[Rd] withTimeout bug, it does not work properly with nlme anymore
maechler at stat.math.ethz.ch
Tue Jan 30 15:17:50 CET 2018
>>>>> Ramiro Barrantes <ramiro at precisionbioassay.com>
>>>>> on Mon, 27 Nov 2017 21:02:52 +0000 writes:
> Hello, I was relying on withTimeout (from R.utils) to help
> me stop nlme when it �hangs�. However, recently this
> stopped working. I am pasting a reproducible example
> below: withTimeout should stop nlme after 10 seconds but
> the code will generate data for which nlme does not
> converge (or takes too long) and withTimeout does not stop
> it. I tried this both on a linux (64 bit, CentOS 7, R
> 3.4.1, nlme 3.1-131 R.util 2.6, and also with R 3.2.5) and
> mac (Sierra 10.13.1, R 3.4.2, same versions or nlme and
> R.utils). It takes over R and I need to use brute-force
> to stop it. As mentioned, this used to work and it is
> very helpful for the purposes of having a loop where nlme
> goes through many models.
> Thank you in advance for any help, Ramiro
as I thought you are reporting a bug about R.utils withTimeout(),
I and maybe others have not reacted.
You've addressed this again in a non-public e-mail,
and indeed the underlying bug is really in nlme which you do
I'm appending a version of your example that is not using R.utils
at all and reproducible hangs for me with R 3.4.3, R 3.4.3
patched and R-devel (and almost surely earlier versions of R
which I did not check.
Indeed, the call to nlme() "stalls" // "hangs" / "freezes" /
... R indeed, and cannot be terminated in a regular way, and, as
you, I do need "brute force" to stop it, killing the R process
As the maintainer of the 'nlme' *is* R-core,
we are asked to fix this, at least making it interruptable.
Still I should not take time for that for the next couple of
weeks as I should fulfill several other day jobs duties,
instead, and so will not promise anything here.
Tested (minimal) patches are welcome!
Here's a version of your script slightly simplified which
exhibits the problem and shows the problem indeed does not
happen in nlminb() -- which I wrongly assumed for a while --
but indeed in nlme's call to own .C() code.
I am looking into fixing this (making it interruptable // detect
the infinite loop).
My guess is that it only happens in degenerate cases like here.
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