From ramiro at precisionbioassay.com  Mon Nov 27 22:02:52 2017
From: ramiro at precisionbioassay.com (Ramiro Barrantes)
Date: Mon, 27 Nov 2017 21:02:52 +0000
Subject: [Rd] withTimeout bug, it does not work properly with nlme anymore
Message-ID: <C7338A7EFF31BB4D831BB06C00887789B9C4AA4D@MBX023-W1-CA-2.exch023.domain.local>

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

library(nlme)
library(R.utils)

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=c(1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4),
id=c("a2","a2","a2","a2","a1","a1","a1","a1","a3","a3","a3","a3","a2","a2","a2","a2","a1","a1","a1","a1","a3","a3","a3","a3","a2","a2","a2","a2","a1","a1","a1","a1","a3","a3","a3","a3","a2","a2","a2","a2","a1","a1","a1","a1","a3","a3","a3","a3","a2","a2","a2","a2","a1","a1","a1","a1","a3","a3","a3","a3","a2","a2","a2","a2","a1","a1","a1","a1","a3","a3","a3","a3","a2","a2","a2","a2","a1","a1","a1","a1","a3","a3","a3","a3","a2","a2","a2","a2","a1","a1","a1","a1","a3","a3","a3","a3"))

fpl.B.range <- function(lx,logbase,A,B,C,D) {
    A/(1+logbase^(-B*(lx-C)))+D
}
myFormula<-list(formula(A~id),formula(B~id),formula(C~id),formula(D~id))
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)


for (i in 1:100) {
    print(paste("Iteration ",i,"...this will stall soon"))
    set.seed(i)
    dat$y <- dat$y+rnorm(nrow(dat), mean = 0, sd = 0.1)
    try({withTimeout(nlme(model=y~fpl.B.range(x,exp(1),A,B,C,D),
                      control=nlmeControl(maxIter=50,pnlsMaxIter=7,msMaxIter=50,niterEM=25),
                          data=dat, na.action=na.omit,
                          fixed=myFormula,random=list(f.block=pdSymm(A+B+C+D~1)),
                          start=INIT),timeout=10)})
}


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[Rd] withTimeout bug, it does not work properly with nlme anymore
Ramiro Barrantes