Sporadic instances of 'errorValue' int 5 | Timed out #76
Description
Related: #75, r-lib/mirai#53. Happens both with and without targets, although most often on GitHub Actions targets R CMD check and in targets pipelines on my local Ubuntu machine.
I am starting to think this issue is specific to Ubuntu. My local Ubuntu installation:
$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.2 LTS"And ubuntu-latest on GitHub Actions is also 22.04.
I wrote a Dockerfile at https://github.com/ropensci/targets/blob/debug-crew/Dockerfile to get set up for reproducible examples on Ubuntu, included below for reference. (I suppose the version in FROM ubuntu:20.04 might need to change.)
# Use the same base image as 'ubuntu-latest'
FROM ubuntu:20.04
# Set environment variables
ENV NOT_CRAN=true
ENV TAR_NOT_CRAN=true
ENV R_KEEP_PKG_SOURCE=yes
ENV R_REMOTES_NO_ERRORS_FROM_WARNINGS=false
ENV TORCH_INSTALL=1
ENV DEBIAN_FRONTEND=noninteractive
ENV TZ=Etc/UTC
ENV LANG=en_US.UTF-8
ENV LANGUAGE=en_US:en
ENV LC_ALL=en_US.UTF-8
ENV _R_CHECK_FORCE_SUGGESTS_=false
# Install system dependencies
RUN apt-get update && \
apt-get install -y --no-install-recommends \
build-essential \
gfortran \
cmake \
git \
emacs \
ca-certificates \
libglpk-dev \
libglpk40 \
libmbedtls-dev \
curl \
htop \
gnupg2 \
lsb-release \
locales \
libxml2-dev \
libssl-dev \
libcurl4-openssl-dev && \
ln -fs /usr/share/zoneinfo/$TZ /etc/localtime && \
dpkg-reconfigure --frontend noninteractive tzdata
# Configure locale
RUN apt-get clean && apt-get update && \
apt-get install -y locales && \
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
dpkg-reconfigure --frontend=noninteractive locales && \
update-locale LANG=en_US.UTF-8
# Install R
RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" > /etc/apt/sources.list.d/cran.list && \
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && \
apt-get update && \
apt-get install -y --no-install-recommends r-base
# Install pandoc from r-lib/actions/setup-pandoc
RUN curl -fsSL https://github.com/jgm/pandoc/releases/download/2.11.4/pandoc-2.11.4-1-amd64.deb -o pandoc.deb && \
dpkg -i pandoc.deb && \
rm pandoc.deb
# Set up R environment
RUN R -e 'install.packages(c("remotes", "rcmdcheck", "languageserver", "pkgload", "testthat", "rmarkdown", "markdown", "knitr"), repos = "https://cloud.r-project.org/")'
# Install nanonext and mirai
RUN R -e 'install.packages(c("nanonext", "mirai"), repos = "https://shikokuchuo.r-universe.dev")'
# Install crew
RUN R -e 'remotes::install_github("wlandau/crew")'
# Install targets
RUN R -e 'remotes::install_github("ropensci/targets")'
# Set up the working directory
WORKDIR /workspace
@shikokuchuo, which systems do you test with?