[R] small object but huge RData file exported

[Jinsong Zhao]

On 2021/10/20 21:05, Duncan Murdoch wrote:
> On 20/10/2021 8:57 a.m., Jinsong Zhao wrote:
>> Hi there,
>>
>> I have a RData file that is obtained by save.image() with size about
>> 74.0 MB (77,608,222 bytes).
>>
>> When load into R, I measured the size of each object with object.size():
>>
>>> object.size(combn.rda.m)
>> 105448 bytes
>>> object.size(cross)
>> 102064 bytes
>>> object.size(denitr.1)
>> 25032 bytes
>>> object.size(rda.denitr.1)
>> 600280 bytes
>>> object.size(xh)
>> 7792 bytes
>>> object.size(xh.x)
>> 6064 bytes
>>> object.size(xh.x.1)
>> 24144 bytes
>>> object.size(xh.x.2)
>> 24144 bytes
>>> object.size(xh.x.3)
>> 24144 bytes
>>> object.size(xh.y)
>> 2384 bytes
>>
>> There are all small objects.
>>
>> If I delete the largest one "rda.denitr.1", and save.image("xx.RData").
>> It has the size of 22.6 KB (23,244 bytes). All seem OK.
>>
>> However, when I save(rda.denitr.1, file = "yy.RData"), then it has the
>> size of 73.9 MB (77,574,869 bytes).
>>
>> I don't know why...
>>
>> Any hint?
> 
> As the docs for object.size() say, "Exactly which parts of the memory 
> allocation should be attributed to which object is not clear-cut."  In 
> particular, if a function or formula has an associated environment, it 
> isn't included, but it is sometimes saved in the image.
> 
> So I'd suspect rda.denitr.1 contains something that references an 
> environment, and it's an environment that would be saved.  (I forget the 
> exact rules, but I think that means it's not the global environment and 
> it's not a package environment.)
> 
> Duncan Murdoch


The rda.denitr.1 is only a list with length 2:
rda.denitr.1[[1]] is a vector with length 10;
rda.denitr.2[[2]] is a list with the length 10. rda.denitr.1[[2]][[1]] 
to rda.denitr.1[[2]][[10]] are small RDA objects generated by rda() from 
vegan package.

If I
 > a <- rda.denitr.1[[2]][[1]]
 > object.size(a)
59896 bytes
 > save(a, file = "abc.RData")
It also has a large size of 73.9 MB (77,536,611 bytes)

Jinsong