Issue creating docker image which installs rstan

I have the following image:

FROM rocker/r-ver:4.1.2

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/


RUN apt-get update 
RUN apt install software-properties-common  -y

# https://github.com/stan-dev/rstan/wiki/Configuring-C-Toolchain-for-Linux
RUN add-apt-repository -y ppa:marutter/rrutter4.0
RUN add-apt-repository -y ppa:c2d4u.team/c2d4u4.0+
RUN apt-get update
RUN apt install -y r-cran-rstan


# https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#installation-of-rstan
RUN Rscript -e 'Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1); install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE)'

After building the image with docker build -f Dockerfile -t docker_r_stan_test . (no errors output), then running: example(stan_model, package = "rstan", run.dontrun = TRUE) I'm expecting to see something similar to what's at: https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#verify-installation

I'm instead getting the output:

Error in find.package(package, lib.loc, verbose = verbose) :
  there is no package called ‘rstan’

I have a similar error trying to use library(rstan):

> library("rstan")
Error in library("rstan") : there is no package called ‘rstan’

I don't understand why rstan isn't installed properly within this image, as it seems I've followed the steps closely

Using Rocker images to install rstan is indeed a good idea, and I demontrated it via (essentially) a single command in this older post on my blog.

Your best bet, really, is to rely on Rocker containers already set up for the c2d4u.team repo. And, as @Oliver noted in a comment to your question, those are not the r-ver images which (for their own valid reason) follow a different internal model (which makes them less ideal for the binaries we show in use here).

First example: rocker/r-ubuntu:20.04

This "simply" relies on the fact that rstan exists here as a binary package r-cran-rstan -- so we install it in one command after updating the apt index.

edd@rob:~$ docker run --rm -ti rocker/r-ubuntu:20.04 bash
root@11e89aea64f6:/# apt update -qq
85 packages can be upgraded. Run 'apt list --upgradable' to see them.
root@11e89aea64f6:/# apt install r-cran-rstan
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  libpng-tools libtbb2 pandoc pandoc-data r-cran-backports r-cran-bh r-cran-brio r-cran-callr
  r-cran-checkmate r-cran-cli r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-data.table
  r-cran-desc r-cran-diffobj r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver
  r-cran-fastmatch r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-inline
  r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lifecycle r-cran-loo r-cran-magrittr
  r-cran-matrixstats r-cran-munsell r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgload
  r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp
  r-cran-rcppeigen r-cran-rcppparallel r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi
  r-cran-scales r-cran-stanheaders r-cran-svglite r-cran-systemfonts r-cran-testthat r-cran-tibble
  r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr
Suggested packages:
  texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context
  wkhtmltopdf librsvg2-bin groff ghc nodejs php python ruby libjs-mathjax node-katex r-cran-devtools
  r-cran-knitr r-cran-rmarkdown r-cran-tinytest r-cran-covr
The following NEW packages will be installed:
  libpng-tools libtbb2 pandoc pandoc-data r-cran-backports r-cran-bh r-cran-brio r-cran-callr
  r-cran-checkmate r-cran-cli r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-data.table
  r-cran-desc r-cran-diffobj r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver
  r-cran-fastmatch r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-inline
  r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lifecycle r-cran-loo r-cran-magrittr
  r-cran-matrixstats r-cran-munsell r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgload
  r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp
  r-cran-rcppeigen r-cran-rcppparallel r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstan
  r-cran-rstudioapi r-cran-scales r-cran-stanheaders r-cran-svglite r-cran-systemfonts r-cran-testthat
  r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr
0 upgraded, 64 newly installed, 0 to remove and 85 not upgraded.
Need to get 60.7 MB of archives.
After this operation, 345 MB of additional disk space will be used.
Do you want to continue? [Y/n] 

Second example: rocker/r-bspm:20.04

It gets even nicer thanks to bspm and its integration (and Inaki and I have an arXiv paper on this) because we can _use install.packages() (via a script) to fetch r-cran-rstan for us:

edd@rob:~$ docker run --rm -ti rocker/r-bspm:20.04 bash                                                  
root@ef07add5e9e7:/# apt update -qq
28 packages can be upgraded. Run 'apt list --upgradable' to see them.                                    
root@ef07add5e9e7:/# install.r rstan
(loaded the methods namespace)                                                                           
Loading required package: utils                                                                          Tracing function "install.packages" in package "utils"                                                   
Install system packages as root...
Reading package lists... Done
Building dependency tree         
Reading state information... Done
Hit http://archive.ubuntu.com/ubuntu focal InRelease                                                     
Hit http://security.ubuntu.com/ubuntu focal-security InRelease                                          
Hit http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal InRelease                                
Hit http://archive.ubuntu.com/ubuntu focal-updates InRelease                                            
Hit http://archive.ubuntu.com/ubuntu focal-backports InRelease                                          
Hit http://ppa.launchpad.net/edd/r-4.0/ubuntu focal InRelease                                           
Hit http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu focal InRelease                                 
Fetched 0 B in 0s (0 B/s)                                                                                
Reading package lists... Done    
Building dependency tree           
Reading state information... Done
Get:1 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal/main amd64 r-cran-backports amd64 1.4.1-
1cran1.2004.0 [94.9 kB]
Get:2 http://archive.ubuntu.com/ubuntu focal/main amd64 libpng-tools amd64 1.6.37-2 [26.1 kB]           
Get:3 http://archive.ubuntu.com/ubuntu focal/universe amd64 pandoc-data all 2.5-3build2 [76.0 kB]       
Get:4 http://archive.ubuntu.com/ubuntu focal/universe amd64 pandoc amd64 2.5-3build2 [15.4 MB] 
[... stuff omitted here for brevity ...]
Setting up r-cran-stanheaders (2.21.0-7-1cran1.2004.0) ...
Setting up r-cran-callr (3.7.0-1cran1.2004.0) ...
Setting up r-cran-tibble (3.1.6-1cran1.2004.0) ...
Setting up r-cran-pkgbuild (1.3.1-1cran1.2004.0) ...
Setting up r-cran-ggplot2 (3.3.5-1cran1.2004.0) ...
Setting up r-cran-rstan (2.21.3-1cran1.2004.0) ...
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...
root@d3045995c945:/# R

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

Loading required package: utils
Tracing function "install.packages" in package "utils"
> library(rstan)
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.21.3, 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)
> 

Note that we use install.r here -- a wrapper for install.packages() from littler -- to point at the R package yet we get the binary. And all its depends. In one command. I think I even posted an animated gif showing just this once ...

The key insight, though, is that none of this is limited to Docker. I am using the bspm approach on one small laptop where I don't want to compile from sources. It works flawlessly, and has for months.

Let us know here or on the r-sig-debian list if you have questions.

Edit: The animated gif I just created is too large to post it here (2mb limit) but fits for Twitter so here it is: https://twitter.com/eddelbuettel/status/1485318710818754567