Hi,
I’m trying to install rstan in a server with Ubuntu and I get the following error, when I run any model.
schools_dat <- list(J = 8,
y = c(28, 8, -3, 7, -1, 1, 18, 12),
sigma = c(15, 10, 16, 11, 9, 11, 10, 18))
fit <- stan(file = '8schools.stan', data = schools_dat)
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! During startup - Warning messages:
1: Setting LC_TIME failed, using “C”
2: Setting LC_MONETARY failed, using “C”
3: Setting LC_PAPER failed, using “C”
4: Setting LC_MEASUREMENT failed, using “C”
In file included from /usr/include/c++/5/thread:35:0,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/functor/map_rect_concurrent.hpp:10,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/functor/map_rect.hpp:13,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:262,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file9b550aef0d1.cpp:8:
/
In addition: Warning message:
running command ‘/usr/lib/R/bin/R CMD SHLIB file9b550aef0d1.cpp 2> file9b550aef0d1.cpp.err.txt’ had status 1
Error in sink(type = “output”) : invalid connection
The IT guy first install the binary version for Ubuntu with r-cran-rstan. But it didn’t work, and then he followed the instructions of https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Linux. And the installation was successful. But I can’t get the models to run. I’ve checked that Rcpp works fine in R. (I just ran a few examples I found).
Details about the server and installation:
- Operating System: Ubuntu 16.04.5 LTS
- RStan Version: 2.18.2
- Output of
writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
CXX14FLAGS=-O3 -march=native -mtune=native -fPIC
CXX14=clang++-3.8
CXXFLAGS+=-flto -Wno-unused-local-typedefs
CXXFLAGS += -DSTAN_THREADS
CXXFLAGS += -pthread
but I also tried with g++
I checked and
g++ -version says 5.4.0
but there is g++, g+±4.9 and g+±5 installed, as well as
clang+±3.8 and clang+±3.6. Can that be a problem?
- Output of
devtools::session_info("rstan")
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 3.4.4 (2018-03-15)
os Ubuntu 16.04.5 LTS
system x86_64, linux-gnu
ui X11
language en_US:en
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Berlin
date 2018-12-04
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.4.4)
backports 1.1.2 2017-12-13 [1] CRAN (R 3.4.4)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.4.4)
BH 1.66.0-1 2018-02-13 [1] CRAN (R 3.4.4)
callr 3.0.0 2018-08-24 [1] CRAN (R 3.4.4)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.4.4)
colorspace 1.3-2 2016-12-14 [1] CRAN (R 3.4.4)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.4.4)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.4.4)
digest 0.6.18 2018-10-10 [1] CRAN (R 3.4.4)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.4.4)
ggplot2 * 3.1.0 2018-10-25 [1] CRAN (R 3.4.4)
glue 1.3.0 2018-07-17 [1] CRAN (R 3.4.4)
gridExtra 2.3 2017-09-09 [2] CRAN (R 3.4.4)
gtable 0.2.0 2016-02-26 [1] CRAN (R 3.4.4)
inline 0.3.15 2018-05-18 [2] CRAN (R 3.4.4)
labeling 0.3 2014-08-23 [2] CRAN (R 3.2.3)
lattice 0.20-38 2018-11-04 [4] CRAN (R 3.4.4)
lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.4.4)
loo 2.0.0 2018-04-11 [1] CRAN (R 3.4.4)
magrittr 1.5 2014-11-22 [2] CRAN (R 3.2.3)
MASS 7.3-51.1 2018-11-01 [4] CRAN (R 3.4.4)
Matrix 1.2-15 2018-11-01 [4] CRAN (R 3.4.4)
matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.4.4)
mgcv 1.8-26 2018-11-21 [4] CRAN (R 3.4.4)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.4.4)
nlme 3.1-137 2018-04-07 [4] CRAN (R 3.4.4)
pillar 1.3.0 2018-07-14 [1] CRAN (R 3.4.4)
pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.4.4)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.4.4)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.4.4)
processx 3.2.0 2018-08-16 [1] CRAN (R 3.4.4)
ps 1.2.1 2018-11-06 [1] CRAN (R 3.4.4)
R6 2.3.0 2018-10-04 [1] CRAN (R 3.4.4)
RColorBrewer 1.1-2 2014-12-07 [2] CRAN (R 3.2.3)
Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.4.4)
RcppEigen 0.3.3.4.0 2018-02-07 [1] CRAN (R 3.4.4)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.4.4)
rlang 0.3.0.1 2018-10-25 [1] CRAN (R 3.4.4)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.4.4)
rstan * 2.18.2 2018-11-07 [3] CRAN (R 3.4.4)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.4.4)
StanHeaders * 2.18.0 2018-10-07 [1] CRAN (R 3.4.4)
stringi 1.2.4 2018-07-20 [1] CRAN (R 3.4.4)
stringr 1.3.1 2018-05-10 [1] CRAN (R 3.4.4)
tibble 1.4.2 2018-01-22 [1] CRAN (R 3.4.4)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.4.4)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.4.4)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.4.4)
[1] /home/nicenboim/R/x86_64-pc-linux-gnu-library/3.4
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library