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Cmdstan #2

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b9e7e84
initial attempt
elbamos Dec 29, 2018
d074098
add cmdstan, other bayesian packages
elbamos Jan 7, 2019
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43 changes: 29 additions & 14 deletions rstan/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,33 +1,48 @@
FROM rocker/verse:latest
MAINTAINER Jeffrey Arnold jeffrey.arnold@gmail.com

ENV STANVERSION 2.18.1

RUN apt-get update \
&& apt-get install -y --no-install-recommends apt-utils ed libnlopt-dev \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/

# Install rstan
RUN install2.r --error --deps TRUE \
rstan \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
RUN apt-get update && apt-get install -y \
clang-4.0 \
llvm-4.0 \
postgresql-client \
jags \
libc++-dev
RUN ln -s /usr/bin/clang++-4.0 /usr/bin/clang++

# Global site-wide config -- neeeded for building packages
RUN mkdir -p $HOME/.R/ \
&& echo "CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -flto -ffat-lto-objects -Wno-unused-local-typedefs \n" >> $HOME/.R/Makevars

# Config for rstudio user
RUN mkdir -p $HOME/.R/ \
&& echo "CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -flto -ffat-lto-objects -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations\n" >> $HOME/.R/Makevars \
&& echo "rstan::rstan_options(auto_write = TRUE)\n" >> /home/rstudio/.Rprofile \
&& echo "options(mc.cores = parallel::detectCores())\n" >> /home/rstudio/.Rprofile
&& echo "CC=clang-4.0" >> $HOME/.R/Makevars \
&& echo "CXX=clang++-4.0" >> $HOME/.R/Makevars \
&& echo "CXX14=clang++-4.0" >> $HOME/.R/Makevars \
&& echo "CXXFLAGS=-O2 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs \n" >> $HOME/.R/Makevars

# Install rstan
RUN install2.r --error --deps TRUE \
rstan \
loo \
RUN install2.r --error rstan --deps TRUE \
bayesplot \
rstanarm \
rjags \
rstantools \
shinystan \
tidybayes \
ggmcmc \
ggeffects \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds

# Config for rstudio user
RUN echo "rstan::rstan_options(auto_write = TRUE)\n" >> /home/rstudio/.Rprofile \
&& echo "options(mc.cores = parallel::detectCores())\n" >> /home/rstudio/.Rprofile

WORKDIR /opt
RUN wget https://github.com/stan-dev/cmdstan/releases/download/v${STANVERSION}/cmdstan-${STANVERSION}.tar.gz && \
tar -xzf cmdstan-${STANVERSION}.tar.gz
WORKDIR /opt/cmdstan-${STANVERSION}
RUN mkdir -p $HOME/.config/cmdstan \
&& echo "CXX=clang++-4.0" >> $HOME/.config/cmdstan/make.local
RUN make build && ln -fs /opt/cmdstan-${STANVERSION}/bin/stanc /usr/bin