Freeze R v4.2.0

geospatial/.gitlab-ci.yml

@@ -47,6 +47,8 @@ build-version:
       --build-arg R_VERSION
       --build-arg NCPUS=$((`nproc`/2+1))
       -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ
       -f geospatial/$R_VERSION.Dockerfile .
     - docker push -a $CI_REGISTRY_IMAGE
   rules:

geospatial/4.2.0.Dockerfile

+ARG R_VERSION=4.2.0
+
+FROM registry.gitlab.b-data.ch/rocker/verse:${R_VERSION}
+
+ARG NCPUS=1
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    gdal-bin \
+    libfftw3-dev \
+    libgdal-dev \
+    libgeos-dev \
+    libgsl0-dev \
+    libhdf4-alt-dev \
+    libhdf5-dev \
+    libjq-dev \
+    libproj-dev \
+    libprotobuf-dev \
+    libnetcdf-dev \
+    libudunits2-dev \
+    netcdf-bin \
+    postgis \
+    protobuf-compiler \
+    sqlite3 \
+    tk-dev \
+    unixodbc-dev \
+  && install2.r --error --skipinstalled -n $NCPUS \
+    RColorBrewer \
+    RNetCDF \
+    classInt \
+    deldir \
+    gstat \
+    hdf5r \
+    lidR \
+    mapdata \
+    maptools \
+    mapview \
+    ncdf4 \
+    proj4 \
+    raster \
+    rgdal \
+    rgeos \
+    rlas \
+    sf \
+    sp \
+    spacetime \
+    spatstat \
+    spatialreg \
+    spdep \
+    stars \
+    terra \
+    tidync \
+    tmap \
+    geosphere \
+  ## Archived on 2022-05-04 as check problems were not corrected in time.
+  && Rscript -e "devtools::install_version('RandomFields', version = '3.3.14')" \
+  ## Archived on 2022-05-04 as requires archived package 'RandomFields'.
+  && Rscript -e "devtools::install_version('geoR', version = '1.8-1')" \
+  ## from bioconductor
+  && R -e "BiocManager::install('rhdf5', update = FALSE, ask = FALSE)" \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/*
+
+## Install wgrib2 for NOAA's NOMADS / rNOMADS forecast files
+#RUN cd /opt \
+#  && wget https://www.ftp.cpc.ncep.noaa.gov/wd51we/wgrib2/wgrib2.tgz \
+#  && tar -xvf wgrib2.tgz \
+#  && rm -rf wgrib2.tgz \
+#  && cd grib2 \
+#  && CC=gcc FC=gfortran make \
+#  && ln -s /opt/grib2/wgrib2/wgrib2 /usr/local/bin/wgrib2

r-ver/.gitlab-ci.yml

@@ -168,6 +168,20 @@ build-manifest:version-linux-multiarch:
           $CI_APP_REPO:$CI_APP_TAG-linux-arm64v8
       fi
       docker manifest push $CI_APP_REPO:$CI_APP_TAG
+    - |
+      docker manifest create $CI_APP_REPO:$VERSION_MAJ_MIN $CI_MANIFEST_LIST
+      if echo $OS_ARCH | grep "linux-arm64v8" >/dev/null ; then
+        docker manifest annotate --variant v8 $CI_APP_REPO:$VERSION_MAJ_MIN \
+          $CI_APP_REPO:$CI_APP_TAG-linux-arm64v8
+      fi
+      docker manifest push $CI_APP_REPO:$VERSION_MAJ_MIN
+    - |
+      docker manifest create $CI_APP_REPO:$VERSION_MAJ $CI_MANIFEST_LIST
+      if echo $OS_ARCH | grep "linux-arm64v8" >/dev/null ; then
+        docker manifest annotate --variant v8 $CI_APP_REPO:$VERSION_MAJ \
+          $CI_APP_REPO:$CI_APP_TAG-linux-arm64v8
+      fi
+      docker manifest push $CI_APP_REPO:$VERSION_MAJ
   rules:
     - if: $CI_COMMIT_BRANCH == "freeze-version"
       changes:

r-ver/4.2.0.Dockerfile

+ARG IMAGE=debian:bullseye
+ARG BLAS=libopenblas-dev
+ARG R_VERSION=4.2.0
+ARG CRAN=https://cran.rstudio.com
+
+FROM registry.gitlab.b-data.ch/r/rsi/${R_VERSION}/${IMAGE} as rsi
+
+FROM ${IMAGE}
+
+LABEL org.opencontainers.image.licenses="GPL-2.0" \
+      org.opencontainers.image.source="https://gitlab.b-data.ch/rocker/docker-stack" \
+      org.opencontainers.image.vendor="b-data GmbH" \
+      org.opencontainers.image.authors="Olivier Benz <olivier.benz@b-data.ch>"
+
+ARG IMAGE
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG BLAS
+ARG R_VERSION
+ARG CRAN
+ARG BUILD_DATE
+
+ENV BASE_IMAGE=${IMAGE} \
+    BUILD_DATE=${BUILD_DATE:-2022-06-23} \
+    R_VERSION=${R_VERSION} \
+    CRAN=${CRAN} \ 
+    LANG=en_US.UTF-8 \
+    TERM=xterm \
+    TZ=Etc/UTC
+
+COPY --from=rsi /usr/local /usr/local
+
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    bash-completion \
+    build-essential \
+    ca-certificates \
+    devscripts \
+    file \
+    fonts-texgyre \
+    g++ \
+    gfortran \
+    gsfonts \
+    libbz2-dev \
+    '^libcurl[3|4]$' \
+    libicu-dev \
+    '^libjpeg.*-turbo.*-dev$' \
+    liblapack-dev \
+    liblzma-dev \
+    ${BLAS} \
+    libpangocairo-1.0-0 \
+    libpaper-utils \
+    '^libpcre[2|3]-dev$' \
+    libpng-dev \
+    libreadline-dev \
+    libtiff5 \
+    locales \
+    pkg-config \
+    unzip \
+    zip \
+    zlib1g \
+  ## Switch BLAS/LAPACK (manual mode)
+  && if [ ${BLAS} = "libopenblas-dev" ]; then \
+    update-alternatives --set libblas.so.3-$(uname -m)-linux-gnu \
+      /usr/lib/$(uname -m)-linux-gnu/openblas-pthread/libblas.so.3; \
+    update-alternatives --set liblapack.so.3-$(uname -m)-linux-gnu \
+      /usr/lib/$(uname -m)-linux-gnu/openblas-pthread/liblapack.so.3; \
+  fi \
+  ## Update locale
+  && sed -i "s/# $LANG/$LANG/g" /etc/locale.gen \
+  && locale-gen \
+  && update-locale LANG=$LANG \
+  ## Add a library directory (for user-installed packages)
+  && mkdir -p /usr/local/lib/R/site-library \
+  && chown root:staff /usr/local/lib/R/site-library \
+  && chmod g+ws /usr/local/lib/R/site-library \
+  ## Set configured CRAN mirror
+  && if [ -z "$BUILD_DATE" ]; then MRAN=$CRAN; \
+   else MRAN=https://mran.microsoft.com/snapshot/${BUILD_DATE}; fi \
+  && echo MRAN=$MRAN >> /etc/environment \
+  && echo "options(repos = c(CRAN='$MRAN'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \
+  ## Use littler installation scripts
+  && Rscript -e "install.packages(c('littler', 'docopt'), repos = '$MRAN')" \
+  && ln -s /usr/local/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
+  && ln -s /usr/local/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
+  && ln -s /usr/local/lib/R/site-library/littler/bin/r /usr/local/bin/r \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/*
+
+CMD ["R"]

rstudio/.gitlab-ci.yml

@@ -45,6 +45,8 @@ build-version:
       cd rstudio && docker build --pull
       --build-arg R_VERSION
       -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ
       -f $R_VERSION.Dockerfile .
     - docker push -a $CI_REGISTRY_IMAGE
   rules:

rstudio/4.2.0.Dockerfile

+ARG IMAGE=debian:bullseye
+ARG R_VERSION=4.2.0
+ARG GIT_VERSION=2.36.1
+ARG RSTUDIO_VERSION=2022.02.3+492
+ARG S6_VERSION=v2.2.0.3
+
+FROM registry.gitlab.b-data.ch/git/gsi/${GIT_VERSION}/${IMAGE} as gsi
+
+FROM registry.gitlab.b-data.ch/r/r-ver:${R_VERSION}
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG GIT_VERSION
+ARG RSTUDIO_VERSION
+ARG S6_VERSION
+
+ENV GIT_VERSION=${GIT_VERSION} \
+    RSTUDIO_VERSION=${RSTUDIO_VERSION} \
+    S6_VERSION=${S6_VERSION} \
+    S6_BEHAVIOUR_IF_STAGE2_FAILS=2 \
+    PATH=/usr/lib/rstudio-server/bin:$PATH
+
+COPY --from=gsi /usr/local /usr/local
+COPY --from=gsi /etc/bash_completion.d /etc/bash_completion.d
+
+## Download and install RStudio server & dependencies
+## Attempts to detect latest version, otherwise falls back to $RSTUDIO_VERSION
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    curl \
+    file \
+    libapparmor1 \
+    libclang-dev \
+    libcurl4-openssl-dev \
+    libedit2 \
+    libpq-dev \
+    libssl-dev \
+    lsb-release \
+    nano \
+    psmisc \
+    procps \
+    python-setuptools \
+    sudo \
+    wget \
+    ## Additional git runtime dependencies
+    libcurl3-gnutls \
+    liberror-perl \
+    ## Additional git runtime recommendations
+    less \
+    ssh-client \
+  && if [ -z "$RSTUDIO_VERSION" ]; \
+    then wget "https://www.rstudio.org/download/latest/stable/server/bionic/rstudio-server-latest-amd64.deb"; \
+    else /bin/bash -c 'wget "http://download2.rstudio.org/server/bionic/amd64/rstudio-server-${RSTUDIO_VERSION/'+'/'-'}-amd64.deb"'; \
+  fi \
+  && dpkg -i rstudio-server-*-amd64.deb \
+  && rm rstudio-server-*-amd64.deb \
+  ## https://github.com/rocker-org/rocker-versioned2/issues/137
+  rm -f /var/lib/rstudio-server/secure-cookie-key \
+  ## Symlink pandoc, pandoc-citeproc so they are available system-wide
+  && if [ -f "/usr/lib/rstudio-server/bin/pandoc/pandoc" ]; then \
+    BUNDLED_PANDOC="/usr/lib/rstudio-server/bin/pandoc/pandoc"; \
+  elif [ -f "/usr/lib/rstudio-server/bin/quarto/bin/pandoc" ]; then \
+    BUNDLED_PANDOC="/usr/lib/rstudio-server/bin/quarto/bin/pandoc"; \
+  elif [ -f "/usr/lib/rstudio-server/bin/quarto/bin/tools/pandoc" ]; then \
+    BUNDLED_PANDOC="/usr/lib/rstudio-server/bin/quarto/bin/tools/pandoc"; \
+  fi \
+  && ln -s "$BUNDLED_PANDOC" /usr/local/bin \
+  && if [ -f "${BUNDLED_PANDOC}-citeproc" ]; then \
+    ln -s "${BUNDLED_PANDOC}-citeproc" /usr/local/bin; \
+  fi \
+  ## Symlink pandoc & standard pandoc templates for use system-wide
+  && PANDOC_TEMPLATES_VERSION=$(pandoc -v | grep -oP "(?<=pandoc\s)[0-9\.]+$") \
+  && wget "https://github.com/jgm/pandoc-templates/archive/${PANDOC_TEMPLATES_VERSION}.tar.gz" -O pandoc-templates.tar.gz \
+  && rm -rf /opt/pandoc/templates \
+  && mkdir -p /opt/pandoc/templates \
+  && tar xvf pandoc-templates.tar.gz \
+  && cp -r pandoc-templates*/* /opt/pandoc/templates && rm -rf pandoc-templates* \
+  && rm -rf /root/.pandoc \
+  && mkdir /root/.pandoc && ln -s /opt/pandoc/templates /root/.pandoc/templates \
+  ## RStudio wants an /etc/R, will populate from $R_HOME/etc
+  && mkdir -p /etc/R \
+  && echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron.site \
+  ## Need to configure non-root user for RStudio
+  && useradd rstudio \
+  && echo "rstudio:rstudio" | chpasswd \
+	&& mkdir /home/rstudio \
+	&& chown rstudio:rstudio /home/rstudio \
+	&& addgroup rstudio staff \
+  ## Prevent rstudio from deciding to use /usr/bin/R if a user apt-get installs a package
+  && echo 'rsession-which-r=/usr/local/bin/R' >> /etc/rstudio/rserver.conf \
+  ## use more robust file locking to avoid errors when using shared volumes:
+  && echo 'lock-type=advisory' >> /etc/rstudio/file-locks \
+  ## Set default branch name to main
+  && git config --system init.defaultBranch main \
+  ## Store passwords for one hour in memory
+  && git config --system credential.helper "cache --timeout=3600" \
+  ## Merge the default branch from the default remote when "git pull" is run
+  && git config --system pull.rebase false \
+  # Push the current branch with the same name on the remote
+  && git config --system push.default simple \
+  ## Set up S6 init system
+  && wget -P /tmp/ https://github.com/just-containers/s6-overlay/releases/download/${S6_VERSION}/s6-overlay-amd64.tar.gz \
+  ## need the modified double tar now, see https://github.com/just-containers/s6-overlay/issues/288
+  && tar hzxf /tmp/s6-overlay-amd64.tar.gz -C / --exclude=usr/bin/execlineb \
+  && tar hzxf /tmp/s6-overlay-amd64.tar.gz -C /usr ./bin/execlineb && $_clean \
+  ## Set up RStudio init scripts
+  && mkdir -p /etc/services.d/rstudio \
+  && echo '#!/usr/bin/with-contenv bash \
+          \n## load /etc/environment vars first: \
+  		    \nfor line in $( cat /etc/environment ) ; do export $line > /dev/null; done \
+          \nexec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0' \
+          > /etc/services.d/rstudio/run \
+  && echo '#!/bin/bash \
+          \nrstudio-server stop' \
+          > /etc/services.d/rstudio/finish \
+  ## Log to syslog
+  && echo '[*] \
+          \nlog-level=warn \
+          \nlogger-type=syslog' \
+          > /etc/rstudio/logging.conf \
+  ## Rocker's default RStudio settings, for better reproducibility
+  && mkdir -p /home/rstudio/.rstudio/monitored/user-settings \
+  && echo 'alwaysSaveHistory="0" \
+          \nloadRData="0" \
+          \nsaveAction="0"' \
+          > /home/rstudio/.rstudio/monitored/user-settings/user-settings \
+  && chown -R rstudio:rstudio /home/rstudio/.rstudio \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/*
+
+COPY userconf.sh /etc/cont-init.d/userconf
+
+## running with "-e ADD=shiny" adds shiny server
+COPY add_shiny.sh /etc/cont-init.d/add
+COPY disable_auth_rserver.conf /etc/rstudio/disable_auth_rserver.conf
+COPY pam-helper.sh /usr/lib/rstudio-server/bin/pam-helper
+
+EXPOSE 8787
+
+CMD ["/init"]

tidyverse/.gitlab-ci.yml

@@ -47,6 +47,8 @@ build-version:
       --build-arg R_VERSION
       --build-arg NCPUS=$((`nproc`/2+1))
       -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ
       -f tidyverse/$R_VERSION.Dockerfile .
     - docker push -a $CI_REGISTRY_IMAGE
   rules:

tidyverse/4.2.0.Dockerfile

+ARG R_VERSION=4.2.0
+
+FROM registry.gitlab.b-data.ch/rocker/rstudio:${R_VERSION}
+
+ARG NCPUS=1
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update \
+  && apt-get -y --no-install-recommends install \
+    cmake \
+    libxml2-dev \
+    libcairo2-dev \
+    libsqlite3-dev \
+    libmariadb-dev \
+    libssh2-1-dev \
+    unixodbc-dev \
+    libsasl2-dev \
+    libtiff-dev \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    libgit2-dev \
+    libxtst6 \
+  && install2.r --error -n $NCPUS BiocManager \
+  && install2.r --error --deps TRUE --skipinstalled -n $NCPUS \
+    tidyverse \
+    dplyr \
+    devtools \
+    formatR \
+  ## dplyr database backends
+  && install2.r --error --skipinstalled -n $NCPUS \
+    arrow \
+    duckdb \
+    fst \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/*

verse/.gitlab-ci.yml

@@ -47,6 +47,8 @@ build-version:
       --build-arg R_VERSION
       --build-arg NCPUS=$((`nproc`/2+1))
       -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ
       -f verse/$R_VERSION.Dockerfile .
     - docker push -a $CI_REGISTRY_IMAGE
   rules:

verse/4.2.0.Dockerfile

+ARG R_VERSION=4.2.0
+ARG CTAN_REPO=https://www.texlive.info/tlnet-archive/2022/06/23/tlnet
+
+FROM registry.gitlab.b-data.ch/rocker/tidyverse:${R_VERSION}
+
+ARG NCPUS=1
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG CTAN_REPO
+
+ENV CTAN_REPO=${CTAN_REPO} \
+    PATH=/opt/TinyTeX/bin/linux:$PATH
+
+## Add LaTeX, rticles and bookdown support
+RUN wget "https://travis-bin.yihui.name/texlive-local.deb" \
+  && dpkg -i texlive-local.deb \
+  && rm texlive-local.deb \
+  && apt-get update \
+  && apt-get install -y --no-install-recommends \
+    cargo \
+    curl \
+    default-jdk \
+    fonts-roboto \
+    ghostscript \
+    hugo \
+    lbzip2 \
+    libbz2-dev \
+    libglpk-dev \
+    libgmp3-dev \
+    libgl1-mesa-dev \
+    libglu1-mesa-dev \
+    libicu-dev \
+    liblzma-dev \
+    libhunspell-dev \
+    libmagick++-dev \
+    libopenmpi-dev \
+    libpoppler-cpp-dev \
+    # librdf0-dev depends on libcurl4-gnutls-dev
+    librdf0-dev \
+    libnode-dev \
+    libzmq3-dev \
+    qpdf \
+    texinfo \
+    vim \
+  ## Install R package redland
+  && install2.r --error --skipinstalled -n $NCPUS redland \
+  ## Explicitly install runtime library sub-deps of librdf0-dev
+  && apt-get install -y \
+	  libcurl4-openssl-dev \
+	  libxslt-dev \
+	  librdf0 \
+	  redland-utils \
+	  rasqal-utils \
+	  raptor2-utils \
+  ## Get rid of librdf0-dev and its dependencies (incl. libcurl4-gnutls-dev)
+	&& apt-get -y autoremove \
+  && rm -rf /var/lib/apt/lists/* \
+  ## Admin-based install of TinyTeX:
+  && wget -qO- "https://yihui.org/tinytex/install-unx.sh" \
+    | sh -s - --admin --no-path \
+  && mv ~/.TinyTeX /opt/TinyTeX \
+  && ln -rs /opt/TinyTeX/bin/$(uname -m)-linux \
+    /opt/TinyTeX/bin/linux \
+  && /opt/TinyTeX/bin/linux/tlmgr path add \
+  && tlmgr update --self \
+  && tlmgr install \
+    ae \
+    cm-super \
+    context \
+    dvipng \
+    listings \
+    makeindex \
+    parskip \
+    pdfcrop \
+  && tlmgr path add \
+  && Rscript -e "tinytex::r_texmf()" \
+  && chown -R root:staff /opt/TinyTeX \
+  && chmod -R g+w /opt/TinyTeX \
+  && chmod -R g+wx /opt/TinyTeX/bin \
+  && echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron.site \
+  && install2.r --error --skipinstalled -n $NCPUS PKI \
+  ## And some nice R packages for publishing-related stuff
+  && install2.r --error --deps TRUE --skipinstalled -n $NCPUS \
+    blogdown \
+    bookdown \
+    distill \
+    rticles \
+    rmdshower \
+    rJava \
+    xaringan \
+  ## Clean up
+  && rm -rf /tmp/*