Freeze R version 4.0.1

geospatial/.gitlab-ci.yml

@@ -5,7 +5,7 @@ services:
 variables:
   DOCKER_DRIVER: overlay2
   DOCKER_TLS_CERTDIR: "/certs"
-  R_VERSION_UPDATE: "false"
+  R_VERSION_UPDATE: "true"
 
 before_script:
   - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
@@ -32,9 +32,9 @@ build-latest:
 build-version:
   stage: build
   script:
-    - cd geospatial && docker build --pull -t $CI_REGISTRY_IMAGE:4.0.0 -f 4.0.0.Dockerfile .
-    - docker push $CI_REGISTRY_IMAGE:4.0.0
+    - cd geospatial && docker build --pull -t $CI_REGISTRY_IMAGE:4.0.1 -f 4.0.1.Dockerfile .
+    - docker push $CI_REGISTRY_IMAGE:4.0.1
   rules:
     - if: $CI_COMMIT_BRANCH == "freeze-version" && $R_VERSION_UPDATE != "true"
       changes:
-        - geospatial/4.0.0.Dockerfile
+        - geospatial/4.0.1.Dockerfile

geospatial/4.0.1.Dockerfile

+FROM registry.gitlab.b-data.ch/rocker/verse:4.0.1
+
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    lbzip2 \
+    libfftw3-dev \
+    libgdal-dev \
+    libgeos-dev \
+    libgsl0-dev \
+    libgl1-mesa-dev \
+    libglu1-mesa-dev \
+    libhdf4-alt-dev \
+    libhdf5-dev \
+    libjq-dev \
+    liblwgeom-dev \
+    libpq-dev \
+    libproj-dev \
+    libprotobuf-dev \
+    libnetcdf-dev \
+    libsqlite3-dev \
+    libssl-dev \
+    libudunits2-dev \
+    netcdf-bin \
+    postgis \
+    protobuf-compiler \
+    sqlite3 \
+    tk-dev \
+    unixodbc-dev \
+  && install2.r --error \
+    RColorBrewer \
+    RandomFields \
+    RNetCDF \
+    classInt \
+    deldir \
+    gstat \
+    hdf5r \
+    lidR \
+    mapdata \
+    maptools \
+    mapview \
+    ncdf4 \
+    proj4 \
+    raster \
+    rgdal \
+    rgeos \
+    rlas \
+    sf \
+    sp \
+    spacetime \
+    spatstat \
+    spdep \
+    geoR \
+    geosphere \
+  ## from bioconductor
+  && R -e "BiocManager::install('rhdf5', update = FALSE, ask = FALSE)" \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/*

r-ver/.gitlab-ci.yml

@@ -6,7 +6,7 @@ variables:
   DOCKER_DRIVER: overlay2
   DOCKER_TLS_CERTDIR: "/certs"
   CRAN: https://cloud.r-project.org
-  R_VERSION_UPDATE: "false"
+  R_VERSION_UPDATE: "true"
 
 before_script:
   - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
@@ -33,12 +33,12 @@ build-latest:
 build-version:
   stage: build
   script:
-    - docker build --pull -t $CI_REGISTRY_IMAGE:4.0.0 -f r-ver/4.0.0.Dockerfile .
-    - docker push $CI_REGISTRY_IMAGE:4.0.0
+    - docker build --pull -t $CI_REGISTRY_IMAGE:4.0.1 -f r-ver/4.0.1.Dockerfile .
+    - docker push $CI_REGISTRY_IMAGE:4.0.1
   rules:
     - if: $CI_COMMIT_BRANCH == "freeze-version"
       changes:
-        - r-ver/4.0.0.Dockerfile
+        - r-ver/4.0.1.Dockerfile
 
 trigger-latest-build-foreign:
   stage: deploy
@@ -75,4 +75,4 @@ trigger-version-build:
   rules:
     - if: $CI_COMMIT_BRANCH == "freeze-version"
       changes:
-        - r-ver/4.0.0.Dockerfile
+        - r-ver/4.0.1.Dockerfile

r-ver/4.0.1.Dockerfile

+FROM debian:buster
+
+LABEL org.label-schema.license="GPL-2.0" \
+      org.label-schema.vcs-url="https://gitlab.b-data.ch/r/docker-stack" \
+      maintainer="Olivier Benz <olivier.benz@b-data.ch>"
+
+ARG R_VERSION
+ARG BUILD_DATE
+
+ENV R_VERSION=${R_VERSION:-4.0.1} \
+    BUILD_DATE=${BUILD_DATE:-2020-06-22} \
+    LC_ALL=en_US.UTF-8 \
+    LANG=en_US.UTF-8 \
+    TERM=xterm
+
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    bash-completion \
+    ca-certificates \
+    file \
+    fonts-texgyre \
+    g++ \
+    gfortran \
+    gsfonts \
+    libblas-dev \
+    libbz2-1.0 \
+    libcurl4 \
+    libicu63 \
+    libjpeg62-turbo \
+    libopenblas-dev \
+    libpangocairo-1.0-0 \
+    libpcre2-8-0 \
+    libpng16-16 \
+    libreadline7 \
+    libtiff5 \
+    liblzma5 \
+    locales \
+    make \
+    unzip \
+    zip \
+    zlib1g \
+  && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
+  && locale-gen en_US.utf8 \
+  && /usr/sbin/update-locale LANG=en_US.UTF-8 \
+  && BUILDDEPS="curl \
+    default-jdk \
+    libbz2-dev \
+    libcairo2-dev \
+    libcurl4-openssl-dev \
+    libpango1.0-dev \
+    libjpeg-dev \
+    libicu-dev \
+    libpcre2-dev \
+    libpng-dev \
+    libreadline-dev \
+    libtiff5-dev \
+    liblzma-dev \
+    libx11-dev \
+    libxt-dev \
+    perl \
+    tcl8.6-dev \
+    tk8.6-dev \
+    texinfo \
+    texlive-extra-utils \
+    texlive-fonts-recommended \
+    texlive-fonts-extra \
+    texlive-latex-recommended \
+    x11proto-core-dev \
+    xauth \
+    xfonts-base \
+    xvfb \
+    zlib1g-dev" \
+  && apt-get install -y --no-install-recommends $BUILDDEPS \
+  && cd tmp/ \
+  ## Download source code
+  && curl -O https://cran.r-project.org/src/base/R-4/R-${R_VERSION}.tar.gz \
+  ## Extract source code
+  && tar -xf R-${R_VERSION}.tar.gz \
+  && cd R-${R_VERSION} \
+  ## Set compiler flags
+  && R_PAPERSIZE=letter \
+    R_BATCHSAVE="--no-save --no-restore" \
+    R_BROWSER=xdg-open \
+    PAGER=/usr/bin/pager \
+    PERL=/usr/bin/perl \
+    R_UNZIPCMD=/usr/bin/unzip \
+    R_ZIPCMD=/usr/bin/zip \
+    R_PRINTCMD=/usr/bin/lpr \
+    LIBnn=lib \
+    AWK=/usr/bin/awk \
+    CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \
+    CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \
+  ## Configure options
+  ./configure --enable-R-shlib \
+               --enable-memory-profiling \
+               --with-readline \
+               --with-blas \
+               --with-tcltk \
+               --disable-nls \
+               --with-recommended-packages \
+  ## Build and install
+  && make \
+  && make install \
+  ## 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 \
+  ## Fix library path
+  #&& sed -i '/^R_LIBS_USER=.*$/d' /usr/local/lib/R/etc/Renviron \
+  && echo "R_LIBS_SITE=\${R_LIBS_SITE-'/usr/local/lib/R/site-library'}" >> /usr/local/lib/R/etc/Renviron \
+  #&& echo "R_LIBS=\${R_LIBS-'/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library'}" >> /usr/local/lib/R/etc/Renviron \
+  ## Set configured CRAN mirror
+  && if [ -z "$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'), repo = '$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 from R source install
+  && cd / \
+  && rm -rf /tmp/* \
+  && apt-get remove --purge -y $BUILDDEPS \
+  && apt-get autoremove -y \
+  && apt-get autoclean -y \
+  && rm -rf /var/lib/apt/lists/*
+
+CMD ["R"]
+

rstudio/.gitlab-ci.yml

@@ -5,7 +5,7 @@ services:
 variables:
   DOCKER_DRIVER: overlay2
   DOCKER_TLS_CERTDIR: "/certs"
-  R_VERSION_UPDATE: "false"
+  R_VERSION_UPDATE: "true"
 
 before_script:
   - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
@@ -32,12 +32,12 @@ build-latest:
 build-version:
   stage: build
   script:
-    - cd rstudio && docker build --pull -t $CI_REGISTRY_IMAGE:4.0.0 -f 4.0.0.Dockerfile .
-    - docker push $CI_REGISTRY_IMAGE:4.0.0
+    - cd rstudio && docker build --pull -t $CI_REGISTRY_IMAGE:4.0.1 -f 4.0.1.Dockerfile .
+    - docker push $CI_REGISTRY_IMAGE:4.0.1
   rules:
     - if: $CI_COMMIT_BRANCH == "freeze-version" && $R_VERSION_UPDATE != "true"
       changes:
-        - rstudio/4.0.0.Dockerfile
+        - rstudio/4.0.1.Dockerfile
 
 trigger-latest-build:
   stage: deploy
@@ -61,4 +61,4 @@ trigger-version-build:
   rules:
     - if: $CI_COMMIT_BRANCH == "freeze-version" && $R_VERSION_UPDATE != "true"
       changes:
-        - rstudio/4.0.0.Dockerfile
+        - rstudio/4.0.1.Dockerfile

rstudio/4.0.1.Dockerfile

+FROM registry.gitlab.b-data.ch/r/r-ver:4.0.1
+
+ARG RSTUDIO_VERSION
+ENV RSTUDIO_VERSION=${RSTUDIO_VERSION:-1.3.959}
+ARG S6_VERSION
+ARG PANDOC_TEMPLATES_VERSION
+ENV S6_VERSION=${S6_VERSION:-v1.21.7.0}
+ENV S6_BEHAVIOUR_IF_STAGE2_FAILS=2
+ENV PATH=/usr/lib/rstudio-server/bin:$PATH
+ENV PANDOC_TEMPLATES_VERSION=${PANDOC_TEMPLATES_VERSION:-2.9}
+
+## Download and install RStudio server & dependencies
+## Attempts to get detect latest version, otherwise falls back to version given in $VER
+## Symlink pandoc, pandoc-citeproc so they are available system-wide
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    curl \
+    file \
+    git \
+    libapparmor1 \
+    libclang-dev \
+    libcurl4-openssl-dev \
+    libedit2 \
+    libssl-dev \
+    lsb-release \
+    multiarch-support \
+    nano \
+    psmisc \
+    procps \
+    python-setuptools \
+    sudo \
+    wget \
+  && if [ -z "$RSTUDIO_VERSION" ]; \
+    then RSTUDIO_URL="https://www.rstudio.org/download/latest/stable/server/bionic/rstudio-server-latest-amd64.deb"; \
+    else RSTUDIO_URL="http://download2.rstudio.org/server/bionic/amd64/rstudio-server-${RSTUDIO_VERSION}-amd64.deb"; fi \
+  && wget -q $RSTUDIO_URL \
+  && dpkg -i rstudio-server-*-amd64.deb \
+  && rm rstudio-server-*-amd64.deb \
+  ## Symlink pandoc & standard pandoc templates for use system-wide
+  && ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc /usr/local/bin \
+  && ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc /usr/local/bin \
+  && git clone --recursive --branch ${PANDOC_TEMPLATES_VERSION} https://github.com/jgm/pandoc-templates \
+  && mkdir -p /opt/pandoc/templates \
+  && cp -r pandoc-templates*/* /opt/pandoc/templates && rm -rf pandoc-templates* \
+  && mkdir /root/.pandoc && ln -s /opt/pandoc/templates /root/.pandoc/templates \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/ \
+  ## RStudio wants an /etc/R, will populate from $R_HOME/etc
+  && mkdir -p /etc/R \
+  ## Write config files in $R_HOME/etc
+  && echo '\n\
+    \n# Configure httr to perform out-of-band authentication if HTTR_LOCALHOST \
+    \n# is not set since a redirect to localhost may not work depending upon \
+    \n# where this Docker container is running. \
+    \nif(is.na(Sys.getenv("HTTR_LOCALHOST", unset=NA))) { \
+    \n  options(httr_oob_default = TRUE) \
+    \n}' >> /usr/local/lib/R/etc/Rprofile.site \
+  && echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron \
+  ## 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 \
+  ## configure git not to request password each time
+  && git config --system credential.helper 'cache --timeout=3600' \
+  && 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 \
+  && tar xzf /tmp/s6-overlay-amd64.tar.gz -C / \
+  && mkdir -p /etc/services.d/rstudio \
+  && echo '#!/usr/bin/with-contenv bash \
+          \n## load /etc/environment vars first: \
+  		  \n for line in $( cat /etc/environment ) ; do export $line ; done \
+          \n exec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0' \
+          > /etc/services.d/rstudio/run \
+  && echo '#!/bin/bash \
+          \n rstudio-server stop' \
+          > /etc/services.d/rstudio/finish \
+  && 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
+
+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

@@ -5,7 +5,7 @@ services:
 variables:
   DOCKER_DRIVER: overlay2
   DOCKER_TLS_CERTDIR: "/certs"
-  R_VERSION_UPDATE: "false"
+  R_VERSION_UPDATE: "true"
 
 before_script:
   - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
@@ -32,12 +32,12 @@ build-latest:
 build-version:
   stage: build
   script:
-    - cd tidyverse && docker build --pull -t $CI_REGISTRY_IMAGE:4.0.0 -f 4.0.0.Dockerfile .
-    - docker push $CI_REGISTRY_IMAGE:4.0.0
+    - cd tidyverse && docker build --pull -t $CI_REGISTRY_IMAGE:4.0.1 -f 4.0.1.Dockerfile .
+    - docker push $CI_REGISTRY_IMAGE:4.0.1
   rules:
     - if: $CI_COMMIT_BRANCH == "freeze-version" && $R_VERSION_UPDATE != "true"
       changes:
-        - tidyverse/4.0.0.Dockerfile
+        - tidyverse/4.0.1.Dockerfile
 
 trigger-latest-build:
   stage: deploy
@@ -61,4 +61,4 @@ trigger-version-build:
   rules:
     - if: $CI_COMMIT_BRANCH == "freeze-version" && $R_VERSION_UPDATE != "true"
       changes:
-        - tidyverse/4.0.0.Dockerfile
+        - tidyverse/4.0.1.Dockerfile

tidyverse/4.0.1.Dockerfile

+FROM registry.gitlab.b-data.ch/rocker/rstudio:4.0.1
+
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+  libxml2-dev \
+  libcairo2-dev \
+  libsqlite-dev \
+  libmariadbd-dev \
+  libmariadbclient-dev \
+  libpq-dev \
+  libssh2-1-dev \
+  unixodbc-dev \
+  libsasl2-dev \
+  && install2.r --error BiocManager \
+  && install2.r --error \
+    --deps TRUE \
+    tidyverse \
+    dplyr \
+    devtools \
+    formatR \
+    remotes \
+    selectr \
+    caTools \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/*

verse/.gitlab-ci.yml

@@ -5,7 +5,7 @@ services:
 variables:
   DOCKER_DRIVER: overlay2
   DOCKER_TLS_CERTDIR: "/certs"
-  R_VERSION_UPDATE: "false"
+  R_VERSION_UPDATE: "true"
 
 before_script:
   - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
@@ -32,12 +32,12 @@ build-latest:
 build-version:
   stage: build
   script:
-    - cd verse && docker build --pull -t $CI_REGISTRY_IMAGE:4.0.0 -f 4.0.0.Dockerfile .
-    - docker push $CI_REGISTRY_IMAGE:4.0.0
+    - cd verse && docker build --pull -t $CI_REGISTRY_IMAGE:4.0.1 -f 4.0.1.Dockerfile .
+    - docker push $CI_REGISTRY_IMAGE:4.0.1
   rules:
     - if: $CI_COMMIT_BRANCH == "freeze-version" && $R_VERSION_UPDATE != "true"
       changes:
-        - verse/4.0.0.Dockerfile
+        - verse/4.0.1.Dockerfile
 
 trigger-latest-build:
   stage: deploy
@@ -61,4 +61,4 @@ trigger-version-build:
   rules:
     - if: $CI_COMMIT_BRANCH == "freeze-version" && $R_VERSION_UPDATE != "true"
       changes:
-        - verse/4.0.0.Dockerfile
+        - verse/4.0.1.Dockerfile

verse/4.0.1.Dockerfile

+FROM registry.gitlab.b-data.ch/rocker/tidyverse:4.0.1
+
+# Version-stable CTAN repo from the tlnet archive at texlive.info, used in the
+# TinyTeX installation: chosen as the frozen snapshot of the TeXLive release
+# shipped for the base Debian image of a given rocker/r-ver tag.
+# Debian buster => TeXLive 2018, frozen release snapshot 2019/02/27
+ARG CTAN_REPO=${CTAN_REPO:-https://www.texlive.info/tlnet-archive/2019/02/27/tlnet}
+ENV CTAN_REPO=${CTAN_REPO}
+
+ENV PATH=$PATH:/opt/TinyTeX/bin/x86_64-linux/
+
+## 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 \
+    less \
+    libbz2-dev \
+    libgl1-mesa-dev \
+    libglu1-mesa-dev \
+    libicu-dev \
+    liblzma-dev \
+    libhunspell-dev \
+    libjpeg-dev \
+    libmagick++-dev \
+    libopenmpi-dev \
+    libpcre2-dev \
+    librdf0-dev \
+    libtiff-dev \
+    libv8-dev \
+    libzmq3-dev \
+    qpdf \
+    ssh \
+    texinfo \
+    vim \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/* \
+  ## Use tinytex for LaTeX installation
+  && install2.r --error tinytex \
+  ## Admin-based install of TinyTeX:
+  && wget -qO- \
+    "https://github.com/yihui/tinytex/raw/master/tools/install-unx.sh" | \
+    sh -s - --admin --no-path \
+  && mv ~/.TinyTeX /opt/TinyTeX \
+  && if /opt/TinyTeX/bin/*/tex -v | grep -q 'TeX Live 2018'; then \
+      ## Patch the Perl modules in the frozen TeX Live 2018 snapshot with the newer
+      ## version available for the installer in tlnet/tlpkg/TeXLive, to include the
+      ## fix described in https://github.com/yihui/tinytex/issues/77#issuecomment-466584510
+      ## as discussed in https://www.preining.info/blog/2019/09/tex-services-at-texlive-info/#comments
+      wget -P /tmp/ ${CTAN_REPO}/install-tl-unx.tar.gz \
+      && tar -xzf /tmp/install-tl-unx.tar.gz -C /tmp/ \
+      && cp -Tr /tmp/install-tl-*/tlpkg/TeXLive /opt/TinyTeX/tlpkg/TeXLive \
+      && rm -r /tmp/install-tl-*; \
+    fi \
+  && /opt/TinyTeX/bin/*/tlmgr path add \
+  && tlmgr install ae inconsolata listings metafont mfware parskip pdfcrop tex xcolor \
+  && tlmgr path add \
+  && Rscript -e "tinytex::r_texmf()" \
+  && chown -R root:staff /opt/TinyTeX \
+  && chmod -R g+w /opt/TinyTeX \
+  && chmod -R g+wx /opt/TinyTeX/bin \
+  && echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron \
+  && install2.r --error PKI \
+  ## And some nice R packages for publishing-related stuff
+  && install2.r --error --deps TRUE \
+    bookdown rticles rmdshower rJava \
+  ## Clean up
+  && rm -rf /tmp/*
+#
+## Consider including:
+# - yihui/printr R package (when released to CRAN)
+# - libgsl0-dev (GSL math library dependencies)