diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index bb39377..a176199 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -19,12 +19,12 @@ jobs: run: | set -x if [[ "${{ github.ref }}" == 'refs/heads/main' ]]; then - # build, test and publish both versions on main. + # build, test and publish all versions on main. # v1 will take ~2 hours - echo 'versions=["v1", "v2"]' >> "$GITHUB_OUTPUT" + echo 'versions=["v1", "v2", "v3"]' >> "$GITHUB_OUTPUT" else - # only build v2 in CI as v1 is too slow - echo 'versions=["v2"]' >> "$GITHUB_OUTPUT" + # only build v2 and v3 in CI as v1 is too slow + echo 'versions=["v2", "v3"]' >> "$GITHUB_OUTPUT" fi tests: needs: matrix @@ -43,7 +43,7 @@ jobs: uses: astral-sh/setup-uv@4db96194c378173c656ce18a155ffc14a9fc4355 - name: check - run: just check + run: just check ${{ matrix.version }} - name: build run: just build ${{ matrix.version }} diff --git a/README.md b/README.md index 345a3b5..1158cdd 100644 --- a/README.md +++ b/README.md @@ -4,30 +4,32 @@ This repo manages the Docker image for the OpenSAFELY R runtime and rstudio-serv images are based on a base Ubuntu LTS version, and come pre-installed with a set of standard R packages. -The current latest version is `v2`, and you should use that unless you have +The current latest version is `v3`, and you should use that unless you have a specific reason. You can use it in your `project.yaml` like so: ``` actions: my_action: - run: r:v2 analysis/my_script.R + run: r:v3 analysis/my_script.R ``` The rstudio images are designed for use with `opensafely launch`. For example, to launch an rstudio-server session (i.e., RStudio running in a browser window) run the following in a Terminal from your research repository. ```sh -opensafely launch rstudio:v2 +opensafely launch rstudio:v3 ``` ## Version List Current available versions for the r image, in reverse chronological order: + - v3: Ubuntu 22.04 and R 4.5.3 - [full package list](v3/packages.md) - v2: Ubuntu 22.04 and R 4.4.3 - [full package list](v2/packages.md) - - v1: Ubuntu 20.04 and R 4.0.5 - [full package list](v1/packages.md) - please note that v1 is deprecated, new projects should use r:v2. + - v1: Ubuntu 20.04 and R 4.0.5 - [full package list](v1/packages.md) - please note that v1 is deprecated, new projects should use r:v3. Current available versions for the rstudio image, in reverse chronological order: + - v3: rstudio-server running r:v3 - v2: rstudio-server running r:v2 - v1: rstudio-server running r:v1 @@ -46,10 +48,10 @@ use `v1` instead of `latest`. We do not plan to add anymore packages to the v1 image. -For the v2 image, the versions of R packages from CRAN tied to a CRAN date. +For the v2 and v3 images, the versions of R packages from CRAN tied to a CRAN date. We can easily install any additional package from the same CRAN date. Additional packages may be requested by creating an issue in the repo. -In the v2 image you can request packages that are not on CRAN. +In the v2 and v3 images you can request packages that are not on CRAN. Occasionally, we will create a new major version of the image with all packages updated to their latest version. We may also possibly remove old and uneeded @@ -58,8 +60,8 @@ incompatible changes, which is occasionally needed. ### User installed R packages -Especially when working in say a Codespace using the rstudio:v2 image you may wish to add some packages for your post release analysis. -The v2 images are configured to allow you to install your own packages, which will be saved to a _.local-packages/r/v2_ directory in your research repository. +Especially when working in say a Codespace using the rstudio:v2 or rstudio:v3 images you may wish to add some packages for your post release analysis. +The v2 and v3 images are configured to allow you to install your own packages, which will be saved to a _.local-packages/r/v#_ directory in your research repository. If the packages is on CRAN, to do this simply run the following. ```r diff --git a/justfile b/justfile index e61e0d2..2a09fc7 100644 --- a/justfile +++ b/justfile @@ -23,9 +23,9 @@ build version: cp ${MAJOR_VERSION}/renv.lock ${MAJOR_VERSION}/renv.lock.bak # cannot use docker compose run as it mangles the output docker run --platform linux/amd64 --rm r:{{ version }} cat /renv/renv.lock > ${MAJOR_VERSION}/renv.lock - elif [ "{{ version }}" = "v2" ]; then + elif [[ "{{ version }}" =~ ^v[23]$ ]]; then # update pkg.lock - cp ${MAJOR_VERSION}/pkg.lock ${MAJOR_VERSION}/pkg.lock.bak + [[ -f ${MAJOR_VERSION}/pkg.lock ]] && cp ${MAJOR_VERSION}/pkg.lock ${MAJOR_VERSION}/pkg.lock.bak || true # cannot use docker compose run as it mangles the output docker run --platform linux/amd64 --rm r:{{ version }} cat /pkg.lock > ${MAJOR_VERSION}/pkg.lock fi @@ -84,5 +84,8 @@ publish-rstudio version: docker push ghcr.io/opensafely-core/rstudio:latest fi -check: - uvx --python 3.13 toml-validator v2/packages.toml +check version: + #!/usr/bin/env bash + if [[ "{{ version }}" =~ ^v[23]$ ]]; then + uvx --python 3.13 toml-validator {{ version }}/packages.toml + fi diff --git a/scripts/local-packages-README.md b/scripts/local-packages-README.Rmd similarity index 55% rename from scripts/local-packages-README.md rename to scripts/local-packages-README.Rmd index 56a1363..1073f13 100644 --- a/scripts/local-packages-README.md +++ b/scripts/local-packages-README.Rmd @@ -1,10 +1,24 @@ +--- +title: "" +output: + github_document: + html_preview: false +--- + +```{r setup, include=FALSE} +v <- Sys.getenv("MAJOR_VERSION") +r_img <- paste0("`r:", v, "`") +rstudio_img <- paste0("`rstudio:", v, "`") +local_dir <- paste0("_.local-packages/r/", v, "_") +``` + # .local-packages a directory for user installed libraries -This directory contains user installed libraries, for say use running OpenSAFELY code in a Codespace or locally. +This directory contains user installed libraries, for say running OpenSAFELY code in a Codespace or locally. ## How to add and remove user installed R packages -The _.local-packages/r/v2_ directory contains user installed R packages to work in the `r:v2` and `rstudio:v2` images. +The `r local_dir` directory contains user installed R packages to work in the `r r_img` and `r rstudio_img` images. You can install additional packages by running @@ -14,7 +28,7 @@ install.packages("PACKAGENAME") or by using the RStudio _Package_ pane _Install_ button. -Note that packages are installed from the same date from CRAN as the other packages in the `r:v2` image. This is to ensure user installed packages work with the other packages in the image (at the time of installation). +Note that packages are installed from the same date from CRAN as the other packages in the `r r_img` image. This is to ensure user installed packages work with the other packages in the image (at the time of installation). If you no longer require a package you can also remove it as follows. diff --git a/scripts/packages.Rmd b/scripts/packages.Rmd index dbd2915..44ac6ad 100644 --- a/scripts/packages.Rmd +++ b/scripts/packages.Rmd @@ -33,7 +33,7 @@ pkgs <- pkgs %>% arrange(Package, .locale = "en") knitr::kable(pkgs, row.names = FALSE) } -if (Sys.getenv("MAJOR_VERSION") == "v2") { +if (Sys.getenv("MAJOR_VERSION") %in% c("v2", "v3")) { suppressMessages(library(dplyr)) pkglock <- jsonlite::fromJSON(paste0("/out/", Sys.getenv("MAJOR_VERSION"), "/pkg.lock")) pkgs <- pkglock[["packages"]] @@ -46,11 +46,12 @@ pkgs <- pkgs %>% mutate( .default = metadataremoterepos ) ) +r_minor_version <- if (Sys.getenv("MAJOR_VERSION") == "v3") "4.5" else "4.4" pkgs <- pkgs %>% mutate( url = case_when( repotype == "cran" ~ paste0(""), - repotype == "cranlike" ~ paste0("<", sub("/bin/linux/noble/4.4/", "/", metadataremoterepos), package, ">") + repotype == "cranlike" ~ paste0("<", sub(paste0("/bin/linux/noble/", r_minor_version, "/"), "/", metadataremoterepos), package, ">") ) ) pkgs <- pkgs %>% diff --git a/scripts/rprofile-site-append-2.R b/scripts/rprofile-site-append-2.R index 9baedcf..cd2123b 100644 --- a/scripts/rprofile-site-append-2.R +++ b/scripts/rprofile-site-append-2.R @@ -1,15 +1,17 @@ # If the local package directory exists set as first entry of R's library path # This is so that install.packages() and remove.packages() will use this directory by default. -if (dir.exists('/workspace/.local-packages/r/v2')) - .libPaths(c('/workspace/.local-packages/r/v2', .libPaths())) +.local_pkg_dir <- paste0('/workspace/.local-packages/r/', Sys.getenv("MAJOR_VERSION")) +if (dir.exists(.local_pkg_dir)) + .libPaths(c(.local_pkg_dir, .libPaths())) # Monkey patch install.packages to create local package directory if it doesn't exist and # create a .gitignore file within in and copy in the README.md. # In R ... passes function arguments through to a subsequent call. install.packages <- function(...) { - if (!dir.exists("/workspace/.local-packages/r/v2")) { - dir.create("/workspace/.local-packages/r/v2", recursive = TRUE) - .libPaths(c("/workspace/.local-packages/r/v2", .libPaths())) + local_pkg_dir <- paste0("/workspace/.local-packages/r/", Sys.getenv("MAJOR_VERSION")) + if (!dir.exists(local_pkg_dir)) { + dir.create(local_pkg_dir, recursive = TRUE) + .libPaths(c(local_pkg_dir, .libPaths())) # create .gitignore file file.create("/workspace/.local-packages/.gitignore") fileconn <- file("/workspace/.local-packages/.gitignore") diff --git a/tests/test-loading-packages.R b/tests/test-loading-packages.R index 08a40ba..e224e54 100644 --- a/tests/test-loading-packages.R +++ b/tests/test-loading-packages.R @@ -7,12 +7,12 @@ npkgs <- length(pkgs) for (i in 1:npkgs) { package <- pkgs[i] - suppressMessages({ - if (!library(package, logical.return = TRUE, character.only = TRUE)) { - stop(paste("Package", package, "failed to load, please investigate")) - } + tryCatch({ + suppressMessages(library(package, character.only = TRUE)) dtch <- paste0("package:", package) detach(dtch, force = TRUE, unload = TRUE, character.only = TRUE) + }, error = function(e) { + stop(paste0("Package ", package, " failed to load: ", conditionMessage(e))) }) } diff --git a/tests/test-preinstalled-user-package-step-1.R b/tests/test-preinstalled-user-package-step-1.R index 462e6c1..fd9c35a 100644 --- a/tests/test-preinstalled-user-package-step-1.R +++ b/tests/test-preinstalled-user-package-step-1.R @@ -1,7 +1,8 @@ # .libPaths() should not have been amended yet -stopifnot(.libPaths()[1] != "/workspace/.local-packages/r/v2") +local_pkg_dir <- paste0("/workspace/.local-packages/r/", Sys.getenv("MAJOR_VERSION")) +stopifnot(.libPaths()[1] != local_pkg_dir) # install package to user library in repo install.packages("tmsens") # .libPaths() should have been amended -stopifnot(.libPaths()[1] == "/workspace/.local-packages/r/v2") +stopifnot(.libPaths()[1] == local_pkg_dir) print("Step 1: installing user package and amending .libPaths() paths test passed") diff --git a/tests/test-preinstalled-user-package-step-2.R b/tests/test-preinstalled-user-package-step-2.R index e235265..05b677b 100644 --- a/tests/test-preinstalled-user-package-step-2.R +++ b/tests/test-preinstalled-user-package-step-2.R @@ -1,5 +1,5 @@ # User library directory should already exist, hence .libPaths() is amended -stopifnot(.libPaths()[1] == "/workspace/.local-packages/r/v2") +stopifnot(.libPaths()[1] == paste0("/workspace/.local-packages/r/", Sys.getenv("MAJOR_VERSION"))) # Load the pre-installed package from previous R session which is now in repo library(tmsens) # Delete /workspace/.local-packages diff --git a/tests/test-user-install-package.R b/tests/test-user-install-package.R index 5dbb9bb..0874085 100644 --- a/tests/test-user-install-package.R +++ b/tests/test-user-install-package.R @@ -34,7 +34,7 @@ library(tmsens) print("Loading user installed package test passed.") print("Library paths") -stopifnot(.libPaths()[1] == "/workspace/.local-packages/r/v2") +stopifnot(.libPaths()[1] == paste0("/workspace/.local-packages/r/", Sys.getenv("MAJOR_VERSION"))) # Test adding a second package works # (again bpbounds chosen because it also has no hard dependencies) diff --git a/tests/test.sh b/tests/test.sh index d312d60..136198d 100755 --- a/tests/test.sh +++ b/tests/test.sh @@ -14,7 +14,7 @@ if [ "${MAJOR_VERSION}" = "v1" ]; then # Test all R packages can be loaded python3 -c "import json; print('\n'.join(json.load(open(\"./$MAJOR_VERSION/renv.lock\"))['Packages']))" | xargs -I {} echo "if (!library({}, warn.conflicts = FALSE, logical.return = TRUE)) {stop(\"Package {} failed to load, please investigate\")}" > .tests.R run_test "${MAJOR_VERSION}" .tests.R -elif [ "${MAJOR_VERSION}" = "v2" ]; then +elif [[ "${MAJOR_VERSION}" =~ ^v[23]$ ]]; then # Test all R packages can be attached then detached run_test "${MAJOR_VERSION}" ./tests/test-loading-packages.R fi @@ -31,8 +31,8 @@ run_test "${MAJOR_VERSION}" ./tests/test-arrow.R # Test loading the 14 base packages run_test "${MAJOR_VERSION}" ./tests/test-loading-base.R -# Test user installed paackages on v2 -if [ "${MAJOR_VERSION}" = "v2" ]; then +# Test user installed paackages on v2 and v3 +if [[ "${MAJOR_VERSION}" =~ ^v[23]$ ]]; then # Test installing and loading in same R session run_test "${MAJOR_VERSION}" ./tests/test-user-install-package.R diff --git a/v2/Dockerfile b/v2/Dockerfile index 52d4cef..a3d62be 100644 --- a/v2/Dockerfile +++ b/v2/Dockerfile @@ -37,6 +37,9 @@ EOF # Finally, build the actual image from the base-r image FROM base-r AS r ARG REPOS="default-arg-to-silence-docker" +ARG MAJOR_VERSION=v2 +ENV MAJOR_VERSION=${MAJOR_VERSION} +RUN echo "MAJOR_VERSION=${MAJOR_VERSION}" >> /usr/lib/R/etc/Renviron.site # Some static metadata for this specific image, as defined by: # https://github.com/opencontainers/image-spec/blob/master/annotations.md#pre-defined-annotation-keys @@ -62,7 +65,9 @@ WORKDIR /workspace # Settings to make it easier for users to add packages RUN --mount=type=bind,source=scripts/rprofile-site-append-2.R,target=/tmp/rprofile-site-append-2.R \ cat /tmp/rprofile-site-append-2.R >> /usr/lib/R/etc/Rprofile.site -COPY scripts/local-packages-README.md /usr/local-packages-README.md +RUN --mount=type=bind,source=scripts/local-packages-README.Rmd,target=/tmp/local-packages-README.Rmd < /etc/apt/sources.list.d/cran.list + /usr/lib/apt/apt-helper download-file 'https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc' /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc + /root/docker-apt-install.sh /tmp/dependencies.txt + ln -sf /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 /usr/lib/R/lib/libRblas.so + ln -sf /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 /usr/lib/R/lib/libRlapack.so +EOF + +# use pak to install packages +ENV PKG_CACHE_DIR=/cache/main +ENV PKG_PACKAGE_CACHE_DIR=/cache/package +ENV PKG_METADATA_CACHE_DIR=/cache/metadata +ARG REPOS="default-arg-to-silence-docker" +ARG CRAN_DATE="default-arg-to-silence-docker" +RUN --mount=type=cache,target=/cache,id=/cache-2204,sharing=locked \ + --mount=type=bind,source=scripts/build-toml.R,target=/tmp/scripts/build-toml.R \ + --mount=type=bind,source=${MAJOR_VERSION}/packages.toml,target=/tmp/packages.toml \ + --mount=type=bind,source=scripts/rprofile-site-append-1.R,target=/tmp/rprofile-site-append-1.R <> /usr/lib/R/etc/Renviron.site + cat /tmp/rprofile-site-append-1.R >> /usr/lib/R/etc/Rprofile.site + Rscript /tmp/scripts/build-toml.R +EOF + + +################################################ +# +# Finally, build the actual image from the base-r image +FROM base-r AS r +ARG REPOS="default-arg-to-silence-docker" +ARG MAJOR_VERSION=v3 +ENV MAJOR_VERSION=${MAJOR_VERSION} +RUN echo "MAJOR_VERSION=${MAJOR_VERSION}" >> /usr/lib/R/etc/Renviron.site + +# Some static metadata for this specific image, as defined by: +# https://github.com/opencontainers/image-spec/blob/master/annotations.md#pre-defined-annotation-keys +# The org.opensafely.action label is used by the jobrunner to indicate this is +# an approved action image to run. +LABEL org.opencontainers.image.title="r" \ + org.opencontainers.image.description="R action for opensafely.org" \ + org.opencontainers.image.source="https://github.com/opensafely-core/r-docker" \ + org.opensafely.action="r" \ + org.opensafely.version="${MAJOR_VERSION}" \ + org.opensafely.cran-date="${CRAN_DATE}" + +# ACTION_EXEC is our default executable +ENV ACTION_EXEC="/usr/bin/Rscript" +# INTERACTIVE_EXEC is used when running w/o any args, implying an interactive session. +# See: https://github.com/opensafely-core/base-docker/blob/main/entrypoint.sh#L5 +ENV INTERACTIVE_EXEC="/usr/bin/R" + +# setup /workspace +RUN mkdir /workspace +WORKDIR /workspace + +# Settings to make it easier for users to add packages +RUN --mount=type=bind,source=scripts/rprofile-site-append-2.R,target=/tmp/rprofile-site-append-2.R \ + cat /tmp/rprofile-site-append-2.R >> /usr/lib/R/etc/Rprofile.site +RUN --mount=type=bind,source=scripts/local-packages-README.Rmd,target=/tmp/local-packages-README.Rmd <> /usr/lib/R/etc/Renviron.site +EOF + +COPY rstudio/rstudio-entrypoint.sh /usr/local/bin/rstudio-entrypoint.sh + +ENV USER=rstudio +ENTRYPOINT ["/usr/local/bin/rstudio-entrypoint.sh"] diff --git a/v3/dependencies.txt b/v3/dependencies.txt new file mode 100644 index 0000000..f0108d0 --- /dev/null +++ b/v3/dependencies.txt @@ -0,0 +1,71 @@ +## Core systemdependencies +tzdata +libopenblas0-pthread +r-base-core=4.5.3-1.2204.0 +r-base-dev=4.5.3-1.2204.0 + +## Package specific dependencies. +# +# Please add comment with the name of the R package that required this package +# to be added for future reference. + +# igraph, XML, xml2 +libxml2 + +# rmarkdown, knitr +pandoc + +# units +libudunits2-0 + +# magick +gsfonts + +## -dev and -bin package dependencies +# +# The following system dependencies are required for some specific R packages. +# However, the documented dependency is the a -dev or -bin package version. +# +# This is due to a quirk of some Debian packaging practices that means some +# work is needed. A not uncommon pattern in apt land is to include the major +# version in the package name, rather than the package version. This is +# typically done to support migration between major versions within a single OS +# lifetime. Because the CRAN system dependencies do not know what the major +# version and thus the name you will have on your OS is, they typically include +# the `-dev` or `-bin` version of the package, which acts like a meta package and will +# pull in the correctly named default major version for the OS. However, it +# frequently pulls in many more packages than the actual library needed. +# +# So, to avoid pulling in more that we need, we figure out the actual name of +# the package, including major version, and depend on just that. Figuring this +# out is manual, but the following can help, from the target Ubuntu version: +# +# debtree $PACKAGE | dot -Tjpg | display +# +# or if that plot is very large it's often the first proper entry of +# +# debtree $PACKAGE +# +# and sometimes grepping can be helpful +# +# debtree $PACKAGE | grep obvious-part-of-package-name* +# +# There is usually a package in the form of $PACKAGEVERSION in the tree which is the +# one we actually need. This will need doing once for every version of base Ubuntu +# image we use for an R version. + +# igraph: documented dependency is libglpk-dev +libglpk40 + +# sf - libgdal-dev +libgdal30 + +# magick: documented dependency is libmagick++-dev +libmagick++-6.q16-8 + +# V8, via daggity: documented dependency is libnode-dev +libnode72 + +# httpgd, via unigd: documented dependency is libtiff-dev +libtiff5 +libtiffxx5 diff --git a/v3/env b/v3/env new file mode 100644 index 0000000..2488f2a --- /dev/null +++ b/v3/env @@ -0,0 +1,6 @@ +MAJOR_VERSION=v3 +BASE=22.04 +RSTUDIO_BASE_URL=https://download2.rstudio.org/server/jammy/amd64/ +RSTUDIO_DEB=rstudio-server-2026.01.2-418-amd64.deb +CRAN_DATE=2026-03-27 +REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/${CRAN_DATE} diff --git a/v3/packages.md b/v3/packages.md new file mode 100644 index 0000000..007484f --- /dev/null +++ b/v3/packages.md @@ -0,0 +1,542 @@ +Package Versions for v3 +================ + +This r:v3 OpenSAFELY image is based on Ubuntu 22.04 with R 4.5.3. + +## R packages + +The image comes pre-installed with a set of R packages listed in the +table below. Some packages may no longer be on CRAN and so their URL +below will link to the archive of that package’s source code. Each image +also contains the 14 base R packages (base, compiler, datasets, +grDevices, graphics, grid, methods, parallel, splines, stats, stats4, +tcltk, tools, and utils) for the respective version of R. + +| Package | Version | Url | +| :-------------------- | :------------ | :--------------------------------------------------------- | +| abind | 1.4-8 | | +| anytime | 0.3.12 | | +| ape | 5.8-1 | | +| arrow | 23.0.1.2 | | +| ash | 1.0-15 | | +| AsioHeaders | 1.30.2-1 | | +| askpass | 1.2.1 | | +| assertthat | 0.2.1 | | +| astsa | 2.5 | | +| aweek | 1.0.3 | | +| backports | 1.5.0 | | +| base64enc | 0.1-6 | | +| base64url | 1.4 | | +| BayesianTools | 0.1.9 | | +| bayesm | 3.1-7 | | +| bayesplot | 1.15.0 | | +| bayestestR | 0.17.0 | | +| bbmle | 1.0.25.1 | | +| bdsmatrix | 1.3-7 | | +| BH | 1.90.0-1 | | +| bigD | 0.3.1 | | +| biglm | 0.9-3 | | +| bigmemory | 4.6.4 | | +| bigmemory.sri | 0.1.8 | | +| binom | 1.1-1.1 | | +| bit | 4.6.0 | | +| bit64 | 4.6.0-1 | | +| bitops | 1.0-9 | | +| blob | 1.3.0 | | +| boot | 1.3-32 | | +| brew | 1.0-10 | | +| brglm2 | 1.0.1 | | +| bridgesampling | 1.2-1 | | +| brms | 2.23.0 | | +| Brobdingnag | 1.2-9 | | +| broom | 1.0.12 | | +| broom.helpers | 1.22.0 | | +| broom.mixed | 0.2.9.7 | | +| bslib | 0.10.0 | | +| butcher | 0.4.0 | | +| ca | 0.71.1 | | +| cachem | 1.1.0 | | +| callr | 3.7.6 | | +| car | 3.1-5 | | +| carData | 3.0-6 | | +| cards | 0.7.1 | | +| cardx | 0.3.2 | | +| caret | 7.0-1 | | +| caTools | 1.18.3 | | +| cellranger | 1.1.0 | | +| checkmate | 2.3.4 | | +| chk | 0.10.0 | | +| class | 7.3-23 | | +| classInt | 0.4-11 | | +| cli | 3.6.5 | | +| clipr | 0.8.0 | | +| clock | 0.7.4 | | +| clue | 0.3-68 | | +| cluster | 2.1.8.2 | | +| cmprsk | 2.2-12 | | +| cobalt | 4.6.2 | | +| coda | 0.19-4.1 | | +| codetools | 0.2-20 | | +| collections | 0.3.12 | | +| colorspace | 2.1-2 | | +| commonmark | 2.0.0 | | +| conflicted | 1.2.0 | | +| consort | 1.2.2 | | +| corpcor | 1.6.10 | | +| corrplot | 0.95 | | +| corrr | 0.4.5 | | +| cowplot | 1.2.0 | | +| coxme | 2.2-22 | | +| cpp11 | 0.5.3 | | +| crayon | 1.5.3 | | +| crosstalk | 1.2.2 | | +| curl | 7.0.0 | | +| dagitty | 0.3-4 | | +| data.table | 1.18.2.1 | | +| datawizard | 1.3.0 | | +| DBI | 1.3.0 | | +| dbplyr | 2.5.2 | | +| dd4d | 0.0.0.9000 | | +| deldir | 2.0-4 | | +| Deriv | 4.2.0 | | +| desc | 1.4.3 | | +| deSolve | 1.42 | | +| detectseparation | 0.3 | | +| dfidx | 0.2-0 | | +| DHARMa | 0.4.7 | | +| diagram | 1.6.5 | | +| DiagrammeR | 1.0.11 | | +| dials | 1.4.2 | | +| DiceDesign | 1.10 | | +| digest | 0.6.39 | | +| distributional | 0.7.0 | | +| doBy | 4.7.1 | | +| doParallel | 1.0.17 | | +| dplyr | 1.2.0 | | +| DT | 0.34.0 | | +| dtplyr | 1.3.3 | | +| dtw | 1.23-1 | | +| dtwclust | 6.0.0 | | +| duckdb | 1.5.1 | | +| e1071 | 1.7-17 | | +| effectsize | 1.0.2 | | +| egg | 0.4.5 | | +| ellipse | 0.5.0 | | +| emmeans | 2.0.2 | | +| emulator | 1.2-24 | | +| enrichwith | 0.4.0 | | +| Epi | 2.64 | | +| epitools | 0.5-10.1 | | +| estimability | 1.5.1 | | +| estimatr | 1.0.6 | | +| etm | 1.1.2 | | +| evaluate | 1.0.5 | | +| exactRankTests | 0.8-36 | | +| expm | 1.0-0 | | +| farver | 2.1.2 | | +| fastDummies | 1.7.5 | | +| fastGHQuad | 1.0.1 | | +| fastglm | 0.0.4 | | +| fastmap | 1.2.0 | | +| fastshap | 0.1.1 | | +| fda | 6.3.0 | | +| fds | 1.8 | | +| finalfit | 1.1.0 | | +| flexclust | 1.5.0 | | +| flexsurv | 2.3.2 | | +| FNN | 1.1.4.1 | | +| fontawesome | 0.5.3 | | +| fontBitstreamVera | 0.1.1 | | +| fontLiberation | 0.1.0 | | +| fontquiver | 0.2.1 | | +| forcats | 1.0.1 | | +| foreach | 1.5.2 | | +| forecast | 9.0.2 | | +| foreign | 0.8-91 | | +| forestplot | 3.2.0 | | +| forestploter | 1.1.3 | | +| Formula | 1.2-5 | | +| formula.tools | 1.7.1 | | +| fracdiff | 1.5-3 | | +| fs | 2.0.1 | | +| furrr | 0.3.1 | | +| future | 1.70.0 | | +| future.apply | 1.20.2 | | +| fuzzyjoin | 0.1.8 | | +| gap | 1.14 | | +| gap.datasets | 0.0.6 | | +| gargle | 1.6.1 | | +| gclus | 1.3.3 | | +| geepack | 1.3.13 | | +| generics | 0.1.4 | | +| geosphere | 1.6-5 | | +| getopt | 1.20.4 | | +| gets | 0.38 | | +| ggalluvial | 0.12.6 | | +| GGally | 2.4.0 | | +| ggdist | 3.3.3 | | +| ggeffects | 2.3.2 | | +| ggfittext | 0.10.3 | | +| ggfortify | 0.4.19 | | +| gggenes | 0.6.0 | | +| ggh4x | 0.3.1 | | +| ggplot2 | 4.0.2 | | +| ggpubr | 0.6.3 | | +| ggrepel | 0.9.8 | | +| ggridges | 0.5.7 | | +| ggsci | 4.2.0 | | +| ggsignif | 0.6.4 | | +| ggstats | 0.13.0 | | +| ggtext | 0.1.2 | | +| ggvenn | 0.1.19 | | +| gh | 1.5.0 | | +| gitcreds | 0.1.2 | | +| glmmTMB | 1.1.14 | | +| glmnet | 4.1-10 | | +| globals | 0.19.1 | | +| glue | 1.8.0 | | +| Gmisc | 3.2.0 | | +| gmm | 1.9-1 | | +| gnm | 1.1-5 | | +| googledrive | 2.1.2 | | +| googlesheets4 | 1.1.2 | | +| gower | 1.0.2 | | +| GPfit | 1.0-9 | | +| gridExtra | 2.3 | | +| gridtext | 0.1.6 | | +| gt | 1.3.0 | | +| gtable | 0.3.6 | | +| gtsummary | 2.5.0 | | +| hardhat | 1.4.2 | | +| haven | 2.5.5 | | +| HDInterval | 0.2.4 | | +| hdrcde | 3.5.0 | | +| here | 1.0.2 | | +| hexbin | 1.28.5 | | +| highr | 0.12 | | +| Hmisc | 5.2-5 | | +| hms | 1.1.4 | | +| htmlTable | 2.4.3 | | +| htmltools | 0.5.9 | | +| htmlwidgets | 1.6.4 | | +| httpgd | 2.1.4 | | +| httpuv | 1.6.17 | | +| httr | 1.4.8 | | +| httr2 | 1.2.2 | | +| IDPmisc | 1.1.21 | | +| ids | 1.0.1 | | +| igraph | 2.2.2 | | +| incidence | 1.7.6 | | +| infer | 1.1.0 | | +| ini | 0.3.1 | | +| inline | 0.3.21 | | +| insight | 1.4.6 | | +| interactions | 1.2.0 | | +| interp | 1.1-6 | | +| ipred | 0.9-15 | | +| isoband | 0.3.0 | | +| iterators | 1.0.14 | | +| janitor | 2.2.1 | | +| jomo | 2.7-6 | | +| jpeg | 0.1-11 | | +| jquerylib | 0.1.4 | | +| jsonlite | 2.0.0 | | +| jtools | 2.3.1 | | +| juicyjuice | 0.1.0 | | +| kableExtra | 1.4.0 | | +| kernlab | 0.9-33 | | +| KernSmooth | 2.23-26 | | +| KMsurv | 0.1-6 | | +| knitr | 1.51 | | +| ks | 1.15.1 | | +| labeling | 0.4.3 | | +| labelled | 2.16.0 | | +| languageserver | 0.3.17 | | +| later | 1.4.8 | | +| lattice | 0.22-9 | | +| latticeExtra | 0.6-31 | | +| lava | 1.8.2 | | +| lazyeval | 0.2.2 | | +| lcmm | 2.2.2 | | +| lhs | 1.2.1 | | +| lifecycle | 1.0.5 | | +| lintr | 3.3.0-1 | | +| listenv | 0.10.1 | | +| litedown | 0.9 | | +| lme4 | 2.0-1 | | +| lmtest | 0.9-40 | | +| lobstr | 1.2.0 | | +| locfit | 1.5-9.12 | | +| loo | 2.9.0 | | +| lpSolveAPI | 5.5.2.0-17.15 | | +| lsoda | 1.2 | | +| lubridate | 1.9.5 | | +| magick | 2.9.1 | | +| magrittr | 2.0.4 | | +| marginaleffects | 0.32.0 | | +| markdown | 2.0 | | +| marqLevAlg | 2.0.8 | | +| MASS | 7.3-65 | | +| MatchIt | 4.7.2 | | +| mathjaxr | 2.0-0 | | +| Matrix | 1.7-5 | | +| MatrixModels | 0.5-4 | | +| matrixStats | 1.5.0 | | +| maxstat | 0.7-26 | | +| mclust | 6.1.2 | | +| medflex | 0.6-11 | | +| memoise | 2.0.1 | | +| metadat | 1.4-0 | | +| metafor | 4.8-0 | | +| mets | 1.3.9 | | +| mgcv | 1.9-4 | | +| mice | 3.19.0 | | +| microbenchmark | 1.5.0 | | +| mime | 0.13 | | +| minqa | 1.2.8 | | +| mitml | 0.4-5 | | +| mitools | 2.4 | | +| mlogit | 1.1-3 | | +| modeldata | 1.5.1 | | +| modelenv | 0.2.0 | | +| ModelMetrics | 1.2.2.2 | | +| modelr | 0.1.11 | | +| modelsummary | 2.6.0 | | +| modeltools | 0.2-24 | | +| msm | 1.8.2 | | +| mstate | 0.3.3 | | +| muhaz | 1.2.6.4 | | +| multcomp | 1.4-30 | | +| multicool | 1.0.1 | | +| mvtnorm | 1.3-6 | | +| naniar | 1.1.0 | | +| NHPoisson | 3.4 | | +| nleqslv | 3.3.6 | | +| nlme | 3.1-168 | | +| nloptr | 2.2.1 | | +| nnet | 7.3-20 | | +| norm | 1.0-11.1 | | +| numDeriv | 2016.8-1.1 | | +| openssl | 2.3.5 | | +| operator.tools | 1.6.3.1 | | +| optparse | 1.7.5 | | +| ordinal | 2025.12-29 | | +| otel | 0.2.0 | | +| padr | 0.6.3 | | +| pammtools | 0.7.4 | | +| pan | 1.9 | | +| pander | 0.6.6 | | +| parallelly | 1.46.1 | | +| parameters | 0.28.3 | | +| parsnip | 1.4.1 | | +| patchwork | 1.3.2 | | +| pbapply | 1.7-4 | | +| pbkrtest | 0.5.5 | | +| pcaPP | 2.0-5 | | +| pch | 2.2 | | +| pec | 2025.06.24 | | +| performance | 0.16.0 | | +| permute | 0.9-10 | | +| PHEindicatormethods | 2.1.1 | | +| pillar | 1.11.1 | | +| pkgbuild | 1.4.8 | | +| pkgconfig | 2.0.3 | | +| pkgload | 1.5.0 | | +| plotly | 4.12.0 | | +| plotrix | 3.8-14 | | +| plyr | 1.8.9 | | +| png | 0.1-9 | | +| polspline | 1.1.25 | | +| polynom | 1.4-1 | | +| posterior | 1.6.1 | | +| pracma | 2.4.6 | | +| predtools | 0.0.3 | | +| prettyunits | 1.2.0 | | +| pROC | 1.19.0.1 | | +| processx | 3.8.6 | | +| prodlim | 2026.03.11 | | +| progress | 1.2.3 | | +| progressr | 0.18.0 | | +| promises | 1.5.0 | | +| proxy | 0.4-29 | | +| ps | 1.9.1 | | +| pscl | 1.5.9 | | +| pseudo | 1.4.3 | | +| Publish | 2025.07.24 | | +| purrr | 1.2.1 | | +| qap | 0.1-2 | | +| qgam | 2.0.0 | | +| quadprog | 1.5-8 | | +| quantmod | 0.4.28 | | +| quantreg | 6.1 | | +| QuickJSR | 1.9.0 | | +| qvcalc | 1.0.4 | | +| R.cache | 0.17.0 | | +| R.methodsS3 | 1.8.2 | | +| R.oo | 1.27.1 | | +| R.utils | 2.13.0 | | +| R6 | 2.6.1 | | +| ragg | 1.5.2 | | +| rainbow | 3.8 | | +| randomForest | 4.7-1.2 | | +| randomForestExplainer | 0.10.1 | | +| ranger | 0.18.0 | | +| rappdirs | 0.3.4 | | +| rbibutils | 2.4.1 | | +| RColorBrewer | 1.1-3 | | +| RConics | 1.1.2 | | +| Rcpp | 1.1.1 | | +| RcppArmadillo | 15.2.4-1 | | +| RcppEigen | 0.3.4.0.2 | | +| RcppParallel | 5.1.11-2 | | +| RcppProgress | 0.4.2 | | +| RcppRoll | 0.3.1 | | +| RcppThread | 2.3.0 | | +| RCurl | 1.98-1.18 | | +| Rdpack | 2.6.6 | | +| rdrobust | 3.0.0 | | +| reactable | 0.4.5 | | +| reactR | 0.6.1 | | +| readr | 2.2.0 | | +| readxl | 1.4.5 | | +| recipes | 1.3.1 | | +| reformulas | 0.4.4 | | +| registry | 0.5-1 | | +| relimp | 1.0-5 | | +| relsurv | 2.3-3 | | +| rematch | 2.0.0 | | +| rematch2 | 2.1.2 | | +| repr | 1.1.7 | | +| reprex | 2.1.1 | | +| reshape2 | 1.4.5 | | +| rex | 1.2.1 | | +| riskRegression | 2026.03.11 | | +| rlang | 1.1.7 | | +| rmarkdown | 2.31 | | +| rms | 8.1-1 | | +| ROI | 1.0-2 | | +| ROI.plugin.lpsolve | 1.0-2 | | +| roxygen2 | 7.3.3 | | +| rpart | 4.1.24 | | +| rpart.plot | 3.1.4 | | +| rprojroot | 2.1.1 | | +| rsample | 1.3.2 | | +| RSpectra | 0.16-2 | | +| rstan | 2.32.7 | | +| rstantools | 2.6.0 | | +| rstatix | 0.7.3 | | +| rstpm2 | 1.7.1 | | +| rstudioapi | 0.18.0 | | +| rvest | 1.0.5 | | +| s2 | 1.1.9 | | +| S7 | 0.2.1 | | +| sandwich | 3.1-1 | | +| sass | 0.4.10 | | +| scales | 1.4.0 | | +| scam | 1.2-22 | | +| SCCS | 1.7 | | +| secretbase | 1.2.0 | | +| segmented | 2.2-1 | | +| selectr | 0.5-1 | | +| seriation | 1.5.8 | | +| sf | 1.1-0 | | +| sfd | 0.1.0 | | +| shades | 1.4.0 | | +| shape | 1.4.6.1 | | +| shapviz | 0.10.3 | | +| shiny | 1.13.0 | | +| shinyjs | 2.1.1 | | +| sjlabelled | 1.2.0 | | +| sjmisc | 2.8.11 | | +| sjPlot | 2.9.0 | | +| sjstats | 0.19.1 | | +| skimr | 2.2.2 | | +| slam | 0.1-55 | | +| slider | 0.3.3 | | +| snakecase | 0.11.1 | | +| sourcetools | 0.1.7-1 | | +| sp | 2.2-1 | | +| spacefillr | 0.4.0 | | +| SparseM | 1.84-2 | | +| sparsevctrs | 0.3.6 | | +| speedglm | 0.3-5 | | +| splines2 | 0.5.4 | | +| SQUAREM | 2026.1 | | +| StanHeaders | 2.32.10 | | +| statmod | 1.5.1 | | +| stringdist | 0.9.17 | | +| stringi | 1.8.7 | | +| stringr | 1.6.0 | | +| styler | 1.11.0 | | +| survey | 4.5 | | +| survival | 3.8-6 | | +| survminer | 0.5.2 | | +| svglite | 2.2.2 | | +| sweep | 0.2.7 | | +| sys | 3.4.3 | | +| systemfonts | 1.3.2 | | +| tables | 0.9.33 | | +| tailor | 0.1.0 | | +| targets | 1.12.0 | | +| tensorA | 0.36.2.1 | | +| textshaping | 1.0.5 | | +| TH.data | 1.1-5 | | +| tibble | 3.3.1 | | +| tictoc | 1.2.1 | | +| tidycmprsk | 1.1.1 | | +| tidymodels | 1.4.1 | | +| tidypredict | 1.1.0 | | +| tidyr | 1.3.2 | | +| tidyselect | 1.2.1 | | +| tidyverse | 2.0.0 | | +| timechange | 0.4.0 | | +| timeDate | 4052.112 | | +| timereg | 2.0.7 | | +| timetk | 2.9.1 | | +| tinytable | 0.16.0 | | +| tinytex | 0.58 | | +| TMB | 1.9.21 | | +| tmvtnorm | 1.7 | | +| TrialEmulation | 0.0.4.9 | | +| tseries | 0.10-61 | | +| tsfeatures | 1.1.1 | | +| tsModel | 0.6-2 | | +| TSP | 1.2.7 | | +| TTR | 0.24.4 | | +| tune | 2.0.1 | | +| twopartm | 0.1.0 | | +| tzdb | 0.5.0 | | +| ucminf | 1.2.2 | | +| unigd | 0.2.0 | | +| units | 1.0-1 | | +| UpSetR | 1.4.0 | | +| urca | 1.3-4 | | +| utf8 | 1.2.6 | | +| uuid | 1.2-2 | | +| V8 | 8.0.1 | | +| vcd | 1.4-13 | | +| vctrs | 0.7.2 | | +| vegan | 2.7-3 | | +| VGAM | 1.1-14 | | +| viridis | 0.6.5 | | +| viridisLite | 0.4.3 | | +| visdat | 0.6.0 | | +| visNetwork | 2.1.4 | | +| vroom | 1.7.0 | | +| warp | 0.2.3 | | +| WeightIt | 1.6.0 | | +| withr | 3.0.2 | | +| wk | 0.9.5 | | +| workflows | 1.3.0 | | +| workflowsets | 1.1.1 | | +| xfun | 0.57 | | +| xgboost | 3.2.1.1 | | +| XML | 3.99-0.23 | | +| xml2 | 1.5.2 | | +| xmlparsedata | 1.0.5 | | +| xtable | 1.8-8 | | +| xts | 0.14.2 | | +| yaml | 2.3.12 | | +| yardstick | 1.3.2 | | +| zip | 2.3.3 | | +| zoo | 1.8-15 | | diff --git a/v3/packages.toml b/v3/packages.toml new file mode 100644 index 0000000..06011cb --- /dev/null +++ b/v3/packages.toml @@ -0,0 +1,215 @@ +title = "R packages and their repositories for v3 of the OpenSAFELY r image" + +# base packages +# rownames(installed.packages(priority = "base")) +# R has 14 base packages which are included in the image: base, compiler, datasets, grDevices, graphics, grid, methods, parallel, splines, stats, stats4, tcltk, tools, utils; these do not need to be listed below +# recommended packages +# rownames(installed.packages(priority = "recommended")) +# R has 15 recommended packages, 14 of which are included in the image: boot, class, cluster, codetools, foreign, KernSmooth, lattice, mgcv, nlme, nnet, rpart, spatial, survival, MASS, Matrix; spatial is currently not included. + +[v1] +packages = [ + "arrow", + "astsa", + "BayesianTools", + "bayesm", + "BH", + "binom", + "blob", + "brglm2", + "brms", + "broom", + "broom.helpers", + "butcher", + "caret", + "caTools", + "cmprsk", + "cobalt", + "consort", + "cowplot", + "coxme", + "cpp11", + "dagitty", + "data.table", + "DBI", + "dbplyr", + "deSolve", + "detectseparation", + "doBy", + "doParallel", + "dplyr", + "dtplyr", + "dtwclust", + "e1071", + "egg", + "emmeans", + "Epi", + "epitools", + "estimatr", + "fastDummies", + "fastshap", + "finalfit", + "flexsurv", + "fontquiver", + "foreach", + "forecast", + "forestploter", + "furrr", + "fuzzyjoin", + "gets", + "ggalluvial", + "GGally", + "ggdist", + "ggfortify", + "ggh4x", + "ggplot2", + "ggvenn", + "gh", + "gitcreds", + "glmmTMB", + "glmnet", + "glue", + "Gmisc", + "gt", + "gtsummary", + "haven", + "HDInterval", + "here", + "hexbin", + "Hmisc", + "hms", + "incidence", + "interactions", + "janitor", + "jsonlite", + "kableExtra", + "knitr", + "labelled", + "latticeExtra", + "lcmm", + "lme4", + "lubridate", + "magick", + "magrittr", + "MatchIt", + "matrixStats", + "metafor", + "mice", + "mlogit", + "modelsummary", + "mstate", + "multcomp", + "mvtnorm", + "naniar", + "NHPoisson", + "optparse", + "pammtools", + "parameters", + "patchwork", + "pch", + "pec", + "PHEindicatormethods", + "plotly", + "plotrix", + "predtools", + "pscl", + "pseudo", + "R.utils", + "randomForest", + "randomForestExplainer", + "Rcpp", + "RcppArmadillo", + "RcppEigen", + "RcppParallel", + "RcppProgress", + "RcppRoll", + "RcppThread", + "rdrobust", + "readxl", + "relsurv", + "riskRegression", + "rlang", + "rmarkdown", + "rms", + "rpart.plot", + "sandwich", + "SCCS", + "segmented", + "sf", + "shapviz", + "shiny", + "skimr", + "splines2", + "stringi", + "stringr", + "survey", + "survminer", + "svglite", + "sweep", + "tictoc", + "tidyr", + "tidyselect", + "tidyverse", + "timetk", + "tsModel", + "twopartm", + "vcd", + "VGAM", + "WeightIt", + "xml2", + "xts", + "zip", + "zoo" +] +comment = "Packages from v1 image. Note that not all packages from v1 are included in v3." + +[v2-additions] +packages = [ + "corrr", + "DiagrammeR", + "infer", + "interp", + "lintr", + "parsnip", + "sjPlot", + "speedglm", + "styler", + "targets", + "tidycmprsk", + "tidymodels", + "tidypredict" +] +comment = "sjPlot requested in issue 160." + +[dummy-data] +packages = "dd4d" +repos = "https://opensafely-core.r-universe.dev/" +comment = "Will's package for simulating dummy data. First added for Will and Becky's workshop at the 2024 OpenSAFELY Symposium." + +[vscode] +packages = [ + "AsioHeaders", + "languageserver", + "httpgd" +] +comment = "Packages to work with the VSCode R extension." + +[trial-emulation] +packages = "TrialEmulation" +comment = "The Bristol group are planning to perform target trial emulation analyses." + +[cardx] +packages = "cardx" +comment = "Requested by Will. This is a soft (Suggests list) dependency of gtsummary, and hence wasn't previously installed." + +[marginaleffects] +packages = "marginaleffects" +comment = "Requested by Will. This is a package to compute and plot marginal effects for fitted statistical models." + +[mediation-package] +packages = "medflex" +comment = "Requested by Ruth Costello. This is a package to for flexible mediation analysis using natural effect models" + +[parglm-replacement] +packages = "fastglm" +comment = "The parglm package was archived on CRAN on 2026-01-29. Tom has identified this as its closest replacement on CRAN on the v3 CRAN_DATE." diff --git a/v3/pkg.lock b/v3/pkg.lock new file mode 100644 index 0000000..7b27eae --- /dev/null +++ b/v3/pkg.lock @@ -0,0 +1,16797 @@ +{ + "lockfile_version": 1, + "os": "Ubuntu 22.04.5 LTS", + "r_version": "R version 4.5.3 (2026-03-11)", + "platform": "x86_64-pc-linux-gnu", + "packages": [ + { + "ref": "cards", + "package": "cards", + "version": "0.7.1", + "type": "standard", + "direct": false, + "binary": true, + "dependencies": ["cli", "dplyr", "glue", "lifecycle", "rlang", "tidyr", "tidyselect"], + "vignettes": false, + "needscompilation": false, + "metadata": { + "RemoteType": "standard", + "RemotePkgRef": "cards", + "RemoteRef": "cards", + "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/2026-03-27", + "RemotePkgPlatform": "x86_64-pc-linux-gnu-ubuntu-22.04", + "RemoteSha": "0.7.1" + }, + "sources": 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