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🟡 Changes recommended
The image has a build-blocking package installation, disabled authentication, unreadable runtime R configuration, and missing publishing integration.
7 open findings
What changed in this PR
Adds a fresh Terra-compatible RStudio image using R 4.6.1 and supporting installation scripts.
Changes:
- Builds and configures R and RStudio Server.
- Adds optional CUDA, Python, geospatial, publishing, and scientific tooling.
- Adds image-inspection helpers and example tests.
| File | Description |
|---|---|
terra-rstudio-anvil/Dockerfile |
Defines the RStudio image. |
terra-rstudio-anvil/CHECK/chk1 |
Pulls and inspects an older image. |
terra-rstudio-anvil/CHECK/chk2 |
Inspects the older image environment. |
terra-rstudio-anvil/CHECK/chk3 |
Pulls the newer reference image. |
terra-rstudio-anvil/CHECK/chk4 |
Inspects the newer image environment. |
terra-rstudio-anvil/CHECK/o4 |
Stores reference inspection output. |
terra-rstudio-anvil/scripts/bin/install2.r |
Installs R packages from the command line. |
terra-rstudio-anvil/scripts/config_R_cuda.sh |
Configures CUDA for R. |
terra-rstudio-anvil/scripts/default_user.sh |
Creates the default RStudio user. |
terra-rstudio-anvil/scripts/experimental/batch_user_creation.sh |
Creates multiple RStudio users. |
terra-rstudio-anvil/scripts/experimental/cuda10.2-tf.sh |
Adds experimental TensorFlow CUDA dependencies. |
terra-rstudio-anvil/scripts/experimental/install_R_binary.sh |
Installs experimental binary R. |
terra-rstudio-anvil/scripts/experimental/install_dev_osgeo.sh |
Builds development OSGeo libraries. |
terra-rstudio-anvil/scripts/experimental/install_geospatial_unstable.sh |
Enables unstable geospatial packages. |
terra-rstudio-anvil/scripts/experimental/install_rl.sh |
Adds reinforcement-learning packages. |
terra-rstudio-anvil/scripts/init_set_env.sh |
Propagates selected runtime variables. |
terra-rstudio-anvil/scripts/init_userconf.sh |
Configures the runtime user. |
terra-rstudio-anvil/scripts/install_R_ppa.sh |
Installs R from a CRAN repository. |
terra-rstudio-anvil/scripts/install_R_source.sh |
Builds R from source. |
terra-rstudio-anvil/scripts/install_cuda-10.1.sh |
Installs CUDA 10.1. |
terra-rstudio-anvil/scripts/install_cuda-11.1.sh |
Installs CUDA 11.1. |
terra-rstudio-anvil/scripts/install_geospatial.sh |
Installs geospatial dependencies. |
terra-rstudio-anvil/scripts/install_julia.sh |
Installs Julia and R integrations. |
terra-rstudio-anvil/scripts/install_jupyter.sh |
Installs Jupyter and an R kernel. |
terra-rstudio-anvil/scripts/install_nvtop.sh |
Builds the GPU monitor. |
terra-rstudio-anvil/scripts/install_pandoc.sh |
Installs or links Pandoc. |
terra-rstudio-anvil/scripts/install_pyenv.sh |
Installs pyenv and pipenv. |
terra-rstudio-anvil/scripts/install_python.sh |
Creates the shared Python environment. |
terra-rstudio-anvil/scripts/install_quarto.sh |
Installs or links Quarto. |
terra-rstudio-anvil/scripts/install_rstudio.sh |
Installs and configures RStudio Server. |
terra-rstudio-anvil/scripts/install_s6init.sh |
Installs the S6 supervisor. |
terra-rstudio-anvil/scripts/install_shiny_server.sh |
Installs Shiny Server. |
terra-rstudio-anvil/scripts/install_tensorflow.sh |
Adds R TensorFlow tooling. |
terra-rstudio-anvil/scripts/install_texlive.sh |
Installs TeX Live. |
terra-rstudio-anvil/scripts/install_tf1_cuda_10_0.sh |
Adds TensorFlow 1 CUDA libraries. |
terra-rstudio-anvil/scripts/install_tidyverse.sh |
Installs tidyverse packages. |
terra-rstudio-anvil/scripts/install_verse.sh |
Adds publishing and development tools. |
terra-rstudio-anvil/scripts/install_wgrib2.sh |
Builds the GRIB utility. |
terra-rstudio-anvil/scripts/rsession.sh |
Launches a standalone R session. |
terra-rstudio-anvil/scripts/setup_R.sh |
Configures R and littler. |
terra-rstudio-anvil/scripts/tests/examples_tf.R |
Exercises an MNIST Keras model. |
terra-rstudio-anvil/scripts/tests/nvblas.R |
Exercises CUDA-backed BLAS. |
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| echo "rsession-which-r=${R_BIN}" > /etc/rstudio/rserver.conf | ||
| ## use more robust file locking to avoid errors when using shared volumes: | ||
| echo "lock-type=advisory" >> /etc/rstudio/file-locks | ||
| echo "auth-none=1" >> /etc/rstudio/rserver.conf |
| @@ -0,0 +1,47 @@ | |||
| # check=skip=SecretsUsedInArgOrEnv | |||
| FROM us.gcr.io/broad-dsp-gcr-public/terra-base:1.0.1 | |||
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| PATH={$PATH:-$PATH:$CUDA_HOME/bin} | ||
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH:-$LD_LIBRARY_PATH:$CUDA_HOME/lib64:$CUDA_HOME/extras/CUPTI/lib64} |
| GEOS_VERSION=${GEOS_VERSION:-"latest"} | ||
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| CRAN_SOURCE=${CRAN_SOURCE:-"https://cloud.r-project.org"} | ||
| echo "options(repos = c(CRAN = '${CRAN}'))" >>"${R_HOME}/etc/Rprofile.site" |
| done | ||
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| ## ensure Renviron.site is only readable/writable by its owner: | ||
| chmod 600 "${R_HOME}/etc/Renviron.site" |
| fi | ||
| } | ||
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| echo "PYTHON_CONFIGURE_OPTS=${PYTHON_CONFIGURE_OPTS}" >>"${R_HOME}/etc/R_environ" |
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| R_DOC_DIR=$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 |
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the terra-rstudio-anvil folder includes a Dockerfile defining a container that works with current Rstudio and R 4.6.1. In May the various stacks did not align, and Rstudio started in a crippled state. Updates in various parts of the stack seem to have resolved the problem.