From plummerm at iarc.fr  Thu May 11 14:23:33 2017
From: plummerm at iarc.fr (Martyn Plummer)
Date: Thu, 11 May 2017 12:23:33 +0000
Subject: [Rd] bug report: nlme model-fitting crashes with R 3.4.0
In-Reply-To: <22804.19722.546929.314493@max.eddelbuettel.com>
References: <106CAE40B5287C47982478041DB6FAC79962728C@HC-MAILBOXC1-N6.healthcare.uiowa.edu>
 <0048a68b-8676-9ec3-76fc-671a5c156996@cmap.polytechnique.fr>
 <22804.19722.546929.314493@max.eddelbuettel.com>
Message-ID: <1494505413.12031.135.camel@iarc.fr>

On Thu, 2017-05-11 at 06:37 -0500, Dirk Eddelbuettel wrote:
> On 11 May 2017 at 10:17, Erwan Le Pennec wrote:
> > ?????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
> 
> That is a known issue with R 3.4.0 -- see NEWS.
> 
> Packages using .C and .Fortran _must_ be recompiled for R 3.4.0. If
> and when
> you do, the example will work again.
> 
> Dirk

However, the issue raised by Erwan on Fedora is a real bug which
affects at least two recommended packages. I know the cause of the
problem and am trying to find out how many packages are affected.

Martyn


[Rd] bug report: nlme model-fitting crashes with R 3.4.0
Martyn Plummer