bug report: nlme model-fitting crashes with R 3.4.0

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bug report: nlme model-fitting crashes with R 3.4.0

langbehn
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
[hidden email]



________________________________
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Re: bug report: nlme model-fitting crashes with R 3.4.0

Erwan Le Pennec
     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
> [hidden email]
>
>
>
> ________________________________
> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you.
> ________________________________
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: bug report: nlme model-fitting crashes with R 3.4.0

Dirk Eddelbuettel

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

--
http://dirk.eddelbuettel.com | @eddelbuettel | [hidden email]

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Re: bug report: nlme model-fitting crashes with R 3.4.0

Martyn Plummer-3
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
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Re: bug report: nlme model-fitting crashes with R 3.4.0

Martyn Plummer-3
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
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> https://stat.ethz.ch/mailman/listinfo/r-devel
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