Segmentation fault (core dumped) Error in inla.inlaprogram.has.crashed() - Ubutu version 14.04.5 LTS
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Moritz Krämer
Jan 13, 2019, 4:34:14 AM1/13/19
to R-inla discussion group
Hi all,
inla model running fine on RStudio on own machine fails when running on Ubuntu version 14.04.5 LTS (GNU/Linux 3.13.0-164-generic x86_64) with error "Segmentation fault (core dumped) Error in inla.inlaprogram.has.crashed()"
Currently using INLA:::inla.dynload.workaround()
and
system(inla.getOption("inla.call")) Segmentation fault (core dumped)
No other specification.
See model and session info below:
"form <- y ~ 0 + f(pred1, model='clinear',range=c(0,Inf),initial=0) +
f(pred2, model='clinear',range=c(0,Inf),initial=0) +
f(pred3, model='clinear',range=c(0,Inf),initial=0) +
f(pred4, model='clinear',range=c(0,Inf),initial=0) +
f(pred5, model='clinear',range=c(0,Inf),initial=0) +
f(pred6, model='clinear',range=c(0,Inf),initial=0) +
f(space, model = spde)
model <- inla(form,
family = 'normal',
data = inla.stack.data(stk.env),
control.predictor = list(A = inla.stack.A(stk.env)),
control.compute = list(waic = TRUE, config = TRUE),
verbose = TRUE,
num.threads = 60)"
─ Session info ────────────────────────────────────────────────────────────────────────
setting value
version R version 3.5.2 (2018-12-20)
os Ubuntu 14.04.5 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_GB.UTF-8
ctype en_GB.UTF-8
tz Europe/London
date 2019-01-13
─ Packages ────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.4.4)
backports 1.1.3 2018-12-14 [1] CRAN (R 3.5.2)
bindr 0.1.1 2018-03-13 [1] CRAN (R 3.4.4)
bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.5.2)
callr 3.1.1 2018-12-21 [1] CRAN (R 3.5.2)
caret * 6.0-81 2018-11-20 [1] CRAN (R 3.5.2)
class 7.3-15 2019-01-01 [4] CRAN (R 3.5.2)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.2)
codetools 0.2-16 2018-12-24 [4] CRAN (R 3.5.2)
colorspace 1.3-2 2016-12-14 [1] CRAN (R 3.5.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.4.4)
data.table * 1.11.8 2018-09-30 [1] CRAN (R 3.5.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.2)
devtools * 2.0.1 2018-10-26 [1] CRAN (R 3.5.2)
digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.2)
doParallel * 1.0.14 2018-09-24 [1] CRAN (R 3.5.2)
dotCall64 * 1.0-0 2018-07-30 [1] CRAN (R 3.5.2)
dplyr * 0.7.8 2018-11-10 [1] CRAN (R 3.5.2)
elasticnet 1.1.1 2018-08-31 [1] CRAN (R 3.5.2)
fields * 9.6 2018-01-29 [1] CRAN (R 3.5.2)
foreach * 1.4.4 2017-12-12 [1] CRAN (R 3.4.4)
foreign 0.8-71 2018-07-20 [4] CRAN (R 3.5.1)
fs 1.2.6 2018-08-23 [1] CRAN (R 3.5.2)
generics 0.0.2 2018-11-29 [1] CRAN (R 3.5.2)
ggplot2 * 3.1.0 2018-10-25 [1] CRAN (R 3.4.4)
glue 1.3.0 2018-07-17 [1] CRAN (R 3.5.2)
gower 0.1.2 2017-02-23 [1] CRAN (R 3.5.2)
gtable 0.2.0 2016-02-26 [1] CRAN (R 3.4.4)
INLA * 18.07.12 2019-01-12 [1] local
ipred * 0.9-8 2018-11-05 [1] CRAN (R 3.5.2)
iterators * 1.0.10 2018-07-13 [1] CRAN (R 3.5.2)
lars 1.2 2013-04-24 [1] CRAN (R 3.5.2)
lattice * 0.20-38 2018-11-04 [4] CRAN (R 3.5.1)
lava 1.6.4 2018-11-25 [1] CRAN (R 3.5.2)
lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.5.2)
lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.5.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.4.4)
maps * 3.3.0 2018-04-03 [1] CRAN (R 3.5.2)
maptools * 0.9-4 2018-09-19 [1] CRAN (R 3.5.2)
MASS 7.3-51.1 2018-11-01 [4] CRAN (R 3.5.1)
Matrix * 1.2-15 2018-11-01 [4] CRAN (R 3.5.1)
MatrixModels 0.4-1 2015-08-22 [1] CRAN (R 3.5.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.4.4)
mgcv * 1.8-26 2018-11-21 [1] CRAN (R 3.5.2)
ModelMetrics 1.2.2 2018-11-03 [1] CRAN (R 3.5.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.2)
nlme * 3.1-137 2018-04-07 [1] CRAN (R 3.5.2)
nnet 7.3-12 2016-02-02 [4] CRAN (R 3.5.0)
pillar 1.3.1 2018-12-15 [1] CRAN (R 3.5.2)
pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.5.2)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.2)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.2)
plyr * 1.8.4 2016-06-08 [1] CRAN (R 3.5.2)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.2)
processx 3.2.1 2018-12-05 [1] CRAN (R 3.5.2)
prodlim 2018.04.18 2018-04-18 [1] CRAN (R 3.5.2)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.2)
purrr * 0.2.5 2018-05-29 [1] CRAN (R 3.5.2)
R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.2)
ranger * 0.10.1 2018-06-04 [1] CRAN (R 3.5.2)
raster * 2.8-4 2018-11-03 [1] CRAN (R 3.5.2)
Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.2)
recipes * 0.1.4 2018-11-19 [1] CRAN (R 3.5.2)
remotes 2.0.2 2018-10-30 [1] CRAN (R 3.5.2)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.5.2)
rgdal 1.3-6 2018-10-16 [1] CRAN (R 3.5.2)
rlang 0.3.1 2019-01-08 [1] CRAN (R 3.5.2)
rpart 4.1-13 2018-02-23 [1] CRAN (R 3.5.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.2)
rstudioapi 0.9.0 2019-01-09 [1] CRAN (R 3.5.2)
scales * 1.0.0 2018-08-09 [1] CRAN (R 3.5.2)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.2)
sp * 1.3-1 2018-06-05 [1] CRAN (R 3.5.2)
spam * 2.2-1 2018-12-20 [1] CRAN (R 3.5.2)
stringi * 1.2.4 2018-07-20 [1] CRAN (R 3.5.2)
stringr 1.3.1 2018-05-10 [1] CRAN (R 3.4.4)
survival 2.43-3 2018-11-26 [4] CRAN (R 3.5.1)
testthat 2.0.1 2018-10-13 [1] CRAN (R 3.5.2)
tibble * 2.0.0 2019-01-04 [1] CRAN (R 3.5.2)
tidyr * 0.8.2 2018-10-28 [1] CRAN (R 3.5.2)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.2)
timeDate 3043.102 2018-02-21 [1] CRAN (R 3.5.2)
usethis * 1.4.0 2018-08-14 [1] CRAN (R 3.5.2)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.4.4)
xgboost * 0.71.2 2018-06-09 [1] CRAN (R 3.5.2)
Helpdesk
Jan 13, 2019, 4:37:45 AM1/13/19
to Moritz Krämer, R-inla discussion group
Hi,
I guess the problems on Ubuntu 14.05 is because its binaries are
compiled on Ubuntu 18.04. You can try the Ubuntu 16.04 or the CentOS
builds, on http://inla.r-inla-download.org/Linux-builds/
the HOWTO file tells how.
An alternative, you can try the static version
library(INLA)
INLA::inla.dynload.workaround()
and check if that works on the (rather old) 14.04
H
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Håvard Rue
Helpdesk
he...@r-inla.org
I guess the problems on Ubuntu 14.05 is because its binaries are
compiled on Ubuntu 18.04. You can try the Ubuntu 16.04 or the CentOS
builds, on http://inla.r-inla-download.org/Linux-builds/
the HOWTO file tells how.
An alternative, you can try the static version
library(INLA)
INLA::inla.dynload.workaround()
and check if that works on the (rather old) 14.04
H
> You received this message because you are subscribed to the Google
> Groups "R-inla discussion group" group.
> To unsubscribe from this group and stop receiving emails from it,
> send an email to r-inla-discussion...@googlegroups.com
> .
> To post to this group, send email to
> r-inla-disc...@googlegroups.com.
> Visit this group at
> https://groups.google.com/group/r-inla-discussion-group.
> For more options, visit https://groups.google.com/d/optout.
--
Håvard Rue
Helpdesk
he...@r-inla.org
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