Building a Docker Image with rstan on rocker/verse - docker

Question

I am planning to run a customized Rstudio with both tidyverse, rmarkdown and rstan pre-installed on Digital Ocean's Docker 17.03.0-ce on 16.04.
On Docker Hub, there is already a pre-built image: Rocker/verse that has tidyverse and rmarkdown functionality. So my plan was to simply get the latest version of Rocker/verse and add a new layer of rstan. I use the dockerfile of jonzelner/rstan and jrnold/rstan and update them as below:
FROM rocker/verse:latest
# Install essentials
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
clang-3.6
# Global site-wide config
RUN mkdir -p $HOME/.R/ \
&& echo "\nCXX=clang++ -ftemplate-depth-256\n" >> $HOME/.R/Makevars \
&& echo "CC=clang\n" >> $HOME/.R/Makevars
# Install rstan
RUN install2.r --error \
inline \
RcppEigen \
StanHeaders \
rstan \
KernSmooth
# Config for rstudio user
RUN mkdir -p /home/rstudio/.R/ \
&& echo "\nCXX=clang++ -ftemplate-depth-256\n" >> /home/rstudio/.R/Makevars \
&& echo "CC=clang\n" >> /home/rstudio/.R/Makevars \
&& echo "CXXFLAGS=-O3\n" >> /home/rstudio/.R/Makevars \
&& echo "\nrstan::rstan_options(auto_write = TRUE)" >> /home/rstudio/.Rprofile \
&& echo "options(mc.cores = parallel::detectCores())" >> /home/rstudio/.Rprofile
# Install loo
RUN install2.r --error \
matrixStats \
loo
However, my attempt to build this image (docker build -t image_name .) ended in error. The results are provided below:
Sending build context to Docker daemon 2.56 kB
Step 1/6 : FROM rocker/verse:latest
---> 7ad7d994bffd
Step 2/6 : RUN apt-get update && apt-get install -y --no-install-recommends clang-3.6
---> Using cache
---> 77473c759438
Step 3/6 : RUN mkdir -p $HOME/.R/ && echo "\nCXX=clang++ -ftemplate-depth-256\n" >> $HOME/.R/Makevars && echo "CC=clang\n" >> $HOME/.R/Makevars
---> Using cache
---> a5b06d28b9fe
Step 4/6 : RUN install2.r --error inline RcppEigen StanHeaders rstan KernSmooth
---> Running in 86b52d5a76f3
trying URL 'https://cran.rstudio.com/src/contrib/inline_0.3.14.tar.gz'
Content type 'unknown' length 18002 bytes (17 KB)
==================================================
downloaded 17 KB
* installing *source* package ‘inline’ ...
** package ‘inline’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (inline)
The downloaded source packages are in
‘/tmp/downloaded_packages’
trying URL 'https://cran.rstudio.com/src/contrib/RcppEigen_0.3.2.9.0.tar.gz'
Content type 'unknown' length 1209128 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
* installing *source* package ‘RcppEigen’ ...
** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
** libs
clang++ -ftemplate-depth-256 -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppEigen.cpp -o RcppEigen.o
/bin/bash: clang++: command not found
/usr/local/lib/R/etc/Makeconf:141: recipe for target 'RcppEigen.o' failed
make: *** [RcppEigen.o] Error 127
ERROR: compilation failed for package ‘RcppEigen’
* removing ‘/usr/local/lib/R/site-library/RcppEigen’
Error in install.packages(pkgs = f, lib = lib, repos = if (isMatchingFile(f)) NULL else rep, :
installation of package ‘RcppEigen’ had non-zero exit status
The command '/bin/sh -c install2.r --error inline RcppEigen StanHeaders rstan KernSmooth' returned a non-zero code: 1
Some similar questions about a package having non-zero exit status have to do with memory, so I tried to increase the Docker memory on my local machine, but still no luck. Is there any thing I can do to successfully build this image?

Answer 1

As you see in the error output, the installation process cannot find the compiler:
/bin/bash: clang++: command not found
Be aware that this is the output from trying to install clang-3.6 in a rocker/verse container:
root#8ea0d98e67c3:/# apt-get install -y --no-install-recommends clang-3.6
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'python-clang-3.6' for regex 'clang-3.6'
0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
It appears that this image doesn't come with Clang 3.6 in its repositories. And this name instead points to python-clang-3.6; Clang bindings for the Python programming language.
Unless you absolutely want 3.6, I would install the plain clang package that points to 3.5, and then re-run the Docker build process.
apt-get install clang