chore: update R version, removes incompatible packages, update docker…

…-stacks image * update R version, removes incompatible packages, unpin version * reduce layers (base), revert changes on legacy * chore: revert unpin versions Author: cheikhgwane <[email protected]> * chore(sonders):pin and update some packages version to match R4.4 * chore(blsq): bump pkgs version * chore: missing versions on base image --------- Co-authored-by: Cheikh Gueye Wane <[email protected]>
BLSQ · Jan 20, 2025 · d588f30 · d588f30
1 parent 75e0c98
commit d588f30
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diff --git a/images/base/Dockerfile b/images/base/Dockerfile
@@ -1,4 +1,4 @@
-FROM quay.io/jupyter/datascience-notebook:2024-01-08
+FROM quay.io/jupyter/datascience-notebook:2025-01-06
 
 LABEL org.opencontainers.image.source=https://github.com/blsq/openhexa-docker-images
 LABEL org.opencontainers.image.description="OpenHEXA Jupyter Notebook image with additional tools and libraries"
@@ -43,13 +43,13 @@ USER ${NB_UID}
 # Set environment variable for Conda cache directory inside the container
 ENV CONDA_PKGS_DIRS=/opt/conda/pkgs
 
-RUN conda install -n base conda-libmamba-solver && \
-  conda config --set solver libmamba
-
-RUN conda install --yes -c conda-forge -c R -c blsqtech -c bioconda \
+RUN conda uninstall r-base && conda install --yes  -c conda-forge -c R -c blsqtech -c bioconda \
+  'r-base=4.4.*' \
+  'r-irkernel=1.3.*' \
+  'nodejs=22.12.*' \
   'fsspec=2023.12.2' \
   'gcsfs=2023.12.2' \
-  'papermill=2.*' \
+  'papermill=2.6.*' \
   # Install openhexa-sdk & openhexa-toolbox from anaconda
   'openhexa.sdk=1.*' \
   'openhexa.toolbox=1.4.*' \

diff --git a/images/blsq-r/Dockerfile b/images/blsq-r/Dockerfile
@@ -22,12 +22,9 @@ RUN wget https://quarto.org/download/latest/quarto-linux-amd64.deb \
     && rm quarto-linux-amd64.deb
 
 
-RUN R -e "install.packages('ggnewscale', dependencies=TRUE, quiet=TRUE, repos='https://cran.r-project.org/')" 
-
 USER ${NB_UID}
 
 RUN conda install --yes -c R \
-  'r-gt=0.10.*'  \
   'r-extrafont=0.19.*'  \
   'r-glue=1.7.*'  \
   'r-here=1.0.*'  \
@@ -98,4 +95,4 @@ RUN conda install --yes -c R \
   'r-fs=1.6.*'  \
   'r-systemfonts=1.1.*'  \
   'r-units=0.8.*' &&\
-  conda clean --all -y
+  conda clean --all -y
diff --git a/images/blsq/Dockerfile b/images/blsq/Dockerfile
@@ -15,23 +15,17 @@ RUN R -e "options(Ncpus = parallel::detectCores()); install.packages(c('GISTools
 USER ${NB_UID}
 WORKDIR $HOME
 
-# R packages on R channel
-RUN conda install --yes -c R \
-  'r-imputets=3.*'  \
-  'r-tsbox=0.3.*' \
-  'r-mmwrweek=0.1.*' &&\
-  conda clean --all -y
-
-RUN conda install --yes -c conda-forge  -c R\
+# Install additional Python and R packages
+RUN conda install --yes  -c conda-forge -c R \
   # Python packages
-  'ruff=0.7.*' \
+  'ruff=0.9.*' \
   'boto3=1.35.*' \
   'python-kaleido=0.2.*' \
   'dateparser=1.2.*' \
   'dask-ml=2022.5.27' \
   'descartes=1.*' \
   'geoalchemy2=0.14.*' \
-  'geopandas=0.14.*' \
+  'geopandas=1.0.*' \
   'lerc=4.*' \
   'plotly=5.*' \
   'slack_sdk=3.*' \
@@ -48,39 +42,33 @@ RUN conda install --yes -c conda-forge  -c R\
   'netCDF4=1.*' \
   'polars=0.20.*' \
   'psycopg2=2.*' \
-  'pyarrow=14.*' \
+  'pyarrow=18.1.*' \
   'rapidfuzz=3.*' \
-  'rpy2=3.*' \
-  'xarray=2023.12.0' \
+  'xarray=2025.1.1' \
   'zarr=2.*' \
   'contextily=1.*' \
   'tabpy=2.*' \
   'docxtpl=0.11.*' \
   # R Packages
-  'r-arrow=14.*' \
+  'r-arrow=18.1.*' \
   'r-getpass=0.*' \
   'r-readxl=1.*' \
-  'r-isotree=0.5.*' \ 
   'r-rcolorbrewer=1.*' \
   'r-rjson=0.2.*' \
-  'r-rpostgres=1.*' \
+  'r-rpostgres=1.4.*' \
   'r-styler=1.*' \
-  'r-tidyverse=2.*' \
   'r-viridis=0.6.*' \
   'r-nloptr=2.*' \
-  'r-rgdal=1.*' \
-  'r-rgeos=0.6.*' \
-  'r-rgooglemaps=1.*' \
-  'r-geojsonio=0.11.*' \
-  'r-ggmap=3.*' \
-  'r-ggthemes=4.*' \
-  'r-hmisc=4.*' \
+  'r-rgeos=0.*' \
+  'r-rgooglemaps=1.5.*' \
+  'r-ggmap=4.0.*'\
+  'r-ggthemes=5.1.*' \
   'r-maptools=1.*' \
   'r-plotly=4.*' \
   'r-raster=3.*' \
   'r-sf=1.*' \
-  'r-stringi=1.*' &&\
-  conda clean --all -y
+  'r-stringi=1.*' \
+  && conda clean --all -y
 
 # Set PYTHONUNBUFFERED to ensure that Python output is sent straight to terminal
 ENV PYTHONUNBUFFERED=1

diff --git a/images/sonder/Dockerfile b/images/sonder/Dockerfile
@@ -11,7 +11,7 @@ USER ${NB_UID}
 WORKDIR $HOME
 RUN conda install --yes -c conda-forge \
   'r-rpostgres=1.4.*' \
-  'r-reticulate=1.34.*'\
+  'r-reticulate=1.40.*'\
   'r-rcolorbrewer=1.*'  \
   'r-rattle=5.5.*' \
   'r-colorspace=2.*' \
@@ -23,7 +23,7 @@ RUN conda install --yes -c conda-forge \
   'r-tibble=3.2.*' \
   'r-gridExtra=2.*' \ 
   'r-factoextra=1.0.*' \
-  'r-modelsummary=1.4.*' \
+  'r-modelsummary=2.2.*' \
   'r-poLCA=1.6.0.*' \ 
   'r-dplyr=1.1.*' \ 
   'r-forcats=1.0.*' \ 
@@ -43,24 +43,21 @@ RUN conda install --yes -c conda-forge \
   'r-corrplot=0.*'\
   'r-haven=2.5.*' \
   'r-survey=4.*'\
-  'r-ggplot2=3.1.*'\ 
-  'r-tidyr=0.8.*' \
+  'r-ggplot2=3.5.*'\ 
+  'r-tidyr=1.3.*' \
   'r-rodbc=1.*' \
-  'r-readxl=1.3.*'\
+  'r-readxl=1.4.*'\
   'r-reshape2=1.4.*' \
-  'r-data.table=1.12.*' \ 
-  'r-psych=1.8.*'  \
+  'r-data.table=1.15.*' \ 
+  'r-psych=2.4.*'  \
   'r-magrittr=2.0.*' \
   'r-stringr=1.5.*' \
-  'r-foreign=0.8_71.*' \
+  'r-foreign=0.*' \
   'r-config=0.3.*' \
-  'r-rgdal=1.*' \
-  'r-rgeos=0.6.*' \
-  'r-rgooglemaps=1.*' \
-  'r-geojsonio=0.11.*' \
-  'r-ggmap=3.*' \
-  'r-ggthemes=4.*' \
-  'r-hmisc=4.*' \
+  'r-rgeos=0.*' \
+  'r-rgooglemaps=1.5.*' \
+  'r-ggmap=4.0.*' \
+  'r-ggthemes=5.1.*' \
   'r-maptools=1.*' \
   'r-plotly=4.*' \
   'r-raster=3.*' \