BioDT · saanavainiocsc · Apr 29, 2025 · Apr 29, 2025 · Apr 29, 2025
diff --git a/container/Dockerfile b/container/Dockerfile
@@ -1,198 +1,70 @@
-ARG CONDA_VERSION=py312_24.7.1-0
-
-#########################################
-# Base
-#########################################
-FROM docker.io/opensuse/leap:15.4 AS base
-
-# Install general utilities:
-#   - R depends on which
-#   - R help needs less
-#   - r-devtools needs tar etc
-RUN zypper refresh && \
-    zypper --non-interactive install \
-        which less \
-        tar gzip unzip \
-        && \
-    zypper clean --all
-
-
-#########################################
-# Conda environment
-#########################################
-FROM base AS conda
-
-# Install conda
-ARG CONDA_VERSION
-RUN curl https://repo.anaconda.com/miniconda/Miniconda3-$CONDA_VERSION-Linux-x86_64.sh -o conda.sh && \
-    bash conda.sh -b -p /conda && \
-    rm conda.sh && \
-    /conda/bin/conda clean -afy
-
-# Create base R environment
-ARG R_VERSION
-RUN . /conda/etc/profile.d/conda.sh && \
-    conda create -p /conda/env -c conda-forge --override-channels --no-default-packages \
-        r-base=$R_VERSION \
-        && \
-    /conda/bin/conda clean -afy
-
-# Install common conda-available packages
-RUN . /conda/etc/profile.d/conda.sh && \
-    conda activate /conda/env && \
-    conda install -c conda-forge --override-channels \
-        r-devtools=2.4.5 \
-        r-remotes=2.4.2.1 \
-        r-rcpp=1.0.12 \
-        r-pbapply=1.7-2 \
-        r-tidyverse=2.0.0 \
-        r-terra=1.7-65 \
-        r-sf=1.0-15 \
-        && \
-    /conda/bin/conda clean -afy
-
-# Install other conda-available packages
-RUN . /conda/etc/profile.d/conda.sh && \
-    conda activate /conda/env && \
-    conda install -c conda-forge --override-channels \
-        r-rcpparmadillo=14.2.2-1 \
-        r-iterators=1.0.14 \
-        r-sp=2.1-3 \
-        r-raster=3.6-26 \
-        r-rgbif=3.8.0 \
-        r-rnaturalearth=1.0.1 \
-        r-rnaturalearthdata=1.0.0 \
-        r-ncdf4=1.22 \
-        r-epi=2.47.1 \
-        r-png=0.1-8 \
-        r-keyring=1.3.2 \
-        r-codetools=0.2-19 \
-        r-geometries=0.2-4 \
-        r-jsonify=1.2.2 \
-        r-rapidjsonr=1.2.0 \
-        r-sfheaders=0.4.4 \
-        r-countrycode=1.6.0 \
-        r-geojsonsf=2.0.3 \
-        r-r.devices=2.17.2 \
-        r-dbi=1.2.3 \
-        r-rlang=1.1.3 \
-        r-glue=1.8.0 \
-        r-withr=3.0.2 \
-        r-fmesher=0.2.0 \
-        r-rgdal=1.6-7 \
-        r-doParallel=1.0.17 \
-        r-foreach=1.5.2 \
-        r-doSNOW=1.0.20 \
-        r-automap=1.1-12 \
-        r-fasterize=1.1.0 \
-        r-stars=0.6-6 \
-        r-ggplot2=3.5.1 \
-        r-ggpubr=0.6.0 \
-        r-tidyr=1.3.1 \
-        r-viridis=0.6.5 \
-        r-cowplot=1.1.3 \
-        r-ggpmisc=0.6.1 \
-        r-gridExtra=2.3 \
-# Packages for capfitogen
-        r-maptools=1.1-8 \
-        r-dismo=1.3-16 \
-        r-rgeos=0.6-4 \
-        r-RJSONIO=1.3-1.9 \
-        r-googleVis=0.7.3 \
-        r-cluster=2.1.8 \
-        r-ade4=1.7-22 \
-        r-labdsv=2.1-0 \
-        r-mclust=6.1.1 \
-        r-clustvarsel=2.3.4 \
-        r-randomForest=4.7-1.2 \
-        r-modeltools=0.2-23 \
-        r-lattice=0.22-6 \
-        r-flexmix=2.3-19 \
-        r-fpc=2.2-13 \
-        r-vegan=2.6-8 \
-        r-adegenet=2.1.10 \
-# Packages for sdm
-        r-dismo=1.3-16 \
-        r-gbm=2.2.2 \
-        r-rjava=1.0-11 \
-        r-glmnet=4.1-8 \
-        r-tree=1.0-44 \
-        r-mda=0.5-5 \
-        r-plotrix=3.8-4 \
-        r-plotmo=3.6.4 \
-        r-earth=5.3.4 \
-        r-ranger=0.17.0 \
-        r-shinybs=0.61.1 \
-        r-crosstalk=1.2.1 \
-        r-rsnns=0.4-17 \
-        r-leaflet=2.2.2 \
-        r-leaflet.providers=2.0.0 \
+FROM docker.io/rocker/r-ver:4.4.1
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update -qy && \
+    apt-get install -qy \
+      curl \
+      gdal-bin \
+      gdal-data \
+      git \
+      libcurl4-openssl-dev \
+      libgdal-dev \
+      libgeos-dev \
+      libicu-dev \
+      libpng-dev \
+      libproj-dev \
+      libsqlite3-dev \
+      libssl-dev \
+      libudunits2-dev \
+      libxt6 \
+      make \
+      pandoc \
+      zlib1g-dev \
+      libsodium-dev \
+      pkg-config \
+      cmake \
+      libfontconfig1-dev \
+      libfreetype6-dev \
+      libharfbuzz-dev \
+      libfribidi-dev \
+      libgsl-dev \
+      tcl8.6-dev \
+      tk8.6-dev \
+      libgit2-dev \
+      default-jdk \
+      libbz2-dev \
+    && apt-get clean
+
+
+# R packages
+RUN Rscript -e 'install.packages("remotes")' && \
+    Rscript -e 'remotes::install_version("renv", version = "1.0.7")'
+
+
+COPY renv.lock renv.lock
+RUN Rscript -e 'renv::restore()'
+
+
+# install INLA
+RUN Rscript -e 'install.packages("INLA", repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)' \
+    && Rscript -e 'install.packages("MatrixModels", type="source")' \
+    && find /usr/local/lib/R/site-library/INLA/ -type f -perm -u+x -exec chmod a+x {} \;
+
+
+# install KrigR
+RUN export R_REMOTES_NO_ERRORS_FROM_WARNINGS="true" \
+    && Rscript -e 'install.packages(c("devtools"), repos="https://cloud.r-project.org")' \
+    && Rscript -e 'devtools::install_github("ErikKusch/KrigR", dependencies=FALSE)'
+
+
+# Docker
+RUN apt-get update -qy && \
+    apt-get install -qy \
+        docker.io \
         && \
-    /conda/bin/conda clean -afy
-
-# Set default CRAN repository
-RUN echo 'options(repos=c(CRAN="https://cloud.r-project.org"))' > /conda/env/lib/R/etc/Rprofile.site
-
-# Install non-conda-available packages
-RUN . /conda/etc/profile.d/conda.sh && \
-    conda activate /conda/env && \
-    Rscript -e 'install.packages(c( \
-        "blockCV", \
-        "ecmwfr", \
-        "giscoR", \
-        "tidyterra", \
-        "geodata", \
-        "mmap" \
-        ))' && \
-    Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/sdm/sdm_1.1-8.tar.gz", repos=NULL, type="source")' && \
-    Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/usdm_2.1-7.tar.gz", repos=NULL, type="source")' && \
-    /conda/bin/conda clean -afy
-
-# Install mraster
-RUN . /conda/etc/profile.d/conda.sh && \
-    conda activate /conda/env && \
-    Rscript -e 'devtools::install_github("babaknaimi/mraster", ref="386058cc11aa169193c1f3dc096ae9bd04736192", dependencies=FALSE)' && \
-    /conda/bin/conda clean -afy
-
-# Install KrigR
-RUN . /conda/etc/profile.d/conda.sh && \
-    conda activate /conda/env && \
-    export R_REMOTES_NO_ERRORS_FROM_WARNINGS="true" && \
-    # dependencies=FALSE so that RcppArmadillo doesn't get reinstalled
-    Rscript -e 'devtools::install_github("ErikKusch/KrigR", ref="760f3cb9c89784f04bea94830279fe2347ecb7ce", dependencies=FALSE)' && \
-    /conda/bin/conda clean -afy
-
-# Install remaining sdm dependencies (should be none)
-RUN . /conda/etc/profile.d/conda.sh && \
-    conda activate /conda/env && \
-    Rscript -e 'sdm::installAll() ' && \
-    /conda/bin/conda clean -afy
-
-# Workaround for memory issues in terra
-ADD terra_max_ram.cpp /opt/
-RUN /conda/env/bin/x86_64-conda-linux-gnu-g++ /opt/terra_max_ram.cpp -shared -fPIC -o /conda/env/lib/terra_max_ram.so && \
-    rm /opt/terra_max_ram.cpp
-
-# ENTRYPOINT ["bash"]
-
-# Clean files not needed runtime
-RUN find -L /conda/env/ -type f -name '*.a' -delete -print && \
-    find -L /conda/env/ -type f -name '*.js.map' -delete -print
-
-#########################################
-# Final container image
-#########################################
-FROM base
-
-COPY --from=conda /conda/env/ /conda/env/
-
-# Workaround for memory issues in terra
-ENV LD_PRELOAD=/conda/env/lib/terra_max_ram.so
+    apt-get clean
 
-ENV PROJ_DATA=/conda/env/share/proj \
-    PATH=/conda/env/bin:$PATH \
-    R_KEYRING_BACKEND=env \
-    LC_ALL=C.UTF-8
 
 ENTRYPOINT ["Rscript"]
 CMD ["--help"]
diff --git a/container/Makefile b/container/Makefile
@@ -1,6 +1,6 @@
 IMAGE_ROOT?=ghcr.io/biodt
 IMAGE=cwr
-IMAGE_VERSION=0.5.3
+IMAGE_VERSION=0.6.0
 R_VERSION=4.3.2