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) <[email protected]>
StatCan · Jan 30, 2025 · ec0aa3f · ec0aa3f
1 parent 9ba95d0
commit ec0aa3f
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Showing 6 changed files with 54 additions and 6 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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