Hi,
I need some additonal packages added to R, which is used in the Jupyter Notebook R Stack.
So far I tried to modify the corresponding Dockerfile (added some packages (r-qboxplot, r-hhi,…))
ARG OWNER=jupyter
ARG BASE_CONTAINER=$OWNER/minimal-notebook
FROM $BASE_CONTAINER
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
USER root
# R pre-requisites
RUN apt-get update --yes && \
apt-get install --yes --no-install-recommends \
fonts-dejavu \
unixodbc \
unixodbc-dev \
r-cran-rodbc \
gfortran \
gcc && \
apt-get clean && rm -rf /var/lib/apt/lists/*
USER ${NB_UID}
# R packages including IRKernel which gets installed globally.
# r-e1071: dependency of the caret R package
RUN mamba install --quiet --yes \
'r-base' \
'r-caret' \
'r-crayon' \
'r-devtools' \
'r-e1071' \
'r-forecast' \
'r-hexbin' \
'r-htmltools' \
'r-htmlwidgets' \
'r-irkernel' \
'r-nycflights13' \
'r-randomforest' \
'r-rcurl' \
'r-rmarkdown' \
'r-rodbc' \
'r-rsqlite' \
'r-shiny' \
'r-tidyverse' \
'r-qboxplot' \
'r-hhi' \
'r-ineq' \
'r-hmisc' \
'r-BSDA' \
'r-moderndive' \
'r-mosaic' \
'r-micEconIndex' \
'unixodbc' && \
mamba clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
# `r-tidymodels` is not easy to install under arm
RUN set -x && \
arch=$(uname -m) && \
if [ "${arch}" == "x86_64" ]; then \
mamba install --quiet --yes \
'r-tidymodels' && \
mamba clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"; \
fi;
Unfortunately, when I try to build this Dockerfile I get the error
#6 5.861 Encountered problems while solving:
#6 5.861 - nothing provides requested r-qboxplot
#6 5.861 - nothing provides requested r-hhi
#6 5.861 - nothing provides requested r-moderndive
#6 5.861 - nothing provides requested r-miceconindex
#6 5.861 - nothing provides r-ggrepel needed by r-mosaic-1.8.3-r40hc72bb7e_0
#6 5.861 - package r-bsda-1.2.0-r40hc72bb7e_0 requires r-base >=4.0,<4.1.0a0, but none of the providers can be installed
Any ideas how to add some additional packages another way?
PS: I’m running jupyterhub via docker-compose as described here
TIA!
Best,
Alex
If you’re absolutely committed to using conda-forge (which is a fine goal, as it would benefit other users), there’s more work ahead.
It’s like it says: those packages aren’t available from conda-forge, and it all starts with staged-recipes.
You can either:
Even as this “works,” the r installed by conda won’t be able to find it.
You may want to everything with the system r, a la: install.R and using that package manager directly.
1 Like
Hi,
thank you very much for your answer. Finally, I managed it by creating a new “private_Dockerfile” which is used for a singleuser:
ARG OWNER=jupyter
ARG BASE_CONTAINER=$OWNER/minimal-notebook
FROM $BASE_CONTAINER
# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
USER root
# R pre-requisites
RUN apt-get update --yes && \
apt-get install --yes --no-install-recommends \
fonts-dejavu \
unixodbc \
unixodbc-dev \
r-cran-rodbc \
gfortran \
gcc && \
apt-get clean && rm -rf /var/lib/apt/lists/*
USER ${NB_UID}
# R packages including IRKernel which gets installed globally.
# r-e1071: dependency of the caret R package
RUN mamba install --quiet --yes \
'r-base' \
'r-caret' \
'r-crayon' \
'r-devtools' \
'r-e1071' \
'r-forecast' \
'r-hexbin' \
'r-htmltools' \
'r-htmlwidgets' \
'r-irkernel' \
'r-nycflights13' \
'r-randomforest' \
'r-rcurl' \
'r-rmarkdown' \
'r-rodbc' \
'r-rsqlite' \
'r-shiny' \
'r-tidyverse' && \
mamba clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
# `r-tidymodels` is not easy to install under arm
RUN set -x && \
arch=$(uname -m) && \
if [ "${arch}" == "x86_64" ]; then \
mamba install --quiet --yes \
'r-tidymodels' && \
mamba clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"; \
fi;
RUN R -e "install.packages('qboxplot',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('hhi',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('ineq',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('hmisc',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('BSDA',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('moderndive',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('mosaic',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('micEconIndex',dependencies=TRUE, repos='http://cran.rstudio.com/')"
…and building it …
docker build -f private_Dockerfile -t jupyterhub-user --build-arg JUPYTERHUB_VERSION=0.9.2 --build-arg DOCKER_NOTEBOOK_IMAGE=jupyter/r-notebook:r-3.6.3 singleuser
and then
docker-compose up -d --build
When I enter the jupyterhub I was suprised to find a new UX:
When I switched back to the standard Dockerfile for singleuser i.e.
make notebook_image
with DOCKER_NOTEBOOK_IMAGE=jupyter/r-notebook:r-3.6.3
I get the “old” UX back:
So, little bit offtopic:
How is it possible to switch between the two different UX?
Does it depend on DOCKER_NOTEBOOK_IMAGE=jupyter/r-notebookXXXXX?
TIA,
Alex
1 Like
jupyterlab running on jupyter_server has been the default UI for some years at this point. At present, it also serves the classic UI, which can be started from the URL /tree.
When opening jupyterlab, you can use the main menu to get to Help » Launch Classic Notebook.
You can pre-configure launching /tree in ~/.jupyter/jupyter_config.json#ServerApp/default_url, a la:
{
"ServerApp": {
"default_url": "/tree"
}
}
1 Like
