From douglas-langbehn at uiowa.edu  Wed May 10 22:59:30 2017
From: douglas-langbehn at uiowa.edu (Langbehn, Douglas)
Date: Wed, 10 May 2017 20:59:30 +0000
Subject: [Rd] bug report: nlme model-fitting crashes with R 3.4.0
Message-ID: <106CAE40B5287C47982478041DB6FAC79962728C@HC-MAILBOXC1-N6.healthcare.uiowa.edu>

lme() and gls() models from the nlme package are all crashing with R.3.4.0. Identical code ran correctly, without error in R 3.3.3 and earlier versions.  The behavior is easily demonstrated using one of the examples form the lme() help file, along with two simple variants. I have commented the errors generated by these calls, as well as the lines of code generating them, in the code example below.

As of today, this bug had not been reported on the R Bugzilla page. I could not submit this report directly to the page because I am not a member, and , as explained in the "Reporting Bugs" link from the  R home page, membership has now been closed due to spamming problems..

############################################################################
library(nlme)
#Using version 3.1-131
#Windows 7 64-bit operating system

fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)

# Error in array(c(rep(1, p), .C(inner_perc_table, as.double(X), as.integer(unlist(grps)),  :
# object 'inner_perc_table' not found
#
#Upon debugging, this error is thrown with line 135 of lme.formula() code.
#
#fixDF <- getFixDF(X, grps, attr(lmeSt, "conLin")$dims$ngrps,

lme(distance ~ age + Sex, data = Orthodont, random = ~ 1|Subject)

# Error in array(c(rep(1, p), .C(inner_perc_table, as.double(X), as.integer(unlist(grps)),  :
# object 'inner_perc_table' not found

gls(distance ~ age + Sex, data = Orthodont,
    correlation = corCompSymm( form = ~ 1 | Subject))

# Error in corMatrix.corCompSymm(object) :
# object 'compSymm_matList' not found
#
#Upon debugging, the error is thrown by line 60 of gls code
#
#glsSt <- Initialize(glsSt, dataMod, glsEstControl)

R.version

# _
# platform       x86_64-w64-mingw32
# arch           x86_64
# os             mingw32
# system         x86_64, mingw32
# status
# major          3
# minor          4.0
# year           2017
# month          04
# day            21
# svn rev        72570
# language       R
# version.string R version 3.4.0 (2017-04-21)
# nickname       You Stupid Darkness

########################################################################
Douglas R Langbehn MD, PhD
Professor
Dept. of Psychiatry and Biostatistics (secondary)
University of Iowa Carver College of Medicine
douglas-langbehn at uiowa.edu



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[Rd] bug report: nlme model-fitting crashes with R 3.4.0
Langbehn, Douglas