From lepennec at cmap.polytechnique.fr  Thu May 11 10:17:24 2017
From: lepennec at cmap.polytechnique.fr (Erwan Le Pennec)
Date: Thu, 11 May 2017 10:17:24 +0200
Subject: [Rd] bug report: nlme model-fitting crashes with R 3.4.0
In-Reply-To: <106CAE40B5287C47982478041DB6FAC79962728C@HC-MAILBOXC1-N6.healthcare.uiowa.edu>
References: <106CAE40B5287C47982478041DB6FAC79962728C@HC-MAILBOXC1-N6.healthcare.uiowa.edu>
Message-ID: <0048a68b-8676-9ec3-76fc-671a5c156996@cmap.polytechnique.fr>

     Dear all,

     I've stumbled a similar issue with the package cluster when 
compiling the 3.4.0 version with the settings of Fedora RPM specs. 
Compiling R with the default setting of configure yields a version that 
works for cluster... and nlme.

     I did not find the exact option that was the cause of this issue 
but I'm willing to help.

     Erwan

PS: This is the reason why R is still at version 3.3.3 on the Fedora 
distribution.

On 10/05/17 22:59, Langbehn, Douglas wrote:
> 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
Erwan Le Pennec