I made a Docker image of Rstudio with Rstan packages and dependencies. I used a When I run my model, it returns an error as shown below:
Sys.setenv(R_FUTURE_RNG_ONMISUSE = "ignore")
MODEL1.nae <- brm(depfactor ~ factor1 + factor2 +
Factor3 + factor4 + factor5 +
(1 | labid) + (1 | subid_unique),
data = data.nae,
family = gaussian,
prior = prior_nae_1,
iter = 4000,
warmup = 2000,
chains = 4,
save_pars = save_pars(all = T),
control = list(adapt_delta = .95),
seed = 456
)
summary(MODEL1.nae)
MODEL2.nae <- brm(depfactor~ factor1 + factor2 +
Factor3 + factor4 +
(1 | labid) + (1 | subid_unique),
data = data.nae,
family = gaussian,
prior = prior_nae_null_1,
iter = 4000,
warmup = 2000,
chains = 4,
save_pars = save_pars(all = T),
control = list(adapt_delta = .95),
seed = 123
)
summary(MODEL2.nae)
Chain 1:
Chain 1: Elapsed Time: 4.1159 seconds (Warm-up)
Chain 1: 1.85004 seconds (Sampling)
Chain 1: 5.96594 seconds (Total)
Chain 1:
Error in unserialize(node$con) :
MultisessionFuture (<none>) failed to receive results from cluster RichSOCKnode #2 (PID 4567 on localhost 'localhost'). The reason reported was 'error reading from connection'. Post-mortem diagnostic: No process exists with this PID, i.e. the localhost worker is no longer alive. Detected a non-exportable reference ('externalptr' of class 'DLLHandle') in one of the globals ('args' of class 'list') used in the future expression. The total size of the 1 globals exported is 158.91 KiB. There is one global: 'args' (158.91 KiB of class 'list')
A snap of my Dockerfile:
FROM rocker/tidyverse:latest
# customizing RStudio
COPY build_imports/.config /home/rstudio/.config
COPY build_imports/.Rprofile /home/rstudio/
# copying the .R folder with Makevars
COPY build_imports/.R /home/rstudio/.R
# rstudio owns ~
RUN chown -R rstudio:rstudio /home/rstudio/
# installing libs
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
clang \
libv8-dev \
libudunits2-dev \
libgdal-dev \
libgeos-dev \
libproj-dev \
libxml2 \
libxml2-dev \
libglpk-dev
# installing rstan
RUN install2.r --error --deps TRUE \
BH\
StanHeaders\
Rcpp \
RcppEigen \
RcppParallel \
inline \
loo \
pkgbuild \
rstan \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
# need to get graph as a dep for igraph
RUN R -e "BiocManager::install('graph')"
# direct installs of a few more deps
RUN install2.r --error --deps TRUE \
igraph \
posterior \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
# cmdstanr as a dep for brms
RUN install2.r --error --deps TRUE -r "https://mc-stan.org/r-packages/" \
cmdstanr \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
RUN install2.r --error --deps TRUE \
brms \
tidybayes \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
RUN install2.r --error --deps TRUE \
janitor \
renv \
here \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
I am not sure of the bug is related to Rstan, or Docker image dependencies or due to memory issue.
Summary:
I have an error from compiling stan.
Description:
I made a Docker image of Rstudio with Rstan packages and dependencies. I used a When I run my model, it returns an error as shown below:
A snap of my Dockerfile:
I am not sure of the bug is related to Rstan, or Docker image dependencies or due to memory issue.