define container that runs R 4.6.1 and Rstudio in terra by vjcitn · Pull Request #524 · DataBiosphere/terra-docker

vjcitn · 2026-10-08T11:47:35Z

This was blocked in May for various reasons possibly related to changes in Rstudio stack.
Now this Dockerfile defines a container that can be used as a community-contributed cloud
environment for terra/anvil.

Explicit build of rstudio on the sudo-enabled base

Following suggestion of using 3.0.0, but noting existence of 3.3.2 at this time. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Removed pam-helper.sh script from Dockerfile.

Removed copying of pam-helper.sh to rstudio-server bin.

A secret was used in an ARG or ENV ... allowing this for now

… rstudio in a jetstream vm. however, the user identity is jupyter and it starts in /home/jupyter when we try to use this as a custom env under "rstudio" terra env control, the build process jumps to the jupyter type environment build process

R452brokenterra can be used in terra but only the console works

Copilot

🟡 Changes recommended

Missing build inputs, lost Bioconductor functionality, and runtime configuration defects remain unresolved.

11 open findings

Replacing terra-jupyter-r drops required R packages and IRkernel · New
Docker build context omits required scripts and installer files · New
Inherited Jupyter ENTRYPOINT prevents s6 and RStudio startup · New
Malformed PATH and CUDA library path handling · New
Rootless startup deletes the configured rserver user · New
rserver uses hardcoded user instead of DEFAULT_USER · New
Unauthenticated HTTP package download permits code tampering · New
Renviron.site permissions block RStudio sessions from reading configuration · New
R environment settings are written to an ignored file · New
PIP_USER=true breaks pip installation in the virtual environment · New
RStudio user lacks write access to the Terra workspace · New

What changed in this PR

Adds a community-contributed R 4.6.1 and RStudio environment for Terra/AnVIL alongside the existing notebook images.

Changes:

Defines the RStudio container and its startup configuration.
Adds installation helpers, examples, and image-inspection scripts.
Revises the Jupyter R and Bioconductor Dockerfiles.

File	Description
terra-rstudio-anvil/scripts/tests/nvblas.R	Adds a GPU matrix benchmark.
terra-rstudio-anvil/scripts/tests/examples_tf.R	Adds a Keras training example.
terra-rstudio-anvil/scripts/setup_R.sh	Configures R, OpenBLAS, and littler.
terra-rstudio-anvil/scripts/rsession.sh	Adds standalone RStudio session startup.
terra-rstudio-anvil/scripts/install_wgrib2.sh	Adds weather-data tooling installation.
terra-rstudio-anvil/scripts/install_verse.sh	Adds publishing packages and dependencies.
terra-rstudio-anvil/scripts/install_tidyverse.sh	Adds tidyverse and database packages.
terra-rstudio-anvil/scripts/install_tf1_cuda_10_0.sh	Adds legacy TensorFlow CUDA dependencies.
terra-rstudio-anvil/scripts/install_texlive.sh	Adds TeX Live installation.
terra-rstudio-anvil/scripts/install_tensorflow.sh	Adds Python and R Keras setup.
terra-rstudio-anvil/scripts/install_shiny_server.sh	Adds Shiny Server installation and startup.
terra-rstudio-anvil/scripts/install_s6init.sh	Installs the s6 supervisor.
terra-rstudio-anvil/scripts/install_rstudio.sh	Installs and configures RStudio Server.
terra-rstudio-anvil/scripts/install_R_source.sh	Builds R from source.
terra-rstudio-anvil/scripts/install_R_ppa.sh	Adds repository-based R installation.
terra-rstudio-anvil/scripts/install_quarto.sh	Installs or exposes Quarto.
terra-rstudio-anvil/scripts/install_python.sh	Configures Python and reticulate.
terra-rstudio-anvil/scripts/install_pyenv.sh	Adds Python version-management setup.
terra-rstudio-anvil/scripts/install_pandoc.sh	Installs Pandoc and templates.
terra-rstudio-anvil/scripts/install_nvtop.sh	Builds GPU monitoring tooling.
terra-rstudio-anvil/scripts/install_jupyter.sh	Adds Jupyter and R kernel setup.
terra-rstudio-anvil/scripts/install_julia.sh	Adds Julia and R integration packages.
terra-rstudio-anvil/scripts/install_geospatial.sh	Adds geospatial libraries and packages.
terra-rstudio-anvil/scripts/install_cuda-11.1.sh	Adds CUDA 11.1 installation.
terra-rstudio-anvil/scripts/install_cuda-10.1.sh	Adds CUDA 10.1 installation.
terra-rstudio-anvil/scripts/init_userconf.sh	Configures runtime users and preferences.
terra-rstudio-anvil/scripts/init_set_env.sh	Propagates selected environment settings.
terra-rstudio-anvil/scripts/experimental/install_rl.sh	Adds reinforcement-learning environment setup.
terra-rstudio-anvil/scripts/experimental/install_R_binary.sh	Adds experimental binary R installation.
terra-rstudio-anvil/scripts/experimental/install_geospatial_unstable.sh	Adds unstable geospatial repository setup.
terra-rstudio-anvil/scripts/experimental/install_dev_osgeo.sh	Builds geospatial libraries from source.
terra-rstudio-anvil/scripts/experimental/cuda10.2-tf.sh	Adds experimental CUDA dependency setup.
terra-rstudio-anvil/scripts/experimental/batch_user_creation.sh	Adds batch account creation.
terra-rstudio-anvil/scripts/default_user.sh	Creates the default application user.
terra-rstudio-anvil/scripts/config_R_cuda.sh	Configures CUDA paths and NVBLAS.
terra-rstudio-anvil/scripts/bin/install2.r	Adds an R package installation helper.
terra-rstudio-anvil/Dockerfile	Defines the Terra RStudio image.
terra-rstudio-anvil/CHECK/o4	Records reference image metadata.
terra-rstudio-anvil/CHECK/chk4	Inspects reference image environment settings.
terra-rstudio-anvil/CHECK/chk3	Pulls the newer reference image.
terra-rstudio-anvil/CHECK/chk2	Inspects older reference image settings.
terra-rstudio-anvil/CHECK/chk1	Pulls and inspects the older image.
terra-jupyter-r/Dockerfile	Updates package versions and dependency installation.
terra-jupyter-bioconductor/Dockerfile	Replaces inheritance with an RStudio-oriented build.

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@@ -1 +1,45 @@
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.7
+FROM us.gcr.io/broad-dsp-gcr-public/terra-base:1.0.0


+ENV R_HOME="/usr/local/lib/R"
+ENV TZ="Etc/UTC"
+
+COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh


+RUN /rocker_scripts/install_rstudio.sh
+
+EXPOSE 8787
+CMD ["/init"]


+PATH={$PATH:-$PATH:$CUDA_HOME/bin}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH:-$LD_LIBRARY_PATH:$CUDA_HOME/lib64:$CUDA_HOME/extras/CUPTI/lib64}


+
+if [ "${RUNROOTLESS}" = "true" ]; then
+    echo "deleting the default user ($DEFAULT_USER) since it is not needed."
+    userdel "$DEFAULT_USER"


@@ -0,0 +1,36 @@
+
+## Tensorflow:
+install.packages('keras', repos='http://cran.us.r-project.org')


+## ensure Renviron.site is only readable/writable by its owner:
+chmod 600 "${R_HOME}/etc/Renviron.site"


+    fi
+}
+
+echo "PYTHON_CONFIGURE_OPTS=${PYTHON_CONFIGURE_OPTS}" >>"${R_HOME}/etc/R_environ"


+# Upgrade version of pip inside the virtualenv
+python3 -m pip --no-cache-dir install --upgrade \


+echo "session-default-working-dir=/home/jupyter" >> /etc/rstudio/rsession.conf
+echo "session-default-new-project-dir=/home/jupyter" >> /etc/rstudio/rsession.conf


vjcitn · 2026-10-08T12:27:25Z

I had only intended to submit changes on one Dockerfile. I will refresh my fork and resubmit.

vjcitn and others added 23 commits March 18, 2026 12:08

Update Dockerfile base image and install scripts

68500af

Explicit build of rstudio on the sudo-enabled base

trying for sudo-capable with rstudio from source

a2d7d68

this will start on a laptop, generating its own password

a3d4a09

PASSWORD set in container

31321f1

Update terra-rstudio-anvil/scripts/install_nvtop.sh

50d1d8c

Following suggestion of using 3.0.0, but noting existence of 3.3.2 at this time. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update terra-rstudio-anvil/scripts/install_cuda-11.1.sh

492c399

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update terra-rstudio-anvil/scripts/install_geospatial.sh

23fbdf2

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update terra-rstudio-anvil/scripts/init_set_env.sh

49bac37

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update terra-rstudio-anvil/scripts/install_rstudio.sh

f9b9929

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

responding to Liz Baldo's review

5650ae7

Remove pam-helper.sh from Dockerfile

030e734

Removed pam-helper.sh script from Dockerfile.

Remove pam-helper.sh installation step

9a6f8d6

Removed copying of pam-helper.sh to rstudio-server bin.

Add skip check for secrets in Dockerfile

1f822da

A secret was used in an ARG or ENV ... allowing this for now

adding RSTUDIO_HOME environment variable

d6c093c

add env var for RSTUDIO_HOME before init

1de786b

some container checking support

32cb9c0

produces a container that starts in AnVIL

38ee898

works for bioc 3.23 but makes a 32GB image!

b9b47a1

some minor changes that still lead to crippled rstudio in terra

a18df18

Merge pull request #1 from vjcitn/r452brokenterra

4e1595b

R452brokenterra can be used in terra but only the console works

changes to use R 4.6.1 and new Rstudio

4c5b6a2

adding zlib installation

630387c

Copilot AI balanced review requested due to automatic review settings October 8, 2026 11:47

Copilot started reviewing on behalf of vjcitn October 8, 2026 11:48

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define container that runs R 4.6.1 and Rstudio in terra - #524

define container that runs R 4.6.1 and Rstudio in terra#524
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		@@ -1 +1,45 @@
		FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.7
		FROM us.gcr.io/broad-dsp-gcr-public/terra-base:1.0.0

		PATH={$PATH:-$PATH:$CUDA_HOME/bin}
		LD_LIBRARY_PATH=${LD_LIBRARY_PATH:-$LD_LIBRARY_PATH:$CUDA_HOME/lib64:$CUDA_HOME/extras/CUPTI/lib64}

		@@ -0,0 +1,36 @@

		## Tensorflow:
		install.packages('keras', repos='http://cran.us.r-project.org')

		## ensure Renviron.site is only readable/writable by its owner:
		chmod 600 "${R_HOME}/etc/Renviron.site"

		# Upgrade version of pip inside the virtualenv
		python3 -m pip --no-cache-dir install --upgrade \

		echo "session-default-working-dir=/home/jupyter" >> /etc/rstudio/rsession.conf
		echo "session-default-new-project-dir=/home/jupyter" >> /etc/rstudio/rsession.conf

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