>>>>> Ramiro Barrantes <ram...@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
Dear 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
mention implicitly.
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
too.
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.
Martin Maechler
ETH Zurich
## From: Ramiro Barrantes <ram...@precisionbioassay.com>
## To: "r-devel@r-project.org" <r-devel@r-project.org>
## Subject: [Rd] withTimeout bug, it does not work properly with nlme anymore
## Date: Mon, 27 Nov 2017 21:02:52 +0000
## 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
## ((Modifications by Martin Maechler)
dat <- data.frame(
x=c(3.69,3.69,3.69,3.69,3.69,3.69,3.69,3.69,3.69,3.69,3.69,3.69,3,3,3,3,3,3,3,3,3,3,3,3,2.3,2.3,2.3,2.3,2.3,2.3,2.3,2.3,2.3,2.3,2.3,2.3,1.61,1.61,1.61,1.61,1.61,1.61,1.61,1.61,1.61,1.61,1.61,1.61,0.92,0.92,0.92,0.92,0.92,0.92,0.92,0.92,0.92,0.92,0.92,0.92,0.22,0.22,0.22,0.22,0.22,0.22,0.22,0.22,0.22,0.22,0.22,0.22,-0.47,-0.47,-0.47,-0.47,-0.47,-0.47,-0.47,-0.47,-0.47,-0.47,-0.47,-0.47,-1.86,-1.86,-1.86,-1.86,-1.86,-1.86,-1.86,-1.86,-1.86,-1.86,-1.86,-1.86),
y=c(0.35,0.69,0.57,1.48,6.08,-0.34,0.53,1.66,0.02,4.4,8.42,3.3,2.32,-2.3,7.52,-2.12,3.41,-4.76,7.9,5.04,10.26,-1.42,7.85,-1.88,3.81,-2.59,4.32,5.7,1.18,
-1.74,1.81,6.16,4.2,-0.39,1.55,-1.4,1.76,-4.14,-2.36,-0.24,4.8,-7.07,1.34,1.98,0.86,-3.96,-0.61,2.68,-1.65,-2.06,3.67,-0.19,2.33,3.78,2.16,0.35,
-5.6,1.32,2.99,4.21,-0.9,4.32,-4.01,2.03,0.9,-0.74,-5.78,5.76,0.52,1.37,-0.9,-4.06,-0.49,-2.39,-2.67,-0.71,-0.4,2.55,0.97,1.96,8.13,-5.93,4.01,0.79,
-5.61,0.29,4.92,-2.89,-3.24,-3.06,-0.23,0.71,0.75,4.6,1.35, -3.35),
f.block = rep(1:4, 24),
id= paste0("a", rep(c(2,1,3),each=4)))
str(dat)
## 'data.frame': 96 obs. of 4 variables:
## $ x : num 3.69 3.69 3.69 3.69 3.69 3.69 3.69 3.69 3.69 3.69 ...
## $ y : num 0.35 0.69 0.57 1.48 6.08 -0.34 0.53 1.66 0.02 4.4 ...
## $ f.block: num 1 2 3 4 1 2 3 4 1 2 ...
## $ id : Factor w/ 3 levels "a1","a2","a3": 2 2 2 2 1 1 1 1 3 3 ...
table(dat$id) # 32 x 3 -- indeed the 2 factors are perfectly balanced:
xtabs(~id + f.block, data=dat)
## This is the version to directly trigger the bug
dd <- dat
set.seed(33)
dd$y <- dat$y + rnorm(nrow(dat), mean = 0, sd = 0.1)
library(nlme, lib = .Library) # <- get R's version not a newer one
cat("nlme version: ", format(packageVersion("nlme")), "\n")
## MM: Barrantes used 'logbase' and 'logbase^(..)' -- I just use exp(..):
fpl.B.range <- function(lx,A,B,C,D) {
A/(1+exp(-B*(lx-C))) + D
}
INIT <- c(A.a1=1, A.a2=0, A.a3=0,
B = 1, B.a2=0, B.a3=0,
C = 0, C.a2=0, C.a3=0,
D = 1, D.a2=0, D.a3=0)
if(FALSE) # for interactive experiments, eval the following
debugonce(nlme.formula)
trace(nlminb, ## show arguments on entry:
quote(print(ls.str())),
exit = quote({cat("exiting nlminb(); port_msg(iv1):\n");
port_msg(iv1); cat("variables:\n"); print(ls.str())}))
## MM: from watching 'htop' I don't see a clear memory leak...
## >>>>>>>>>>>>>>>Careful: This does "freeze R" : >>>>>>>>>>>>>>>>>
nlme(y ~ fpl.B.range(x, A,B,C,D), data = dd,
fixed = list(A~id, B~id, C~id, D~id),
random = list(f.block = pdSymm(A+B+C+D ~ 1)),
start = INIT,
control= nlmeControl(## NB: msMaxIter=200, ## gives singularity error at
iter.55
msVerbose=TRUE), #==> passed as 'trace' to nlminb()
verbose = TRUE) -> res
## Shows that nlminb() is entered, then
## prints 50 iterations, and then *AGAIN* number 50 (!!)
## and then shows how nlminb() *is* exited, then shows -- thanks to verbose=TRUE
## **Iteration 1
## LME step: Loglik: -245.5092, nlminb iterations: 50
## reStruct parameters:
## f.block1 f.block2 f.block3 f.block4 f.block5 f.block6 f.block7
f.block8 f.block9 f.block10
## 2.3611369 -0.8382860 13.0713658 -1.0197240 -1.1551335 -0.3378552 5.4881588
-0.4035375 -3.3995335 14.7498195
## and then
## it stalls, I need to kill the R process
## -- [on lynne Fedora 26 (4.14.11-200.fc26.x86_64), Jan.2018]
## in R 3.4.3 and R 3.4.3 patched with nlme 3.1.131
## and R-devel with nlme 3.1.135
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