getME function crashes

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everything's fine for me with the development version of lme4 (github)

 > library(arm)
Le chargement a n?cessit? le package : MASS
Le chargement a n?cessit? le package : Matrix
Le chargement a n?cessit? le package : lme4
Le chargement a n?cessit? le package : lattice

arm (Version 1.6-09, built: 2013-9-23)

Working directory is D:/Analyses

 > library(lme4)
 > set.seed (1)
 > J <- 15
 > n <- J*(J+1)/2
 > group <- rep (1:J, 1:J)
 > mu.a <- 5
 > sigma.a <- 2
 > a <- rnorm (J, mu.a, sigma.a)
 > b <- -3
 > x <- rnorm (n, 2, 1)
 > y <- rbinom (n, 1, invlogit (a[group] + b*x))
 > mod <- glmer (y ~ x + (1 | group), family=binomial(link="logit"))
 > getME(mod, "L")
'MatrixFactorization' of Formal class 'dCHMsimpl' [package "Matrix"] 
with 10 slots
   ..@ x       : num [1:15] 1.22 1.22 1.1 1.44 1.74 ...
   ..@ p       : int [1:16] 0 1 2 3 4 5 6 7 8 9 ...
   ..@ i       : int [1:15] 0 1 2 3 4 5 6 7 8 9 ...
   ..@ nz      : int [1:15] 1 1 1 1 1 1 1 1 1 1 ...
   ..@ nxt     : int [1:17] 1 2 3 4 5 6 7 8 9 10 ...
   ..@ prv     : int [1:17] 16 0 1 2 3 4 5 6 7 8 ...
   ..@ colcount: int [1:15] 1 1 1 1 1 1 1 1 1 1 ...
   ..@ perm    : int [1:15] 0 1 2 3 4 5 6 7 8 9 ...
   ..@ type    : int [1:4] 2 1 0 1
   ..@ Dim     : int [1:2] 15 15
 > sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arm_1.6-09      lme4_1.1-1      lattice_0.20-25 Matrix_1.1-0 
MASS_7.3-29

loaded via a namespace (and not attached):
[1] abind_1.4-1    coda_0.16-1    fortunes_1.5-1 grid_3.0.2 
minqa_1.2.1    nlme_3.1-111
[7] splines_3.0.2  tools_3.0.2

Idem with the 64-bit version of R

Renaud

Le 07/11/2013 17:31, Johannes Radinger a ?crit :
Hi,

Actually I tried to use the sim function from the package "arm" to get
posterior simulations of beta from a merMod.
But somehow this function crashed and I could trace the problem back to the
function getME(model,"L") which is
the cause for the crash.
For example here an example dataset for a binomial model (glmer) from the
sim function in the 'arm'-package:

set.seed (1)
J<- 15
n<- J*(J+1)/2
group<- rep (1:J, 1:J)
mu.a<- 5
sigma.a<- 2
a<- rnorm (J, mu.a, sigma.a)
b<- -3
x<- rnorm (n, 2, 1)
y<- rbinom (n, 1, invlogit (a[group] + b*x))

mod<- glmer (y ~ x + (1 | group), family=binomial(link="logit"))

When I now run getME(mod, "L") my R session completely crashes with
following error:
*** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
  1: .Call(merPredDL, ptr())
  2: PR$L()
  3: getME(mod, "L")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

I am running following setup:

R version 3.0.2 (2013-09-25)
Platform: i686-pc-linux-gnu (32-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arm_1.6-09      lme4_1.0-5      lattice_0.20-24 Matrix_1.1-0
MASS_7.3-29

loaded via a namespace (and not attached):
[1] abind_1.4-0   coda_0.16-1   grid_3.0.2    minqa_1.2.1   nlme_3.1-111
splines_3.0.2 tools_3.0.2

Can anyone reproduce this problem?

/Johannes

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_______________________________________________
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Renaud Lancelot
Directeur adjoint / Deputy director
http://umr-cmaee.cirad.fr/
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CIRAD, UMR CMAEE, Campus International de Baillarguet TA A-DIR / B
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Head of epidemiology team
EDENext Project, coordinator: http://www.edenext.eu/

Tel.  +33 4 67 59 37 17  -  Fax  +33 4 67 59 37 98
Secr. +33 4 67 59 37 37  - Cell. +33 6 77 52 08 69
I couldn't reproduce, but that is not entirely surprising with memory 
bugs. Apart from changing invlogit to plogis, I successfully ran your 
example with the following session info.  The difference could be that I 
was using a development version of lme4, but I doubt that would make a 
difference...checking...no, the cran version works for me too.

Steve

 > sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] lme4_1.1-1   Matrix_1.1-0

loaded via a namespace (and not attached):
[1] MASS_7.3-29     grid_3.0.2      lattice_0.20-23 minqa_1.2.1
[5] nlme_3.1-111    splines_3.0.2
 >
Hi,

Actually I tried to use the sim function from the package "arm" to get
posterior simulations of beta from a merMod.
But somehow this function crashed and I could trace the problem back to the
function getME(model,"L") which is
the cause for the crash.
For example here an example dataset for a binomial model (glmer) from the
sim function in the 'arm'-package:

set.seed (1)
J <- 15
n <- J*(J+1)/2
group <- rep (1:J, 1:J)
mu.a <- 5
sigma.a <- 2
a <- rnorm (J, mu.a, sigma.a)
b <- -3
x <- rnorm (n, 2, 1)
y <- rbinom (n, 1, invlogit (a[group] + b*x))

mod <- glmer (y ~ x + (1 | group), family=binomial(link="logit"))

When I now run getME(mod, "L") my R session completely crashes with
following error:
*** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
  1: .Call(merPredDL, ptr())
  2: PR$L()
  3: getME(mod, "L")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

I am running following setup:

R version 3.0.2 (2013-09-25)
Platform: i686-pc-linux-gnu (32-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arm_1.6-09      lme4_1.0-5      lattice_0.20-24 Matrix_1.1-0
MASS_7.3-29

loaded via a namespace (and not attached):
[1] abind_1.4-0   coda_0.16-1   grid_3.0.2    minqa_1.2.1   nlme_3.1-111
splines_3.0.2 tools_3.0.2

Can anyone reproduce this problem?

/Johannes

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_______________________________________________
R-sig-mixed-models at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

Johannes,

on Linux-64, with the same version of R and the same version of 
all loaded packages, your example code runs fine. Apart from 
Windows-32, the only difference I've spotted is  that a module 
named "tools_3.0.2" does not appear in my sessionInfo(), but 
that might be platform dependant.

Hugo

On Thu, 7 Nov 2013 17:31:41 +0100

Hi,

Actually I tried to use the sim function from the package "arm" to get
posterior simulations of beta from a merMod.
But somehow this function crashed and I could trace the problem back to the
function getME(model,"L") which is
the cause for the crash.
For example here an example dataset for a binomial model (glmer) from the
sim function in the 'arm'-package:

set.seed (1)
J <- 15
n <- J*(J+1)/2
group <- rep (1:J, 1:J)
mu.a <- 5
sigma.a <- 2
a <- rnorm (J, mu.a, sigma.a)
b <- -3
x <- rnorm (n, 2, 1)
y <- rbinom (n, 1, invlogit (a[group] + b*x))

mod <- glmer (y ~ x + (1 | group), family=binomial(link="logit"))

When I now run getME(mod, "L") my R session completely crashes with
following error:
*** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: .Call(merPredDL, ptr())
 2: PR$L()
 3: getME(mod, "L")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

I am running following setup:

R version 3.0.2 (2013-09-25)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arm_1.6-09      lme4_1.0-5      lattice_0.20-24 Matrix_1.1-0
MASS_7.3-29

loaded via a namespace (and not attached):
[1] abind_1.4-0   coda_0.16-1   grid_3.0.2    minqa_1.2.1   nlme_3.1-111
splines_3.0.2 tools_3.0.2

Can anyone reproduce this problem?

/Johannes

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_______________________________________________
R-sig-mixed-models at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
--
This are the exact symptoms of having a mismatch between your Matrix,
RcppEigen, and lme4 versions ... try reinstalling them in that order.

  Ben Bolker
everything's fine for me with the development version of lme4 (github)

library(arm)
Le chargement a n?cessit? le package : MASS
Le chargement a n?cessit? le package : Matrix
Le chargement a n?cessit? le package : lme4
Le chargement a n?cessit? le package : lattice

arm (Version 1.6-09, built: 2013-9-23)

Working directory is D:/Analyses

library(lme4)
set.seed (1)
J <- 15
n <- J*(J+1)/2
group <- rep (1:J, 1:J)
mu.a <- 5
sigma.a <- 2
a <- rnorm (J, mu.a, sigma.a)
b <- -3
x <- rnorm (n, 2, 1)
y <- rbinom (n, 1, invlogit (a[group] + b*x))
mod <- glmer (y ~ x + (1 | group), family=binomial(link="logit"))
getME(mod, "L")
'MatrixFactorization' of Formal class 'dCHMsimpl' [package "Matrix"]
with 10 slots
  ..@ x       : num [1:15] 1.22 1.22 1.1 1.44 1.74 ...
  ..@ p       : int [1:16] 0 1 2 3 4 5 6 7 8 9 ...
  ..@ i       : int [1:15] 0 1 2 3 4 5 6 7 8 9 ...
  ..@ nz      : int [1:15] 1 1 1 1 1 1 1 1 1 1 ...
  ..@ nxt     : int [1:17] 1 2 3 4 5 6 7 8 9 10 ...
  ..@ prv     : int [1:17] 16 0 1 2 3 4 5 6 7 8 ...
  ..@ colcount: int [1:15] 1 1 1 1 1 1 1 1 1 1 ...
  ..@ perm    : int [1:15] 0 1 2 3 4 5 6 7 8 9 ...
  ..@ type    : int [1:4] 2 1 0 1
  ..@ Dim     : int [1:2] 15 15
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arm_1.6-09      lme4_1.1-1      lattice_0.20-25 Matrix_1.1-0
MASS_7.3-29

loaded via a namespace (and not attached):
[1] abind_1.4-1    coda_0.16-1    fortunes_1.5-1 grid_3.0.2
minqa_1.2.1    nlme_3.1-111
[7] splines_3.0.2  tools_3.0.2

Idem with the 64-bit version of R

Renaud

Le 07/11/2013 17:31, Johannes Radinger a ?crit :
Hi,

Actually I tried to use the sim function from the package "arm" to get
posterior simulations of beta from a merMod.
But somehow this function crashed and I could trace the problem back
to the
function getME(model,"L") which is
the cause for the crash.
For example here an example dataset for a binomial model (glmer) from the
sim function in the 'arm'-package:

set.seed (1)
J<- 15
n<- J*(J+1)/2
group<- rep (1:J, 1:J)
mu.a<- 5
sigma.a<- 2
a<- rnorm (J, mu.a, sigma.a)
b<- -3
x<- rnorm (n, 2, 1)
y<- rbinom (n, 1, invlogit (a[group] + b*x))

mod<- glmer (y ~ x + (1 | group), family=binomial(link="logit"))

When I now run getME(mod, "L") my R session completely crashes with
following error:
*** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
  1: .Call(merPredDL, ptr())
  2: PR$L()
  3: getME(mod, "L")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

I am running following setup:

R version 3.0.2 (2013-09-25)
Platform: i686-pc-linux-gnu (32-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arm_1.6-09      lme4_1.0-5      lattice_0.20-24 Matrix_1.1-0
MASS_7.3-29

loaded via a namespace (and not attached):
[1] abind_1.4-0   coda_0.16-1   grid_3.0.2    minqa_1.2.1   nlme_3.1-111
splines_3.0.2 tools_3.0.2

Can anyone reproduce this problem?

/Johannes

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https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

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