From plummerm at iarc.fr  Thu May 11 18:19:51 2017
From: plummerm at iarc.fr (Martyn Plummer)
Date: Thu, 11 May 2017 16:19:51 +0000
Subject: [Rd] bug report: nlme model-fitting crashes with R 3.4.0
In-Reply-To: <1494505413.12031.135.camel@iarc.fr>
References: <106CAE40B5287C47982478041DB6FAC79962728C@HC-MAILBOXC1-N6.healthcare.uiowa.edu>
 <0048a68b-8676-9ec3-76fc-671a5c156996@cmap.polytechnique.fr>
 <22804.19722.546929.314493@max.eddelbuettel.com>
 <1494505413.12031.135.camel@iarc.fr>
Message-ID: <1494519584.10161.2.camel@iarc.fr>

On Thu, 2017-05-11 at 12:23 +0000, Martyn Plummer wrote:
> 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.

Sorry for the false alarm. Dirk is right and the problem is the binary
incompatibility between 3.4.0 and 3.3.3.

If you try building the R source RPM with R 3.4.0 *without using a
chroot* then you get interference from the installed version of R (i.e.
3.3.3) when the %check section of the spec file is run. This is not a
bug in the spec file because you are not supposed to build an SRPM this
way.

If you build the SRPM *using mock* (the chroot tool used by Red Hat)
then the build fails for a completely different reason. The chroot is
not set up with time zone information and this triggers one of the
regression tests.

I'm filing a bug report with Red Hat. So hopefully we will see RPMs of
R 3.4.0 for Fedora soon.

Martyn



> Martyn
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


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