Compare revisions

Olivier Benz · Olivier Benz · Olivier Benz · Olivier Benz · Olivier Benz · Olivier Benz
--- a/CUDA.md
+++ b/CUDA.md
@@ -88,7 +88,7 @@ cd base && docker build \
  --build-arg BASE_IMAGE=ubuntu \
  --build-arg BASE_IMAGE_TAG=22.04 \
  --build-arg BUILD_ON_IMAGE=glcr.b-data.ch/cuda/r/ver \
-  --build-arg R_VERSION=4.4.2 \
+  --build-arg R_VERSION=4.4.3 \
  --build-arg CUDA_IMAGE_FLAVOR=devel \
  -t jupyterlab/cuda/r/base \
  -f latest.Dockerfile .

--- a/CUDA_VERSION_MATRIX.md
+++ b/CUDA_VERSION_MATRIX.md
@@ -6,6 +6,7 @@ Topmost entry = Tag `latest`

 | R     | Python  | SAGA[^1] | CUDA   | cuBLAS    | cuDNN     | NCCL   | TensorRT[^2]            | Linux distro |
 |:------|:--------|:---------|:-------|:----------|:----------|:-------|:------------------------|:-------------|
+| 4.4.3 | 3.12.9  | 7.3.0    | 12.8.0 | 12.8.3.14 | 8.9.7.29  | 2.25.1 | 10.8.0.43/<br>10.3.0.26 | Ubuntu 22.04 |
 | 4.4.2 | 3.12.9  | 7.3.0    | 12.8.0 | 12.8.3.14 | 8.9.7.29  | 2.25.1 | 10.8.0.43/<br>10.3.0.26 | Ubuntu 22.04 |
 | 4.4.1 | 3.12.7  | 7.3.0    | 12.6.2 | 12.6.3.3  | 8.9.7.29  | 2.23.4 | 10.6.0.26/<br>10.3.0.26 | Ubuntu 22.04 |
 | 4.4.0 | 3.12.4  | 7.3.0    | 12.5.0 | 12.5.2.13 | 8.9.7.29  | 2.21.5 | 10.0.1.6                | Ubuntu 22.04 |
@@ -41,7 +42,6 @@ given.
 | CUDA   | Linux driver version | Windows driver version[^6] |
 |:-------|:---------------------|:---------------------------|
 | 12.8.0 | ≥ 570.26             | ≥ 570.65                   |
-| 12.6.3 | ≥ 560.35.05          | ≥ 561.17                   |
 | 12.6.2 | ≥ 560.35.03          | ≥ 560.94                   |
 | 12.5.0 | ≥ 555.42.02          | ≥ 555.85                   |
 | 11.8.0 | ≥ 520.61.05          | ≥ 520.06                   |
@@ -58,7 +58,6 @@ Only works with
 | CUDA   | Driver version 535[^7] | Driver version 470[^8] |
 |:-------|:----------------------:|:----------------------:|
 | 12.8.0 | 🟢                      | 🔵                      |
-| 12.6.3 | 🟢                      | 🔵                      |
 | 12.6.2 | 🟢                      | 🔵                      |
 | 12.5.0 | 🟢                      | 🔵                      |
 | 11.8.0 | 🟡                      | 🟢                      |

--- a/README.md
+++ b/README.md
@@ -154,7 +154,7 @@ To install docker, follow the instructions for your platform:

 ```bash
 cd base && docker build \
-  --build-arg R_VERSION=4.4.2 \
+  --build-arg R_VERSION=4.4.3 \
  -t jupyterlab/r/base \
  -f latest.Dockerfile .
 ```

--- a/VERSION_MATRIX.md
+++ b/VERSION_MATRIX.md
@@ -8,7 +8,8 @@ Topmost entry = Tag `latest`

 | R     | Python  | Jupyter Hub | Jupyter Lab | code‑server (Code) | RStudio       | Neovim | Git    | Git LFS | Pandoc | CRAN date  | Linux distro |
 |:------|:--------|:------------|:------------|:-------------------|:--------------|:-------|:-------|:--------|:-------|:-----------|:-------------|
-| 4.4.2 | 3.12.9  | 5.2.1       | 4.3.5       | 4.97.2 (1.97.2)    | 2024.12.1+563 | 0.10.4 | 2.48.1 | 3.6.1   | 3.4    |            | Debian 12    |
+| 4.4.3 | 3.12.9  | 5.2.1       | 4.3.5       | 4.97.2 (1.97.2)    | 2024.12.1+563 | 0.10.4 | 2.48.1 | 3.6.1   | 3.4    | 2025‑02‑28 | Debian 12    |
+| 4.4.2 | 3.12.9  | 5.2.1       | 4.3.5       | 4.97.2 (1.97.2)    | 2024.12.1+563 | 0.10.4 | 2.48.1 | 3.6.1   | 3.4    | 2025‑02‑28 | Debian 12    |
 | 4.4.1 | 3.12.7  | 5.2.1       | 4.2.5       | 4.93.1 (1.93.1)    | 2024.09.0+375 | 0.10.2 | 2.47.0 | 3.5.1   | 3.2    | 2024‑10‑31 | Debian 12    |
 | 4.4.0 | 3.12.4  | 5.0.0       | 4.2.2       | 4.90.0 (1.90.0)    | 2024.04.2+764 | n/a    | 2.45.2 | 3.5.1   | 3.1.11 | 2024‑06‑14 | Debian 12    |
 | 4.3.3 | 3.11.9  | 4.1.5       | 4.1.6       | 4.23.0 (1.88.0)    | n/a           | n/a    | 2.44.0 | 3.5.1   | 3.1.11 | 2024‑04‑24 | Debian 12    |
@@ -24,7 +25,8 @@ Topmost entry = Tag `latest`

 | R     | CTAN date  | Quarto      |
 |:------|:-----------|:------------|
-| 4.4.2 |            | 1.6.42      |
+| 4.4.3 |            | 1.6.42      |
+| 4.4.2 | 2025‑02‑28 | 1.6.42      |
 | 4.4.1 | 2024‑10‑31 | 1.5.57      |
 | 4.4.0 | 2024‑06‑14 | 1.4.555     |
 | 4.3.3 | 2024‑04‑24 | 1.4.553     |
@@ -40,7 +42,8 @@ Topmost entry = Tag `latest`

 | R     | QGIS   | SAGA  | OTB[^1] |
 |:------|:-------|:------|:--------|
-| 4.4.2 | 3.40.3 | 9.1.3 | 9.1.0   |
+| 4.4.3 | 3.42.0 | 9.1.3 | 9.1.0   |
+| 4.4.2 | 3.42.0 | 9.1.3 | 9.1.0   |
 | 4.4.1 | 3.40.0 | 9.1.3 | 9.1.0   |
 | 4.4.0 | 3.36.3 | 9.1.3 | 9.0.0   |
 | 4.3.3 | 3.36.2 | 9.1.3 | 9.0.0   |

--- a/base/.gitlab-ci.yml
+++ b/base/.gitlab-ci.yml
 .env:
  variables:
-    R_VERSION: "4.4.2"
+    R_VERSION: "4.4.3"
    RSTUDIO_VERSION: "2024.12.1+563"
    TAG_VERSION_MAJ_MIN: "false"
    TAG_VERSION_MAJ: "false"

--- a/base/4.4.2.Dockerfile
+++ b/base/4.4.2.Dockerfile
--- a/base/latest.Dockerfile
+++ b/base/latest.Dockerfile
@@ -419,19 +419,10 @@ RUN apt-get update \
      >> $(which radian)_; \
    echo "$(which radian) \"\${@}\"" >> $(which radian)_; \
  fi \
-  ## Install httpgd
-  ## Archived on 2025-02-14 as requires archived package 'unigd'.
-  && install2.r --error --skipinstalled -n $NCPUS \
-    unigd \
-    AsioHeaders \
-  && curl -sLO https://cran.r-project.org/src/contrib/Archive/httpgd/httpgd_2.0.2.tar.gz \
-  && R CMD INSTALL httpgd_2.0.2.tar.gz \
-  && rm httpgd_2.0.2.tar.gz \
  ## Install the R kernel for Jupyter, languageserver and httpgd
  && install2.r --error --deps TRUE --skipinstalled -n $NCPUS \
    IRkernel \
    languageserver \
-    httpgd \
  && Rscript -e "IRkernel::installspec(user = FALSE, displayname = paste('R', Sys.getenv('R_VERSION')))" \
  ## Get rid of libcairo2-dev and its dependencies (incl. python3)
  && apt-get -y purge libcairo2-dev \

--- a/common/subtags/devtools/4.4.2.Dockerfile
+++ b/common/subtags/devtools/4.4.2.Dockerfile
+ARG BASE_IMAGE=debian
+ARG BASE_IMAGE_TAG=12
+ARG BUILD_ON_IMAGE
+ARG R_VERSION=4.4.2
+
+ARG NODE_VERSION=20.18.1
+ARG CODE_BUILTIN_EXTENSIONS_DIR=/opt/code-server/lib/vscode/extensions
+
+FROM glcr.b-data.ch/nodejs/nsi/${NODE_VERSION}/${BASE_IMAGE}:${BASE_IMAGE_TAG} AS nsi
+
+FROM ${BUILD_ON_IMAGE}:${R_VERSION}
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG BUILD_ON_IMAGE
+
+ARG NODE_VERSION
+ARG CODE_BUILTIN_EXTENSIONS_DIR
+ARG BUILD_START
+
+ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION} \
+    NODE_VERSION=${NODE_VERSION} \
+    BUILD_DATE=${BUILD_START}
+
+## Prevent Corepack showing the URL when it needs to download software
+ENV COREPACK_ENABLE_DOWNLOAD_PROMPT=0
+
+## Install Node.js
+COPY --from=nsi /usr/local /usr/local
+
+USER root
+
+ENV HOME=/root
+
+WORKDIR ${HOME}
+
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    bats \
+    libkrb5-dev \
+    libsecret-1-dev \
+    libx11-dev \
+    libxkbfile-dev \
+    libxt6 \
+    quilt \
+    rsync \
+  && if [ -n "$PYTHON_VERSION" ]; then \
+    ## make some useful symlinks that are expected to exist
+    ## ("/usr/bin/python" and friends)
+    for src in pydoc3 python3 python3-config; do \
+      dst="$(echo "$src" | tr -d 3)"; \
+      if [ -s "/usr/bin/$src" ] && [ ! -e "/usr/bin/$dst" ]; then \
+        ln -svT "$src" "/usr/bin/$dst"; \
+      fi \
+    done; \
+  fi \
+  ## Clean up Node.js installation
+  && bash -c 'rm -f /usr/local/bin/{docker-entrypoint.sh,yarn*}' \
+  && bash -c 'mv /usr/local/{CHANGELOG.md,LICENSE,README.md} \
+    /usr/local/share/doc/node' \
+  ## Enable corepack (Yarn, pnpm)
+  && corepack enable \
+  ## Install nFPM
+  && echo 'deb [trusted=yes] https://repo.goreleaser.com/apt/ /' \
+    | tee /etc/apt/sources.list.d/goreleaser.list \
+  && apt-get update \
+  && apt-get install -y --no-install-recommends nfpm \
+  ## Install code-server extensions
+  && code-server --extensions-dir "$CODE_BUILTIN_EXTENSIONS_DIR" \
+    --install-extension dbaeumer.vscode-eslint \
+  && code-server --extensions-dir "$CODE_BUILTIN_EXTENSIONS_DIR" \
+    --install-extension esbenp.prettier-vscode \
+  && code-server --extensions-dir "$CODE_BUILTIN_EXTENSIONS_DIR" \
+    --install-extension ms-python.black-formatter \
+  && code-server --extensions-dir "$CODE_BUILTIN_EXTENSIONS_DIR" \
+    --install-extension timonwong.shellcheck \
+  ## Enable shellcheck system-wide
+  && ln -sf "$CODE_BUILTIN_EXTENSIONS_DIR"/timonwong.shellcheck-*/binaries/*/*/shellcheck \
+    /usr/local/bin/shellcheck \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/* \
+    "$HOME/.config" \
+    "$HOME/.local"
+
+## Switch back to ${NB_USER} to avoid accidental container runs as root
+USER ${NB_USER}
+
+ENV HOME=/home/${NB_USER}
+
+WORKDIR ${HOME}
--- a/geospatial/.gitlab-ci.yml
+++ b/geospatial/.gitlab-ci.yml
 .env:
  variables:
-    R_VERSION: "4.4.2"
+    R_VERSION: "4.4.3"
    TAG_VERSION_MAJ_MIN: "false"
    TAG_VERSION_MAJ: "false"


--- a/geospatial/4.4.2.Dockerfile
+++ b/geospatial/4.4.2.Dockerfile
+ARG BUILD_ON_IMAGE=glcr.b-data.ch/jupyterlab/r/verse
+ARG R_VERSION=4.4.2
+
+FROM ${BUILD_ON_IMAGE}:${R_VERSION}
+
+ARG NCPUS=1
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG BUILD_ON_IMAGE
+ARG BUILD_START
+
+ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION} \
+    BUILD_DATE=${BUILD_START}
+
+USER root
+
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    libfftw3-dev \
+    libgdal-dev \
+    libgeos-dev \
+    libgsl0-dev \
+    #libgl1-mesa-dev \
+    #libglu1-mesa-dev \
+    libhdf4-alt-dev \
+    #libhdf5-dev \
+    libjq-dev \
+    #libpq-dev \
+    libproj-dev \
+    libprotobuf-dev \
+    libnetcdf-dev \
+    #libsqlite3-dev \
+    #libssl-dev \
+    libudunits2-dev \
+    nco \
+    netcdf-bin \
+    postgis \
+    protobuf-compiler \
+    sqlite3 \
+    tk-dev \
+    #unixodbc-dev
+  && install2.r --error --skipinstalled -n $NCPUS \
+    #RColorBrewer \
+    RNetCDF \
+    classInt \
+    deldir \
+    gstat \
+    hdf5r \
+    lidR \
+    mapdata \
+    mapview \
+    ncdf4 \
+    proj4 \
+    raster \
+    rlas \
+    sf \
+    sfarrow \
+    sp \
+    spacetime \
+    spatstat \
+    spatialreg \
+    spdep \
+    stars \
+    terra \
+    tidync \
+    tmap \
+    geoR \
+    geosphere \
+  ## from bioconductor
+  && R -e "BiocManager::install('rhdf5', update = FALSE, ask = FALSE)" \
+  ## Strip libraries of binary packages installed from P3M
+  && RLS=$(Rscript -e "cat(Sys.getenv('R_LIBS_SITE'))") \
+  && strip ${RLS}/*/libs/*.so \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/*
+
+## Switch back to ${NB_USER} to avoid accidental container runs as root
+USER ${NB_USER}
--- a/qgisprocess/.gitlab-ci.yml
+++ b/qgisprocess/.gitlab-ci.yml
 .env:
  variables:
-    R_VERSION: "4.4.2"
+    R_VERSION: "4.4.3"
    QGIS_VERSION: "3.42.0"
    OTB_VERSION: "9.1.0"
    TAG_VERSION_MAJ_MIN: "false"

--- a/qgisprocess/4.4.2.Dockerfile
+++ b/qgisprocess/4.4.2.Dockerfile
+ARG BASE_IMAGE=debian
+ARG BASE_IMAGE_TAG=12
+ARG BUILD_ON_IMAGE=glcr.b-data.ch/jupyterlab/r/geospatial
+ARG R_VERSION=4.4.2
+ARG QGIS_VERSION=3.42.0
+
+ARG SAGA_VERSION
+ARG OTB_VERSION
+## OTB_VERSION=9.1.0
+
+ARG PROC_SAGA_NG_VERSION
+
+FROM ${BASE_IMAGE}:${BASE_IMAGE_TAG} AS files
+
+ARG OTB_VERSION
+
+ARG NB_UID=1000
+ENV NB_GID=100
+
+RUN mkdir /files
+
+COPY conf/user /files
+COPY scripts /files
+
+RUN if [ "$(uname -m)" = "x86_64" ]; then \
+    ## QGIS: Set OTB application folder and OTB folder
+    qgis3Ini="/files/var/backups/skel/.local/share/QGIS/QGIS3/profiles/default/QGIS/QGIS3.ini"; \
+    echo "\n[Processing]" >> ${qgis3Ini}; \
+    if [ -z "${OTB_VERSION}" ]; then \
+      echo "Configuration\OTB_APP_FOLDER=/usr/lib/otb/applications" >> \
+        ${qgis3Ini}; \
+      echo "Configuration\OTB_FOLDER=/usr\n" >> ${qgis3Ini}; \
+    else \
+      echo "Configuration\OTB_APP_FOLDER=/usr/local/lib/otb/applications" >> \
+        ${qgis3Ini}; \
+      echo "Configuration\OTB_FOLDER=/usr/local\n" >> ${qgis3Ini}; \
+    fi \
+  fi \
+  && chown -R ${NB_UID}:${NB_GID} /files/var/backups/skel \
+  ## Ensure file modes are correct when using CI
+  ## Otherwise set to 777 in the target image
+  && find /files -type d -exec chmod 755 {} \; \
+  && find /files -type f -exec chmod 644 {} \; \
+  && find /files/usr/local/bin -type f -exec chmod 755 {} \;
+
+FROM glcr.b-data.ch/qgis/qgissi/${QGIS_VERSION}/${BASE_IMAGE}:${BASE_IMAGE_TAG} AS qgissi
+FROM glcr.b-data.ch/saga-gis/saga-gissi${SAGA_VERSION:+/}${SAGA_VERSION:-:none}${SAGA_VERSION:+/$BASE_IMAGE}${SAGA_VERSION:+:$BASE_IMAGE_TAG} AS saga-gissi
+FROM glcr.b-data.ch/orfeotoolbox/otbsi${OTB_VERSION:+/}${OTB_VERSION:-:none}${OTB_VERSION:+/$BASE_IMAGE}${OTB_VERSION:+:$BASE_IMAGE_TAG} AS otbsi
+
+FROM ${BUILD_ON_IMAGE}:${R_VERSION}
+
+ARG NCPUS=1
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG BUILD_ON_IMAGE
+ARG QGIS_VERSION
+ARG SAGA_VERSION
+ARG OTB_VERSION
+ARG PROC_SAGA_NG_VERSION
+ARG BUILD_START
+
+ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION} \
+    QGIS_VERSION=${QGIS_VERSION} \
+    SAGA_VERSION=${SAGA_VERSION} \
+    OTB_VERSION=${OTB_VERSION} \
+    BUILD_DATE=${BUILD_START}
+
+USER root
+
+ENV HOME=/root \
+    ## GRASS GIS: Make sure the distro's python is used
+    GRASS_PYTHON=/usr/bin/python3
+
+WORKDIR ${HOME}
+
+## Install QGIS
+COPY --from=qgissi /usr /usr
+## Install SAGA GIS
+COPY --from=saga-gissi /usr /usr
+## Install Orfeo Toolbox
+COPY --from=otbsi /usr/local /usr/local
+ENV GDAL_DRIVER_PATH=${OTB_VERSION:+disable} \
+    OTB_APPLICATION_PATH=${OTB_VERSION:+/usr/local/lib/otb/applications} \
+    OTB_INSTALL_DIR=${OTB_VERSION:+/usr/local}
+ENV OTB_APPLICATION_PATH=${OTB_APPLICATION_PATH:-/usr/lib/otb/applications} \
+    OTB_INSTALL_DIR=${OTB_INSTALL_DIR:-/usr}
+
+RUN apt-get update \
+  && apt-get -y install --no-install-recommends \
+    ## Multimedia files trancoding
+    ffmpeg \
+    ## QGIS: Additional runtime dependencies
+    '^libexiv2-[0-9]+$' \
+    '^libgdal[0-9]+$' \
+    libgeos-c1v5 \
+    '^libgsl[0-9]+$' \
+    libjs-jquery \
+    libjs-leaflet \
+    '^libprotobuf-lite[0-9]+$' \
+    libqca-qt5-2-plugins \
+    '^libqscintilla2-qt5-[0-9]+$' \
+    libqt5core5a \
+    libqt5gui5 \
+    libqt5keychain1 \
+    libqt5multimediawidgets5 \
+    libqt5network5 \
+    libqt5quickwidgets5 \
+    libqt5serialport5 \
+    libqt5sql5 \
+    libqt5webkit5 \
+    libqt5widgets5 \
+    libqt5xml5 \
+    libqwt-qt5-6 \
+    '^libspatialindex[0-9]+$' \
+    '^libzip[0-9]+$' \
+    ocl-icd-libopencl1 \
+    qt3d-assimpsceneimport-plugin \
+    qt3d-defaultgeometryloader-plugin \
+    qt3d-gltfsceneio-plugin \
+    qt3d-scene2d-plugin \
+    qt5-image-formats-plugins \
+    ## QGIS: Python 3 Support
+    gdal-bin \
+    libfcgi0ldbl \
+    libsqlite3-mod-spatialite \
+    python3-gdal \
+    python3-jinja2 \
+    python3-lxml \
+    python3-matplotlib \
+    python3-owslib \
+    python3-plotly \
+    python3-psycopg2 \
+    python3-pygments \
+    python3-pyproj \
+    python3-pyqt5 \
+    python3-pyqt5.qsci \
+    python3-pyqt5.qtmultimedia \
+    python3-pyqt5.qtpositioning \
+    python3-pyqt5.qtserialport \
+    python3-pyqt5.qtsql \
+    python3-pyqt5.qtsvg \
+    python3-pyqt5.qtwebkit \
+    python3-sip \
+    python3-yaml \
+    qttools5-dev-tools \
+    ## QGIS: Additional runtime recommendations
+    grass \
+    ## QGIS: Additional runtime suggestions
+    gpsbabel \
+    ## SAGA GIS: Supplementary runtime dependencies [^1]
+    libdxflib3 \
+    libhpdf-2.3.0 \
+    libsvm3 \
+    libwxgtk3.*-dev \
+    $(test -z "${SAGA_VERSION}" && echo "saga") \
+  ## Orfeo Toolbox: Supplementary runtime dependencies
+  && if [ "$(uname -m)" = "x86_64" ]; then \
+    apt-get -y install --no-install-recommends \
+      '^libboost-filesystem[0-9].[0-9]+.[0-9]$' \
+      '^libboost-serialization[0-9].[0-9]+.[0-9]$' \
+      libglew2.* \
+      '^libinsighttoolkit4.[0-9]+$' \
+      libmuparser2v5 \
+      libmuparserx4.* \
+      '^libopencv-core[0-9][0-9.][0-9][a-z]?$' \
+      '^libopencv-ml[0-9][0-9.][0-9][a-z]?$' \
+      libtinyxml-dev \
+      $(test -z "${OTB_VERSION}" && echo "otb-* monteverdi"); \
+    if [ ! -z "${OTB_VERSION}" ]; then \
+      if [ "$(echo ${OTB_VERSION} | cut -c 1)" -lt "8" ]; then \
+        apt-get -y install --no-install-recommends \
+          '^libopenthreads[0-9]+$' \
+          libossim1; \
+      fi; \
+      ## Orfeo Toolbox: Clean up installation
+      bash -c 'rm -rf /usr/local/{otbenv.profile,recompile_bindings.sh,tools}'; \
+      if [ -f /usr/local/README ]; then \
+        mv /usr/local/README /usr/local/share/doc/otb; \
+      fi; \
+      if [ -f /usr/local/LICENSE ]; then \
+        mv /usr/local/LICENSE /usr/local/share/doc/otb; \
+      fi \
+    else \
+      mkdir -p /usr/lib/otb; \
+      ln -rs /usr/lib/$(uname -m)-linux-gnu/otb/applications \
+        /usr/lib/otb/applications; \
+    fi \
+  fi \
+  ## GRASS GIS: Configure dynamic linker run time bindings
+  && echo "$(grass --config path)/lib" | tee /etc/ld.so.conf.d/libgrass.conf \
+  && ldconfig \
+  ## SAGA GIS: Add en_GB.UTF-8 and update locale
+  && sed -i "s/# $LANG/$LANG/g" /etc/locale.gen \
+  && sed -i "s/# en_GB.UTF-8/en_GB.UTF-8/g" /etc/locale.gen \
+  && locale-gen \
+  ## [^1]: SAGA GIS: libvigraimpex11 is not available for jammy
+  && if $(! grep -q "jammy" /etc/os-release); then \
+    apt-get -y install --no-install-recommends '^libvigraimpex[0-9]+$'; \
+  fi \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/* \
+    ${HOME}/.cache \
+    ${HOME}/.grass*
+
+## Install QGIS related stuff
+RUN apt-get update \
+  ## Install QGIS-Plugin-Manager
+  && apt-get -y install --no-install-recommends python3-pip \
+  && export PIP_BREAK_SYSTEM_PACKAGES=1 \
+  && /usr/bin/pip install qgis-plugin-manager \
+  ## Install qgisprocess, the R interface to QGIS
+  && install2.r --error --skipinstalled -n $NCPUS qgisprocess \
+  ## Strip libraries of binary packages installed from P3M
+  && RLS=$(Rscript -e "cat(Sys.getenv('R_LIBS_SITE'))") \
+  && strip ${RLS}/*/libs/*.so \
+  ## Clean up
+  && if [ ! -z "$PYTHON_VERSION" ]; then \
+    apt-get -y purge python3-pip; \
+    apt-get -y autoremove; \
+  fi \
+  && rm -rf /var/lib/apt/lists/* \
+    ${HOME}/.cache \
+    ${HOME}/.config \
+    ${HOME}/.local
+
+## Switch back to ${NB_USER} to avoid accidental container runs as root
+USER ${NB_USER}
+
+ENV HOME=/home/${NB_USER} \
+    ## Qt: Support running on headless computer
+    QT_QPA_PLATFORM=offscreen
+
+WORKDIR ${HOME}
+
+## Copy files as late as possible to avoid cache busting
+COPY --from=files /files /
+COPY --from=files /files/var/backups/skel ${HOME}
+
+  ## QGIS: Install plugin 'Processing Saga NextGen Provider'
+RUN mkdir -p ${HOME}/.local/share/QGIS/QGIS3/profiles/default/python/plugins \
+  && cd ${HOME}/.local/share/QGIS/QGIS3/profiles/default/python/plugins \
+  && qgis-plugin-manager init \
+  && qgis-plugin-manager update \
+  && qgis-plugin-manager install 'Processing Saga NextGen Provider'=="${PROC_SAGA_NG_VERSION:-0.0.7}" \
+  ## QGIS: Enable plugins
+  && qgis_process plugins enable processing_saga_nextgen \
+  && qgis_process plugins enable grassprovider \
+  && if [ "$(uname -m)" = "x86_64" ]; then \
+    ## QGIS: Install and enable OTB plugin
+    qgis-plugin-manager install 'OrfeoToolbox Provider'; \
+    qgis_process plugins enable orfeoToolbox_provider; \
+  fi \
+  && rm -rf .cache_qgis_plugin_manager \
+  ## Clean up
+  && rm -rf \
+    ${HOME}/.cache/QGIS \
+    ${HOME}/.cache/qgis_process_ \
+    ${HOME}/.config \
+    ${HOME}/.grass* \
+  ## Create backup of QGIS settings
+  && cp -a ${HOME}/.local/share/QGIS /var/backups/skel/.local/share
+
+ENV PYTHONPATH=${PYTHONPATH:+$PYTHONPATH:}${OTB_VERSION:+/usr/local/lib/otb/python}
--- a/tidyverse/.gitlab-ci.yml
+++ b/tidyverse/.gitlab-ci.yml
 .env:
  variables:
-    R_VERSION: "4.4.2"
+    R_VERSION: "4.4.3"
    TAG_VERSION_MAJ_MIN: "false"
    TAG_VERSION_MAJ: "false"


--- a/tidyverse/4.4.2.Dockerfile
+++ b/tidyverse/4.4.2.Dockerfile
+ARG BUILD_ON_IMAGE=glcr.b-data.ch/jupyterlab/r/base
+ARG R_VERSION=4.4.2
+
+FROM ${BUILD_ON_IMAGE}:${R_VERSION}
+
+ARG NCPUS=1
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG BUILD_ON_IMAGE
+ARG BUILD_START
+
+ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION} \
+    BUILD_DATE=${BUILD_START}
+
+USER root
+
+RUN apt-get update \
+  && apt-get -y install --no-install-recommends \
+    cmake \
+    default-libmysqlclient-dev \
+    #libxml2-dev \
+    libfribidi-dev \
+    libgit2-dev \
+    libharfbuzz-dev \
+    libpq-dev \
+    libsasl2-dev \
+    libsqlite3-dev \
+    libssh2-1-dev \
+    #libtiff-dev \
+    libxtst6 \
+    unixodbc-dev \
+  && install2.r --error --skipinstalled -n $NCPUS BiocManager \
+  && install2.r --error --deps TRUE --skipinstalled -n $NCPUS \
+    tidyverse \
+    dplyr \
+    devtools \
+    formatR \
+  ## dplyr database backends
+  && install2.r --error --skipinstalled -n $NCPUS \
+    arrow \
+    duckdb \
+    fst \
+  ## Get rid of libharfbuzz-dev and its dependencies (incl. python3)
+  && apt-get -y purge libharfbuzz-dev \
+  && apt-get -y autoremove \
+  && apt-get -y install --no-install-recommends libharfbuzz-icu0 \
+  ## Strip libraries of binary packages installed from P3M
+  && RLS=$(Rscript -e "cat(Sys.getenv('R_LIBS_SITE'))") \
+  && strip ${RLS}/*/libs/*.so \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/*
+
+## Switch back to ${NB_USER} to avoid accidental container runs as root
+USER ${NB_USER}
--- a/verse/.gitlab-ci.yml
+++ b/verse/.gitlab-ci.yml
 .env:
  variables:
-    R_VERSION: "4.4.2"
+    R_VERSION: "4.4.3"
    CTAN_REPO_BUILD_LATEST: "https://mirror.init7.net/ctan/systems/texlive/tlnet"
    TAG_VERSION_MAJ_MIN: "false"
    TAG_VERSION_MAJ: "false"

--- a/verse/4.4.2.Dockerfile
+++ b/verse/4.4.2.Dockerfile
+ARG BUILD_ON_IMAGE=glcr.b-data.ch/jupyterlab/r/tidyverse
+ARG R_VERSION=4.4.2
+ARG CODE_BUILTIN_EXTENSIONS_DIR=/opt/code-server/lib/vscode/extensions
+ARG QUARTO_VERSION=1.6.42
+ARG CTAN_REPO=https://www.texlive.info/tlnet-archive/2025/02/28/tlnet
+
+FROM ${BUILD_ON_IMAGE}:${R_VERSION}
+
+ARG NCPUS=1
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG BUILD_ON_IMAGE
+ARG CODE_BUILTIN_EXTENSIONS_DIR
+ARG QUARTO_VERSION
+ARG CTAN_REPO
+ARG CTAN_REPO_BUILD_LATEST
+ARG BUILD_START
+
+USER root
+
+ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION} \
+    QUARTO_VERSION=${QUARTO_VERSION} \
+    BUILD_DATE=${BUILD_START}
+
+ENV HOME=/root \
+    PATH=/opt/TinyTeX/bin/linux:/opt/quarto/bin:$PATH
+
+WORKDIR ${HOME}
+
+## Add LaTeX, rticles and bookdown support
+RUN dpkgArch="$(dpkg --print-architecture)" \
+  && apt-get update \
+  && apt-get install -y --no-install-recommends \
+    default-jdk \
+    fonts-roboto \
+    ghostscript \
+    hugo \
+    lbzip2 \
+    libbz2-dev \
+    libglpk-dev \
+    libgmp3-dev \
+    libgl1-mesa-dev \
+    libglu1-mesa-dev \
+    libharfbuzz-dev \
+    libhunspell-dev \
+    libicu-dev \
+    liblzma-dev \
+    #libpcre2-dev \
+    libmagick++-dev \
+    libopenmpi-dev \
+    libpoppler-cpp-dev \
+    librdf0-dev \
+    ## Installing libnode-dev uninstalls nodejs
+    ## https://github.com/jeroen/V8/issues/100
+    #libnode-dev \
+    librsvg2-bin \
+    qpdf \
+    texinfo \
+    ## Python: For h5py wheels (arm64)
+    libhdf5-dev \
+  ## Install R package redland
+  && install2.r --error --skipinstalled -n $NCPUS redland \
+  ## Explicitly install runtime library sub-deps of librdf0-dev
+  && apt-get install -y \
+    libcurl4-openssl-dev \
+    libxslt-dev \
+    librdf0 \
+    redland-utils \
+    rasqal-utils \
+    raptor2-utils \
+  ## Get rid of librdf0-dev and its dependencies (incl. libcurl4-gnutls-dev)
+  && apt-get -y autoremove \
+  ## Install quarto
+  && curl -sLO https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${dpkgArch}.tar.gz \
+  && mkdir -p /opt/quarto \
+  && tar -xzf quarto-${QUARTO_VERSION}-linux-${dpkgArch}.tar.gz -C /opt/quarto --no-same-owner --strip-components=1 \
+  && rm quarto-${QUARTO_VERSION}-linux-${dpkgArch}.tar.gz \
+  ## Exempt quarto from address space limit
+  && sed -i 's/"${QUARTO_DENO}"/prlimit -v=unlimited: "${QUARTO_DENO}"/g' \
+    /opt/quarto/bin/quarto \
+  ## Remove quarto pandoc
+  && rm /opt/quarto/bin/tools/$(uname -m)/pandoc \
+  ## Link to system pandoc
+  && ln -s /usr/bin/pandoc /opt/quarto/bin/tools/$(uname -m)/pandoc \
+  ## Tell APT about the TeX Live installation
+  ## by building a dummy package using equivs
+  && apt-get install -y --no-install-recommends equivs \
+  && cd /tmp \
+  && wget https://github.com/scottkosty/install-tl-ubuntu/raw/master/debian-control-texlive-in.txt \
+  && equivs-build debian-* \
+  && mv texlive-local*.deb texlive-local.deb \
+  && dpkg -i texlive-local.deb \
+  && apt-get -y purge equivs \
+  && apt-get -y autoremove \
+  ## Admin-based install of TinyTeX
+  && CTAN_REPO_ORIG=${CTAN_REPO} \
+  && CTAN_REPO=${CTAN_REPO_BUILD_LATEST:-$CTAN_REPO} \
+  && export CTAN_REPO \
+  && wget -qO- "https://yihui.org/tinytex/install-unx.sh" \
+    | sh -s - --admin --no-path \
+  && mv ${HOME}/.TinyTeX /opt/TinyTeX \
+  && sed -i "s|${HOME}/.TinyTeX|/opt/TinyTeX|g" \
+    /opt/TinyTeX/texmf-var/fonts/conf/texlive-fontconfig.conf \
+  && ln -rs /opt/TinyTeX/bin/$(uname -m)-linux \
+    /opt/TinyTeX/bin/linux \
+  && /opt/TinyTeX/bin/linux/tlmgr path add \
+  && tlmgr update --self \
+  ## TeX packages as requested by the community
+  && curl -sSLO https://yihui.org/gh/tinytex/tools/pkgs-yihui.txt \
+  && tlmgr install $(cat pkgs-yihui.txt | tr '\n' ' ') \
+  && rm -f pkgs-yihui.txt \
+  ## TeX packages as in rocker/verse
+  && tlmgr install \
+    context \
+    pdfcrop \
+  ## TeX packages as in jupyter/scipy-notebook
+  && tlmgr install \
+    cm-super \
+    dvipng \
+  ## TeX packages specific for nbconvert
+  && tlmgr install \
+    oberdiek \
+    titling \
+  && tlmgr path add \
+  && tlmgr option repository ${CTAN_REPO_ORIG} \
+  && Rscript -e "tinytex::r_texmf()" \
+  && chown -R root:${NB_GID} /opt/TinyTeX \
+  && chmod -R g+w /opt/TinyTeX \
+  && chmod -R g+wx /opt/TinyTeX/bin \
+  ## Make the TeX Live fonts available as system fonts
+  && cp /opt/TinyTeX/texmf-var/fonts/conf/texlive-fontconfig.conf \
+    /etc/fonts/conf.d/09-texlive.conf \
+  && fc-cache -fsv \
+  && 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 \
+    quarto \
+    rticles \
+    rJava \
+    xaringan \
+  ## Install Cairo: R Graphics Device using Cairo Graphics Library
+  ## Install magick: Advanced Graphics and Image-Processing in R
+  && install2.r --error --skipinstalled -n $NCPUS \
+    Cairo \
+    magick \
+  ## Get rid of libharfbuzz-dev
+  && apt-get -y purge libharfbuzz-dev \
+  ## Get rid of libmagick++-dev
+  && apt-get -y purge libmagick++-dev \
+  ## and their dependencies (incl. python3)
+  && apt-get -y autoremove \
+  && apt-get -y install --no-install-recommends \
+    '^libmagick\+\+-6.q16-[0-9]+$' \
+    imagemagick \
+  ## Install code-server extensions
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension quarto.quarto \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension James-Yu.latex-workshop \
+  && if [ -n "${RSTUDIO_VERSION}" ]; then \
+    ## Check for quarto redundancy
+    if [ -d /opt/quarto ]; then \
+      ## Remove RStudio quarto
+      rm -rf /usr/lib/rstudio-server/bin/quarto; \
+      ## Link to system quarto
+      ln -s /opt/quarto /usr/lib/rstudio-server/bin/quarto; \
+    fi \
+  fi \
+  ## Strip libraries of binary packages installed from P3M
+  && RLS=$(Rscript -e "cat(Sys.getenv('R_LIBS_SITE'))") \
+  && strip ${RLS}/*/libs/*.so \
+  ## Update default PATH settings in /etc/profile.d/00-reset-path.sh
+  && sed -i 's|/opt/code-server/bin|/opt/TinyTeX/bin/linux:/opt/quarto/bin:/opt/code-server/bin|g' /etc/profile.d/00-reset-path.sh \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/* \
+    ${HOME}/.config \
+    ${HOME}/.local \
+    ${HOME}/.vscode-remote \
+    ${HOME}/.wget-hsts
+
+## Switch back to ${NB_USER} to avoid accidental container runs as root
+USER ${NB_USER}
+
+ENV CTAN_REPO=${CTAN_REPO}
+
+ENV HOME=/home/${NB_USER}
+
+WORKDIR ${HOME}
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