Bioc323 by vjcitn · Pull Request #520 · DataBiosphere/terra-docker

vjcitn · 2026-05-12T22:31:40Z

The dockerfile and scripts in this branch create R 4.6.0 and can install Bioconductor 3.23. Rstudio starts up but we have seen problems:

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

Copilot

Pull request overview

Adds a new terra-rstudio-anvil image definition and supporting install/init scripts to build R from source and run RStudio Server (plus optional components like Python/reticulate, TensorFlow/Keras, geospatial, TeX, Quarto, etc.). The PR also modifies terra-jupyter-bioconductor in a way that appears to switch it away from being a Jupyter/Leonardo-focused image.

Changes:

Introduce a new terra-rstudio-anvil/Dockerfile that builds R from source, installs littler tooling, and installs/configures RStudio Server via s6-overlay.
Add a large suite of terra-rstudio-anvil/scripts/* installer and init scripts (R, RStudio, s6 init, Python venv/reticulate, tidyverse/verse/geospatial, TeX, Pandoc/Quarto, CUDA helpers, etc.), plus a couple of ad-hoc R test scripts.
Replace terra-jupyter-bioconductor/Dockerfile with a new build that installs RStudio/s6 rather than extending terra-jupyter-r.

Reviewed changes

Copilot reviewed 42 out of 43 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
terra-rstudio-anvil/scripts/tests/nvblas.R	Adds an R snippet intended to test NVBLAS via `LD_PRELOAD`.
terra-rstudio-anvil/scripts/tests/examples_tf.R	Adds an example Keras MNIST training script.
terra-rstudio-anvil/scripts/setup_R.sh	Sets CRAN defaults, HTTP user agent, OpenBLAS switching, and installs littler.
terra-rstudio-anvil/scripts/rsession.sh	Adds a standalone `rsession` launcher script.
terra-rstudio-anvil/scripts/install_wgrib2.sh	Installs `wgrib2` from upstream tarball.
terra-rstudio-anvil/scripts/install_verse.sh	Installs broader “verse” dependencies incl. TeX tooling and R packages.
terra-rstudio-anvil/scripts/install_tidyverse.sh	Installs tidyverse and common DB/IO-related packages.
terra-rstudio-anvil/scripts/install_tf1_cuda_10_0.sh	Installs CUDA 10.0 runtime libs needed for TF 1.x compatibility.
terra-rstudio-anvil/scripts/install_texlive.sh	Installs TeX Live via CTAN and configures PATH/permissions.
terra-rstudio-anvil/scripts/install_tensorflow.sh	Installs Python support + R `keras`.
terra-rstudio-anvil/scripts/install_shiny_server.sh	Installs Shiny Server and configures it under s6.
terra-rstudio-anvil/scripts/install_s6init.sh	Installs s6-overlay.
terra-rstudio-anvil/scripts/install_rstudio.sh	Installs RStudio Server, configures rserver/rsession, and s6 services.
terra-rstudio-anvil/scripts/install_R_source.sh	Builds and installs R from source tarball.
terra-rstudio-anvil/scripts/install_R_ppa.sh	Installs R from CRAN Ubuntu repo via apt (PPA-style approach).
terra-rstudio-anvil/scripts/install_quarto.sh	Installs or symlinks Quarto CLI (bundled or standalone).
terra-rstudio-anvil/scripts/install_python.sh	Creates a Python venv, installs `reticulate`, and adjusts BLAS on focal.
terra-rstudio-anvil/scripts/install_pyenv.sh	Installs pyenv and pipenv to enable multiple Python versions.
terra-rstudio-anvil/scripts/install_pandoc.sh	Installs or symlinks Pandoc (bundled or standalone) plus templates.
terra-rstudio-anvil/scripts/install_nvtop.sh	Builds and installs `nvtop` from source.
terra-rstudio-anvil/scripts/install_jupyter.sh	Installs Jupyter + IRkernel and TeX deps for nbconvert.
terra-rstudio-anvil/scripts/install_julia.sh	Installs Julia and R bindings (JuliaCall, JuliaConnectoR).
terra-rstudio-anvil/scripts/install_geospatial.sh	Installs system geospatial libs and a wide set of R geospatial packages.
terra-rstudio-anvil/scripts/install_cuda-11.1.sh	Installs/pins CUDA 11.1 runtime+dev packages and some TensorRT symlinks.
terra-rstudio-anvil/scripts/install_cuda-10.1.sh	Installs/pins CUDA 10.1 packages and TF-related dependencies.
terra-rstudio-anvil/scripts/init_userconf.sh	s6 cont-init script to manage user creation/rootless behavior/passwords.
terra-rstudio-anvil/scripts/init_set_env.sh	s6 cont-init script to propagate selected env vars into `Renviron.site`.
terra-rstudio-anvil/scripts/experimental/install_rl.sh	Experimental: creates a venv and installs RL-related Python packages.
terra-rstudio-anvil/scripts/experimental/install_R_binary.sh	Experimental: installs R via apt in a separate script variant.
terra-rstudio-anvil/scripts/experimental/install_geospatial_unstable.sh	Experimental: adds ubuntugis-unstable and installs geospatial stack.
terra-rstudio-anvil/scripts/experimental/install_dev_osgeo.sh	Experimental: builds GDAL/GEOS/PROJ from source and installs R packages.
terra-rstudio-anvil/scripts/experimental/cuda10.2-tf.sh	Experimental: ad-hoc CUDA/TensorRT installation commands.
terra-rstudio-anvil/scripts/experimental/batch_user_creation.sh	Experimental: create multiple OS users from an env var.
terra-rstudio-anvil/scripts/default_user.sh	Creates default `rstudio` user and sets baseline RStudio prefs.
terra-rstudio-anvil/scripts/config_R_cuda.sh	Configures CUDA/NVBLAS environment for R and RStudio.
terra-rstudio-anvil/scripts/bin/install2.r	Adds `install2.r` helper (littler-based) for installing R packages.
terra-rstudio-anvil/Dockerfile	New Dockerfile building the RStudio Anvil image.
terra-rstudio-anvil/CHECK/o4	Adds captured diagnostic output (docker inspect excerpt).
terra-rstudio-anvil/CHECK/chk4	Adds a diagnostic command snippet (docker inspect/grep env).
terra-rstudio-anvil/CHECK/chk3	Adds a diagnostic command snippet (docker pull).
terra-rstudio-anvil/CHECK/chk2	Adds a diagnostic command snippet (docker inspect/grep env).
terra-rstudio-anvil/CHECK/chk1	Adds a diagnostic command snippet (docker pull/inspect labels).
terra-jupyter-bioconductor/Dockerfile	Replaces prior base image with a new build flow that installs R/RStudio tooling.

Comments suppressed due to low confidence (1)

terra-rstudio-anvil/scripts/experimental/install_dev_osgeo.sh:120

apt_install is designed to accept package names, but it’s being called with apt flags and a local .deb path (apt_install -y -V ./apache-arrow-apt-source-...deb). dpkg -s will treat -y as a package name, and the install step may fail. Install the local .deb with dpkg -i (or apt-get install ./file.deb) outside of apt_install, then run apt-get update.

## geoparquet support
wget https://apache.jfrog.io/artifactory/arrow/"$(lsb_release --id --short | tr '[:upper:]' '[:lower:]')"/apache-arrow-apt-source-latest-"$(lsb_release --codename --short)".deb
apt_install -y -V ./apache-arrow-apt-source-latest-"$(lsb_release --codename --short)".deb
apt-get update && apt-get install -y -V libarrow-dev libparquet-dev libarrow-dataset-dev

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+CUDA_HOME=${CUDA_HOME:-/usr/local/cuda}
+PATH={$PATH:-$PATH:$CUDA_HOME/bin}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH:-$LD_LIBRARY_PATH:$CUDA_HOME/lib64:$CUDA_HOME/extras/CUPTI/lib64}
+NVBLAS_CONFIG_FILE=${NVBLAS_CONFIG_FILE:-/etc/nvblas.conf}


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


+R_DOC_DIR=$R_HOME/doc
+R_INCLUDE_DIR=$R_HOME/include
+R_SHARE_DIR=$R_HOME/share
+RSTUDIO_DEFAULT_R_VERSION_HOME=$R_HOME
+RSTUDIO_DEFAULT_R_VERSION=$R_VERSION
+PATH=$PATH:/usr/lib/rstudio-server/bin
+rsession --standalone=1 \


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


+ENV PASSWORD="bioc"
+


+GEOS_VERSION=${GEOS_VERSION:-"latest"}
+
+CRAN_SOURCE=${CRAN_SOURCE:-"https://cloud.r-project.org"}
+echo "options(repos = c(CRAN = '${CRAN}'))" >>"${R_HOME}/etc/Rprofile.site"


+COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
+RUN /rocker_scripts/install_R_source.sh
+
+ENV CRAN="https://cloud.r-project.org"
+ENV LANG=en_US.UTF-8
+
+COPY scripts/bin/ /rocker_scripts/bin/
+COPY scripts/setup_R.sh /rocker_scripts/setup_R.sh
+RUN <<EOF
+if grep -q "1000" /etc/passwd; then
+    userdel --remove "$(id -un 1000)";
+fi
+/rocker_scripts/setup_R.sh
+EOF


+FROM us.gcr.io/broad-dsp-gcr-public/terra-base:1.0.0
+
+USER root
+


+            "Env": [
+                "PATH=/opt/venv/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/bin",
+                "NVARCH=x86_64",
+                "NVIDIA_REQUIRE_CUDA=cuda>=12.6 brand=unknown,driver>=470,driver<471 brand=grid,driver>=470,driver<471 brand=tesla,driver>=470,driver<471 brand=nvidia,driver>=470,driver<471 brand=quadro,driver>=470,driver<471 brand=quadrortx,driver>=470,driver<471 brand=nvidiartx,driver>=470,driver<471 brand=vapps,driver>=470,driver<471 brand=vpc,driver>=470,driver<471 brand=vcs,driver>=470,driver<471 brand=vws,driver>=470,driver<471 brand=cloudgaming,driver>=470,driver<471 brand=unknown,driver>=535,driver<536 brand=grid,driver>=535,driver<536 brand=tesla,driver>=535,driver<536 brand=nvidia,driver>=535,driver<536 brand=quadro,driver>=535,driver<536 brand=quadrortx,driver>=535,driver<536 brand=nvidiartx,driver>=535,driver<536 brand=vapps,driver>=535,driver<536 brand=vpc,driver>=535,driver<536 brand=vcs,driver>=535,driver<536 brand=vws,driver>=535,driver<536 brand=cloudgaming,driver>=535,driver<536 brand=unknown,driver>=550,driver<551 brand=grid,driver>=550,driver<551 brand=tesla,driver>=550,driver<551 brand=nvidia,driver>=550,driver<551 brand=quadro,driver>=550,driver<551 brand=quadrortx,driver>=550,driver<551 brand=nvidiartx,driver>=550,driver<551 brand=vapps,driver>=550,driver<551 brand=vpc,driver>=550,driver<551 brand=vcs,driver>=550,driver<551 brand=vws,driver>=550,driver<551 brand=cloudgaming,driver>=550,driver<551",
+                "NV_CUDA_CUDART_VERSION=12.6.77-1",


+git clone https://github.com/Syllo/nvtop.git
+cd nvtop
+# Pin to a specific known-good version to ensure reproducible builds
+git checkout v3.0.0
+mkdir -p build && cd build
+cmake .. -DNVML_RETRIEVE_HEADER_ONLINE=True
+make
+make install
+cd ../..
+
+# Clean up
+rm -rf /var/lib/apt/lists/* nvtop


vjcitn and others added 19 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

use R 4.6.0 and Bioc 3.23 ... but rstudio only works a little in terra

2999d91

Copilot AI review requested due to automatic review settings May 12, 2026 22:31

Copilot AI reviewed May 12, 2026

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trying lots of things

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Bioc323#520

Bioc323#520
vjcitn wants to merge 20 commits into
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		## ensure Renviron.site is only readable/writable by its owner:
		chmod 600 "${R_HOME}/etc/Renviron.site"


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

		FROM us.gcr.io/broad-dsp-gcr-public/terra-base:1.0.0

		USER root

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