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2020 Nov 25
1
[External] Re: .Internal(quit(...)): system call failed: Cannot allocate memory
...t happens to manifest when there is 4e8+ unique characters/factors in
> an R session. I am able to reproduce it using data.table and dplyr
> (0.8.4 because 1.0.0+ fails even sooner), but using base R is not easy
> because of the size. I described briefly problem in:
> https://github.com/h2oai/db-benchmark/issues/110
Because of the design of R's character vectors, with each element
allocated separately, R is never going to be great at handling huge
numbers of distinct strings. But it can do an adequate job given
enough memory to work with.
When I run your GitHub issue example on a...
2020 Nov 24
0
.Internal(quit(...)): system call failed: Cannot allocate memory
...try one more time.
It happens to manifest when there is 4e8+ unique characters/factors in
an R session. I am able to reproduce it using data.table and dplyr
(0.8.4 because 1.0.0+ fails even sooner), but using base R is not easy
because of the size. I described briefly problem in:
https://github.com/h2oai/db-benchmark/issues/110
It would help if gcinfo() could take FALSE/TRUE/2L where 2L will print
even more information about gc, like how much time the each gc()
process took, how many objects it has to check on each level.
Best regards,
Jan
On Tue, Nov 24, 2020 at 1:05 PM Tomas Kalibera <tom...
2020 Nov 24
2
.Internal(quit(...)): system call failed: Cannot allocate memory
On 11/24/20 11:27 AM, Jan Gorecki wrote:
> Thanks Bill for checking that.
> It was my impression that warnings are raised from some internal
> system calls made when quitting R. At that point I don't have much
> control over checking the return status of those.
> Your suggestion looks good to me.
>
> Tomas, do you think this could help? could this be implemented?
I think