Dear Uwe,
(When replying to your message, I sent the reply to r-devel and not
r-package-devel, as Martin Meachler suggested that this thread would be
a better fit for r-devel.)
Thanks. In the example below I used rm() explicitly, but in general
users wouldn't do that.
One of the reasons for the large number of file handles is that
sometimes unnamed temporary objects are created. For example:
> library(ldat)
> libraty(lvec)
>
> a <- lvec(10, "integer")
OPENFILE '/tmp/RtmpVqkDsw/file32145169fb06/lvec3214753f2af0'
> b <- as_rvec(a[1:3])
OPENFILE '/tmp/RtmpVqkDsw/file32145169fb06/lvec32146a50f383'
OPENFILE '/tmp/RtmpVqkDsw/file32145169fb06/lvec3214484b652c'
> print(b)
[1] 0 0 0
>
>
> gc()
CLOSEFILE '/tmp/RtmpVqkDsw/file32145169fb06/lvec3214484b652c'
CLOSEFILE '/tmp/RtmpVqkDsw/file32145169fb06/lvec32146a50f383'
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 796936 42.6 1442291 77.1 1168576 62.5
Vcells 1519523 11.6 4356532 33.3 4740854 36.2
For debugging, I log when files are opened and closed. The call a[1:3]
(which creates a slice of a) creates two temporary objects [1]. These
are only deleted when I explicitly call gc() or on some other random
moment in time.
I hope this illustrates the problem better.
Best,
Jan
[1] One improvement would be to create less temporary files; often these
contain only very little information that is better kept in memory. But
that is only a partial solution.
On 07-08-18 15:24, Uwe Ligges wrote:
Why not add functionality that allows to delete object + runs cleanup code?
Best,
Uwe Ligges
On 07.08.2018 14:26, Jan van der Laan wrote:
In my package I open handles to temporary files from c++, handles to
them are returned to R through vptr objects. The files are deleted
then the corresponding R-object is deleted and the garbage collector
runs:
a <- lvec(10, "integer")
rm(a)
Then when the garbage collector runs the file is deleted. However, on
some platforms (probably with lower limits on the maximum number of
file handles a process can have open), I run into the problem that the
garbage collector doesn't run often enough. In this case that means
that another package of mine using this package generates an error
when its tests are run.
The simplest solution is to add some calls to gc() in my tests. But a
more general/automatic solution would be nice.
I thought about something in the lines of
robust_lvec <- function(...) {
tryCatch({
lvec(...)
}, error = function(e) {
gc()
lvec(...) # duplicated code
})
}
e.g. try to open a file, when that fails call the garbage collector
and try again. However, this introduces duplicated code (in this case
only one line, but that can be more), and doesn't help if it is
another function that tries to open a file.
Is there a better solution?
Thanks!
Jan
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