From ec0aa3fa842af96911a30f70b6df85614502dd2f Mon Sep 17 00:00:00 2001 From: Bryan Paget <8212170+bryanpaget@users.noreply.github.com> Date: Thu, 30 Jan 2025 08:46:40 -0500 Subject: [PATCH] Bryan update r 4.4.1 (#742) * feat: R 4.4.2 * feat: R 4.4.2 * feat: R 4.4.2 * feat: R 4.4.2 * feat: R 4.4.2 * feat: R 4.4.1 * feat: revert to older rstudio-server * Update 6_rstudio-server.Dockerfile --------- Co-authored-by: Paget, Bryan (StatCan) --- docker-bits/6_rstudio.Dockerfile | 10 +++++++++- output/jupyterlab-cpu/Dockerfile | 10 +++++++++- output/jupyterlab-pytorch/Dockerfile | 10 +++++++++- output/jupyterlab-tensorflow/Dockerfile | 10 +++++++++- output/rstudio/Dockerfile | 10 +++++++++- output/sas/Dockerfile | 10 +++++++++- 6 files changed, 54 insertions(+), 6 deletions(-) diff --git a/docker-bits/6_rstudio.Dockerfile b/docker-bits/6_rstudio.Dockerfile index 7fe5ba430..79d1d25a2 100644 --- a/docker-bits/6_rstudio.Dockerfile +++ b/docker-bits/6_rstudio.Dockerfile @@ -15,9 +15,16 @@ ENV PATH=$PATH:/usr/lib/rstudio-server/bin ENV SPARK_HOME="/opt/conda/lib/python3.11/site-packages/pyspark" # Install some default R packages -RUN mamba install --quiet --yes \ +# rpy2 is installed by upstream, I don't know if anyone uses it. +# ryp2 was causing problems with R 4.4.1, so I removed it from the +# mamba install. rpy2 is reinstalled with pip below. +# when we next upgrade R, let's try to restore rpy2 to its original state +# which means just remove mamba remove rpy2 and remove pip install rpy2 +RUN mamba remove rpy2 && \ + mamba install --quiet --yes \ 'r-arrow' \ 'r-aws.s3' \ + 'r-base=4.4.1' \ 'r-catools' \ 'r-e1071' \ 'r-hdf5r' \ @@ -29,6 +36,7 @@ RUN mamba install --quiet --yes \ 'r-sparklyr' \ 'r-tidyverse' \ && \ + pip install rpy2 && \ clean-layer.sh && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER diff --git a/output/jupyterlab-cpu/Dockerfile b/output/jupyterlab-cpu/Dockerfile index 6108be20c..8d53116c9 100644 --- a/output/jupyterlab-cpu/Dockerfile +++ b/output/jupyterlab-cpu/Dockerfile @@ -252,9 +252,16 @@ ENV PATH=$PATH:/usr/lib/rstudio-server/bin ENV SPARK_HOME="/opt/conda/lib/python3.11/site-packages/pyspark" # Install some default R packages -RUN mamba install --quiet --yes \ +# rpy2 is installed by upstream, I don't know if anyone uses it. +# ryp2 was causing problems with R 4.4.1, so I removed it from the +# mamba install. rpy2 is reinstalled with pip below. +# when we next upgrade R, let's try to restore rpy2 to its original state +# which means just remove mamba remove rpy2 and remove pip install rpy2 +RUN mamba remove rpy2 && \ + mamba install --quiet --yes \ 'r-arrow' \ 'r-aws.s3' \ + 'r-base=4.4.1' \ 'r-catools' \ 'r-e1071' \ 'r-hdf5r' \ @@ -266,6 +273,7 @@ RUN mamba install --quiet --yes \ 'r-sparklyr' \ 'r-tidyverse' \ && \ + pip install rpy2 && \ clean-layer.sh && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER diff --git a/output/jupyterlab-pytorch/Dockerfile b/output/jupyterlab-pytorch/Dockerfile index c4729bc67..a3501d102 100644 --- a/output/jupyterlab-pytorch/Dockerfile +++ b/output/jupyterlab-pytorch/Dockerfile @@ -274,9 +274,16 @@ ENV PATH=$PATH:/usr/lib/rstudio-server/bin ENV SPARK_HOME="/opt/conda/lib/python3.11/site-packages/pyspark" # Install some default R packages -RUN mamba install --quiet --yes \ +# rpy2 is installed by upstream, I don't know if anyone uses it. +# ryp2 was causing problems with R 4.4.1, so I removed it from the +# mamba install. rpy2 is reinstalled with pip below. +# when we next upgrade R, let's try to restore rpy2 to its original state +# which means just remove mamba remove rpy2 and remove pip install rpy2 +RUN mamba remove rpy2 && \ + mamba install --quiet --yes \ 'r-arrow' \ 'r-aws.s3' \ + 'r-base=4.4.1' \ 'r-catools' \ 'r-e1071' \ 'r-hdf5r' \ @@ -288,6 +295,7 @@ RUN mamba install --quiet --yes \ 'r-sparklyr' \ 'r-tidyverse' \ && \ + pip install rpy2 && \ clean-layer.sh && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER diff --git a/output/jupyterlab-tensorflow/Dockerfile b/output/jupyterlab-tensorflow/Dockerfile index f869e732f..c151f9643 100644 --- a/output/jupyterlab-tensorflow/Dockerfile +++ b/output/jupyterlab-tensorflow/Dockerfile @@ -381,9 +381,16 @@ ENV PATH=$PATH:/usr/lib/rstudio-server/bin ENV SPARK_HOME="/opt/conda/lib/python3.11/site-packages/pyspark" # Install some default R packages -RUN mamba install --quiet --yes \ +# rpy2 is installed by upstream, I don't know if anyone uses it. +# ryp2 was causing problems with R 4.4.1, so I removed it from the +# mamba install. rpy2 is reinstalled with pip below. +# when we next upgrade R, let's try to restore rpy2 to its original state +# which means just remove mamba remove rpy2 and remove pip install rpy2 +RUN mamba remove rpy2 && \ + mamba install --quiet --yes \ 'r-arrow' \ 'r-aws.s3' \ + 'r-base=4.4.1' \ 'r-catools' \ 'r-e1071' \ 'r-hdf5r' \ @@ -395,6 +402,7 @@ RUN mamba install --quiet --yes \ 'r-sparklyr' \ 'r-tidyverse' \ && \ + pip install rpy2 && \ clean-layer.sh && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER diff --git a/output/rstudio/Dockerfile b/output/rstudio/Dockerfile index 45a2560b3..74dcc2048 100644 --- a/output/rstudio/Dockerfile +++ b/output/rstudio/Dockerfile @@ -252,9 +252,16 @@ ENV PATH=$PATH:/usr/lib/rstudio-server/bin ENV SPARK_HOME="/opt/conda/lib/python3.11/site-packages/pyspark" # Install some default R packages -RUN mamba install --quiet --yes \ +# rpy2 is installed by upstream, I don't know if anyone uses it. +# ryp2 was causing problems with R 4.4.1, so I removed it from the +# mamba install. rpy2 is reinstalled with pip below. +# when we next upgrade R, let's try to restore rpy2 to its original state +# which means just remove mamba remove rpy2 and remove pip install rpy2 +RUN mamba remove rpy2 && \ + mamba install --quiet --yes \ 'r-arrow' \ 'r-aws.s3' \ + 'r-base=4.4.1' \ 'r-catools' \ 'r-e1071' \ 'r-hdf5r' \ @@ -266,6 +273,7 @@ RUN mamba install --quiet --yes \ 'r-sparklyr' \ 'r-tidyverse' \ && \ + pip install rpy2 && \ clean-layer.sh && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER diff --git a/output/sas/Dockerfile b/output/sas/Dockerfile index 796cb3e74..9d602b1e1 100644 --- a/output/sas/Dockerfile +++ b/output/sas/Dockerfile @@ -412,9 +412,16 @@ ENV PATH=$PATH:/usr/lib/rstudio-server/bin ENV SPARK_HOME="/opt/conda/lib/python3.11/site-packages/pyspark" # Install some default R packages -RUN mamba install --quiet --yes \ +# rpy2 is installed by upstream, I don't know if anyone uses it. +# ryp2 was causing problems with R 4.4.1, so I removed it from the +# mamba install. rpy2 is reinstalled with pip below. +# when we next upgrade R, let's try to restore rpy2 to its original state +# which means just remove mamba remove rpy2 and remove pip install rpy2 +RUN mamba remove rpy2 && \ + mamba install --quiet --yes \ 'r-arrow' \ 'r-aws.s3' \ + 'r-base=4.4.1' \ 'r-catools' \ 'r-e1071' \ 'r-hdf5r' \ @@ -426,6 +433,7 @@ RUN mamba install --quiet --yes \ 'r-sparklyr' \ 'r-tidyverse' \ && \ + pip install rpy2 && \ clean-layer.sh && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER