stan-dev / stan-dev/rstan

internal compiler error when installing in docker container

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R
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Description

Summary:

I'm pretty new to R and docker. When installing rstan into my docker container, I am getting the following error: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See file:///usr/share/doc/gcc-6/README.Bugs for instructions.
make: *** [lang__grammars__statement_grammar_inst.o] Error 4

Reproducible Steps:

FROM rocker/shiny
EXPOSE 3838
RUN Rscript --verbose -e "R.Version()"
RUN apt-get update; apt-get -y install clang libboost-all-dev libcurl4-openssl-dev libxml2-dev libcurl4-openssl-dev libssl-dev libmariadbclient-dev libpq-dev tcl8.6-dev tk8.6-dev
RUN update-alternatives --config c++
COPY . /srv/shiny-server
RUN echo "r <- getOption('repos'); r['CRAN'] <- 'https://cran.rstudio.com'; options(repos = r);" > ~/.Rprofile
RUN Rscript --verbose -e "capabilities('tcltk')"
RUN Rscript --verbose -e "update.packages(checkBuilt = TRUE, ask = FALSE)"
RUN Rscript --verbose -e "install.packages('rstan',dependencies = TRUE)"

Console Output

error.txt

RStan Version:

rstan_2.18.2.tar.gz

R Version:

R version 3.5.2 (2018-12-20)

Operating System:

PRETTY_NAME="Debian GNU/Linux 9 (stretch)"
NAME="Debian GNU/Linux"
VERSION_ID="9"
VERSION="9 (stretch)"
ID=debian

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the listed Docker build steps from the issue, especially the RStan installation command, and inspect error.txt alongside the compiler output. Compare the environment details for rocker/shiny, Debian 9, R 3.5.2, and rstan 2.18.2; done means the installation completes or the project has a documented, reproducible diagnosis.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, r
Domain
build-system, devops
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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