Langbehn, Douglas
2017-May-10 20:59 UTC
[Rd] bug report: nlme model-fitting crashes with R 3.4.0
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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[[alternative HTML version deleted]]
Erwan Le Pennec
2017-May-11 08:17 UTC
[Rd] bug report: nlme model-fitting crashes with R 3.4.0
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
>
>
>
> ________________________________
> 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]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
Dirk Eddelbuettel
2017-May-11 11:37 UTC
[Rd] bug report: nlme model-fitting crashes with R 3.4.0
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 | edd at debian.org