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| ## Emacs, make this -*- mode: sh; -*- | ||
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| FROM ubuntu:noble | ||
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| LABEL org.label-schema.license="GPL-2.0" \ | ||
| org.label-schema.vcs-url="https://github.com/rocker-org/" \ | ||
| org.label-schema.vendor="Rocker Project" \ | ||
| maintainer="Dirk Eddelbuettel <[email protected]>" | ||
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| ## Set a default user. Available via runtime flag `--user docker` | ||
| ## Add user to 'staff' group, granting them write privileges to /usr/local/lib/R/site.library | ||
| ## User should also have & own a home directory (for rstudio or linked volumes to work properly). | ||
| RUN useradd -s /bin/bash -m docker \ | ||
| && usermod -a -G staff docker \ | ||
| ## Refresh apt, install minimal tools | ||
| && apt-get update \ | ||
| && apt-get install -y --no-install-recommends \ | ||
| ca-certificates \ | ||
| locales \ | ||
| wget \ | ||
| ## Install key and setup R repo at CRAN | ||
| && wget -q -O - https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \ | ||
| | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \ | ||
| && echo "deb [arch=amd64 signed-by=/etc/apt/trusted.gpg.d/cran_ubuntu_key.asc] https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" \ | ||
| > /etc/apt/sources.list.d/cran.list \ | ||
| ## Install key and setup r2u repo, also set 'pin preference' | ||
| && wget -q -O - https://r2u.stat.illinois.edu/ubuntu/dirk_eddelbuettel_pubkey.asc \ | ||
| | tee -a /etc/apt/trusted.gpg.d/dirk_eddelbuettel_pubkey.asc \ | ||
| && echo "deb [arch=amd64 signed-by=/etc/apt/trusted.gpg.d/dirk_eddelbuettel_pubkey.asc] https://r2u.stat.illinois.edu/ubuntu noble main" \ | ||
| > /etc/apt/sources.list.d/r2u.list \ | ||
| && echo "Package: *" > /etc/apt/preferences.d/99r2u \ | ||
| && echo "Pin: release o=CRAN-Apt Project" >> /etc/apt/preferences.d/99r2u \ | ||
| && echo "Pin: release l=CRAN-Apt Packages" >> /etc/apt/preferences.d/99r2u \ | ||
| && echo "Pin-Priority: 700" >> /etc/apt/preferences.d/99r2u \ | ||
| ## Configure default locale, see https://github.com/rocker-org/rocker/issues/19 | ||
| && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \ | ||
| && locale-gen en_US.utf8 \ | ||
| && /usr/sbin/update-locale LANG=en_US.UTF-8 | ||
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| ## Set some variables | ||
| ENV LC_ALL en_US.UTF-8 | ||
| ENV LANG en_US.UTF-8 | ||
| ENV DEBIAN_FRONTEND noninteractive | ||
| ENV TZ UTC | ||
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| # Now install R and littler, and create a link for littler in /usr/local/bin | ||
| # Default CRAN repo is now set by R itself, and littler knows about it too | ||
| RUN apt-get update \ | ||
| && apt-get install -y --no-install-recommends \ | ||
| r-base \ | ||
| r-base-dev \ | ||
| r-recommended \ | ||
| ## Install bspm for r2u as well as remotes and docopt used in littler script | ||
| r-cran-docopt \ | ||
| r-cran-littler \ | ||
| r-cran-remotes \ | ||
| ## Install python support for bspm | ||
| python3-dbus \ | ||
| python3-gi \ | ||
| python3-apt \ | ||
| ## But install bspm from source | ||
| && Rscript -e 'install.packages("bspm")' \ | ||
| ## Support user-level installation of R packages | ||
| && chown root:staff "/usr/local/lib/R/site-library" \ | ||
| && chmod g+ws "/usr/local/lib/R/site-library" \ | ||
| ## Install a number littler scripts | ||
| && ln -s /usr/lib/R/site-library/littler/examples/build.r /usr/local/bin/build.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/check.r /usr/local/bin/check.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/installBioc.r /usr/local/bin/installBioc.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/installDeps.r /usr/local/bin/installDeps.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/installRub.r /usr/local/bin/installRub.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/tt.r /usr/local/bin/tt.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/tttf.r /usr/local/bin/tttf.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/tttl.r /usr/local/bin/tttl.r \ | ||
| && ln -s /usr/lib/R/site-library/littler/examples/update.r /usr/local/bin/update.r \ | ||
| ## Configure bspm and set one helpful apt default | ||
| && echo "options(bspm.version.check=FALSE)" >> /etc/R/Rprofile.site \ | ||
| && echo "suppressMessages(bspm::enable())" >> /etc/R/Rprofile.site \ | ||
| && echo 'APT::Install-Recommends "false";' > /etc/apt/apt.conf.d/90local-no-recommends \ | ||
| && rm -rf /tmp/downloaded_packages/ /tmp/*.rds \ | ||
| && rm -rf /var/lib/apt/lists/* |