I am running into an issue where I am able to run my rstan code interactively (e.g., in jupyter notebook), but when I run the same script in the command line through Rscript I receive the following error:
Loading required package: ggplot2
Loading required package: StanHeaders
rstan (Version 2.18.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from /shared/centos7/gcc/10.1.0/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/immintrin.h:55,
from /home/shawn/anaconda3/envs/crowdsourcing-r/lib/R/library/RcppEigen/include/Eigen/Core:210,
from /home/shawn/anaconda3/envs/crowdsourcing-r/lib/R/library/RcppEigen/include/Eigen/Dense:1,
from /home/shawn/anaconda3/envs/crowdsourcing-r/lib/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4,
from /home/shawn/anaconda3/envs/crowdsourcing-r/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4,
from /home/shawn/anaconda3/envs/crowdsourcing-r/lib/R/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4,
from /home/shawn/anaconda3/envs/crowdsourcing-r/lib/R/library/StanHeaders/include/stan/math/rev/core.hpp:14,
Calls: stan ... cxxfunctionplus -> <Anonymous> -> cxxfunction -> compileCode
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command '/home/shawn/anaconda3/envs/crowdsourcing-r/lib/R/bin/R CMD SHLIB file35914625e290.cpp 2> file35914625e290.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection
Calls: stan -> stan_model -> cxxfunctionplus -> sink
Execution halted
Below is the barebone script I am using:
library(rstan)
y <- rbinom(20, size = 1, prob = 0.3)
bernoulli_string <- "
data {
int n;
int y[n];
}
parameters {
real<lower=0, upper=1> theta;
}
model {
y ~ bernoulli(theta);
}"
stan_samples <- stan(model_code = bernoulli_string, data = list(y = y, n = length(y)) )
stan_samples
Below are some system info. The session info and Makevars are identical when I run it interactively and through the command line.
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 3.6.3 (2020-02-29)
os CentOS Linux 7 (Core)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2021-07-12
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
backports 1.2.1 2020-12-09 [1] CRAN (R 3.6.3)
BH 1.69.0-1 2019-01-07 [1] CRAN (R 3.6.0)
callr 3.7.0 2021-04-20 [1] CRAN (R 3.6.3)
checkmate 1.9.1 2019-01-15 [1] CRAN (R 3.6.0)
cli 2.5.0 2021-04-26 [1] CRAN (R 3.6.3)
colorspace 2.0-1 2021-05-04 [1] CRAN (R 3.6.3)
crayon 1.4.1 2021-02-08 [1] CRAN (R 3.6.3)
desc 1.3.0 2021-03-05 [1] CRAN (R 3.6.3)
digest 0.6.27 2020-10-24 [1] CRAN (R 3.6.3)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 3.6.3)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.6.0)
farver 2.1.0 2021-02-28 [1] CRAN (R 3.6.3)
ggplot2 * 3.3.3 2020-12-30 [1] CRAN (R 3.6.3)
glue 1.4.2 2020-08-27 [1] CRAN (R 3.6.3)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.3)
inline 0.3.15 2018-05-18 [1] CRAN (R 3.6.0)
isoband 0.2.4 2021-03-03 [1] CRAN (R 3.6.3)
labeling 0.4.2 2020-10-20 [1] CRAN (R 3.6.3)
lattice 0.20-44 2021-05-02 [1] CRAN (R 3.6.3)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 3.6.3)
loo 2.1.0 2019-03-13 [1] CRAN (R 3.6.0)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 3.6.3)
MASS 7.3-54 2021-05-03 [1] CRAN (R 3.6.3)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.2)
matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.6.0)
mgcv 1.8-28 2019-03-21 [1] CRAN (R 3.6.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.3)
nlme 3.1-152 2021-02-04 [1] CRAN (R 3.6.3)
pillar 1.6.1 2021-05-16 [1] CRAN (R 3.6.3)
pkgbuild 1.0.3 2019-03-20 [1] CRAN (R 3.6.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.3)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.3)
processx 3.5.2 2021-04-30 [1] CRAN (R 3.6.3)
ps 1.6.0 2021-02-28 [1] CRAN (R 3.6.3)
R6 2.5.0 2020-10-28 [1] CRAN (R 3.6.3)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.3)
Rcpp 1.0.6 2021-01-15 [1] CRAN (R 3.6.3)
RcppEigen 0.3.3.5.0 2018-11-24 [1] CRAN (R 3.6.0)
rlang 0.4.11 2021-04-30 [1] CRAN (R 3.6.3)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 3.6.3)
rstan * 2.18.2 2018-11-07 [1] CRAN (R 3.6.0)
scales 1.1.1 2020-05-11 [1] CRAN (R 3.6.3)
StanHeaders * 2.18.1 2019-01-28 [1] CRAN (R 3.6.0)
tibble 3.1.2 2021-05-16 [1] CRAN (R 3.6.3)
utf8 1.2.1 2021-03-12 [1] CRAN (R 3.6.3)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 3.6.3)
viridisLite 0.4.0 2021-04-13 [1] CRAN (R 3.6.3)
withr 2.4.2 2021-04-18 [1] CRAN (R 3.6.3)
# --------
# Makevars
# --------
CXX14FLAGS=-O3 -march=native -mtune=native -fPIC
CXX14=/shared/centos7/gcc/8.1.0/bin/g++
LDFLAGS+=-L/shared/centos7/gcc/8.1.0/lib64, -L/shared/centos7/gcc/8.1.0/libexec/gcc/x86_64-pc-linux-gnu/8.1.0, -L/shared/centos7/gcc/8.1.0/lib/gcc/x86_64-pc-linux-gnu/8.1.0,-rpath
CFLAGS+=-I/shared/centos7/gcc/8.1.0/lib/gcc/x86_64-pc-linux-gnu/8.1.0/include, -I/shared/centos7/gcc/8.1.0/include/c++/8.1.0, -I/shared/centos7/gcc/8.1.0/include/c++/8.1.0/x86_64-pc-linux-gnu,-rpath
# Make using all cores (set # to # of cores on your machine)
MAKE=make -j4