at csiro.au (Bill.Venables at csiro.au)
Date: Sun, 11 Jul 2010 12:10:05 +1000
Subject: [Rd] Large discrepancies in the same object being saved
	to	.RData
In-Reply-To: <1BDAE2969943D540934EE8B4EF68F95FB26EB6E6D3@EXNSW-MBX03.nexus.csiro.au>
References: <62C82B39B8A85E4B95A18F7F7B852F87057236625D@exvic-mbx03.nexus.csiro.au>
	<4C346F1A.8060302@gmail.com>
	<AANLkTimUSBF4mQpc7ZC0kovoBTUiSgwPIiM_acr9ds2H@mail.gmail.com>
	<4C391204.3040601@gmail.com>
	<1BDAE2969943D540934EE8B4EF68F95FB26EB6E6D3@EXNSW-MBX03.nexus.csiro.au>
Message-ID: <1BDAE2969943D540934EE8B4EF68F95FB26EB66350@EXNSW-MBX03.nexus.csiro.au>

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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[Rd] Large discrepancies in the same object being saved to .RData
Bill.Venables at csiro.au