diff --git a/.gitignore b/.gitignore index 3b57fba..5f3e5d6 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,8 @@ renv.lock.bak renv/ .tests.R +.tests-base.R +pkg.lock.bak # rstudio-server directories *.config diff --git a/README.md b/README.md index e7117e8..7a95013 100644 --- a/README.md +++ b/README.md @@ -8,19 +8,28 @@ Docker image for running R code in OpenSAFELY, both locally and in production. * docker-compose * [just](https://github.com/casey/just) +And the tests additionally require + +* curl +* python3 + ## Building ```sh -just build +just build VERSION ``` -Under the hood, this builds `./Dockerfile` using docker-compose and buildkit. +where `VERSION` is either v1 or v2. + +Under the hood, this builds `VERSION/Dockerfile` using docker-compose and buildkit. -We currently build a lot of packages, so an initial build on a fresh checkout +In v1, we currently build a lot of packages, so an initial build on a fresh checkout can take a long time (e.g. an hour). However, to alleviate this, the -Dockerfile is carefully designed to use local buildkit cache, so subequent +v1/Dockerfile is carefully designed to use local buildkit cache, so subequent rebuilds should be very fast. +In v2, where possible we install binary R packages for Linux from the Posit Public Package Manager. + ## Adding new packages :warning: To do this you will need: @@ -41,10 +50,18 @@ experience to approve the package. ### Install the package within Docker +#### Under v1 + To add a package, by default it will be installed from CRAN. ```sh -just add-package PACKAGE +just add-package-v1 PACKAGE +``` + +If you need to install a package from another CRAN-like repository, specify its URL as the REPOS argument. + +```sh +just add-package-v1 PACKAGE REPOS ``` If you need to install a package from another CRAN-like repository, specify its URL as the REPOS argument. @@ -54,7 +71,7 @@ just add-package PACKAGE REPOS ``` This will attempt to install and build the package and its dependencies, and -update the `renv.lock`. It will then rebuild the R image with the new lock file +update the `v1/renv.lock`. It will then rebuild the R image with the new lock file and test it. Note that the first time you do this it will need to compile every @@ -62,6 +79,18 @@ included R package (because you won't have the R package builds cached locally). This can take **several hours**. (When we solve the caching problem here we'll be able to do this all in CI.) +#### Under v2 + +Add the package to _v2/packages.csv_. In this file, the first column is the package name, and the second column is for the repository. If the package is on CRAN simply leave the second column blank after the comma. If the package is not on CRAN please add it to the by adding it to the _packages.json_ file in , then enter the relevant Linux binary package URL, likely `https://opensafely-core.r-universe.dev/bin/linux/noble/4.4/`. + +If the package requires any runtime dependencies add those to _v2/dependencies.txt_ + +Then build the v2 image. + +```sh +just build v2 +``` + ### Push the new Docker image to Github Container Registry You will need to configure authentication to GitHub's container registry first. @@ -70,13 +99,13 @@ See [GitHub's documentation](https://docs.github.com/en/packages/working-with-a- When you have authentication configured, run: ```sh -just publish +just publish VERSION ``` ### Commit changes to this repository Commit and push the small resulting change (should only be a few extra -lines in `packages.csv` and `renv.lock`) to a branch, then get the changes +lines in `VERSION/packages.csv`, `VERSION/packages.md`, and `VERSION/renv.lock`) to a branch, then get the changes merged via pull request. The review is a trivial exercise because the Docker image has already been @@ -93,19 +122,19 @@ separately in the tech team manual. If you don't have access, ask in #### System dependencies If the package requires any system build dependencies (e.g. -dev packages with -headers), they should be added to `build-dependencies.txt`. If it requires -runtime dependencies, they should be added to `dependencies.txt`. Packages +headers), they should be added to `VERSION/build-dependencies.txt`. If it requires +runtime dependencies, they should be added to `VERSION/dependencies.txt`. Packages don't advertise their system dependencies, so you may need to figure them out by trying to add the package and reading any error output on failure. -#### Installing an older version +#### Installing an older version in the v1 image only If the package still fails to build, you may be able to install an older version. Find a previous version at `https://cran.r-project.org/src/contrib/Archive/{PACKAGE}/`, and attempt to install it specifically with ```sh -just add-package PACKAGE@VERSION +just add-package v1 PACKAGE@VERSION ``` ## Building, testing, and publishing the rstudio image @@ -113,17 +142,62 @@ just add-package PACKAGE@VERSION The rstudio image is based on the r image including rstudio-server. To build run ```sh -just build-rstudio +just build-rstudio VERSION ``` To test that rstudio-server appears at `http://localhost:8787` run ```sh -just test-rstudio +just test-rstudio VERSION ``` And then push the new rstudio image to the GitHub container registry with ```sh -just publish-rstudio +just publish-rstudio VERSION +``` + +## How to update the version of R and the packages + +In v2, we choose a date from which to install the packages from CRAN, we strongly recommend that the version of R in the image was the release version of R on this date. R release dates can be found on the [R wikipedia page](https://en.wikipedia.org/wiki/R_(programming_language)#Version_names). + +In v2, when installing packages we use a Posit Public Package Manager (PPPM) snapshot repository on the chosen `CRAN_DATE`. + +We use a fixed date because CRAN follows a rolling release model. +As such we know that on a particular date CRAN has tested these package versions with the release version of R. +Hence this is an extremely stable approach to choosing a set of package versions. +And we can add additional packages at their versions on this date reliably (and without updating dependency packages already included in the image). + +The CRAN apt repository for R is available [here](https://cran.r-project.org/bin/linux/ubuntu/noble-cran40/) (note you may need to amend the Ubuntu codename in the URL if using a newer base image), find the package number you require and edit the number in _v2/dependencies.txt_ and _v2/build-dependencies.txt_. + +Then amend the `CRAN_DATE` and `REPOS` arguments in _v2/env_. + +To update run + +```sh +just build v2 +``` + +To test the updated image run + +```sh +just test v2 ``` + +### How to choose a version of R and CRAN date + +Choose a version of R. + +Choose a CRAN date when that version of R. + +Essentially we follow a very similar approach to the versioned stack of the Rocker project. They list their R versions and CRAN dates on their [wiki](https://github.com/rocker-org/rocker-versioned2/wiki/Versions). + +We recommend not choosing a date within the first week of a new version of R being released, because there may be alot of packages updated on CRAN during this time. + +You then need to check that a PPPM snapshot repository exists for your chosen date. Navigate to and inspect your chosen date. Set this as the `REPOS` argument in _v2/env_. + +If you choose a version of R that is not the current version of R we recommend following the rocker approach and choosing the CRAN date as the day before the next version of R was released. For example, if choosing R 4.4.1, R 4.4.2 was released on 2024-10-31 and so we would choose 2024-10-30 as the CRAN date. + +You can find out when the next release of R is scheduled for on the [R developer page](https://developer.r-project.org/). + +We set the `HTTPUserAgent` in the appropriate places so that we obtain binary R packages for Linux from the PPPM. There is additional information about this on the [PPPM website](https://p3m.dev/__docs__/admin/serving-binaries/#binary-user-agents). diff --git a/docker-compose.yaml b/docker-compose.yaml index 415a801..5ad784b 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -1,13 +1,14 @@ services: # used to build the production image r: - image: r + image: r:${MAJOR_VERSION} build: context: . + dockerfile: ${MAJOR_VERSION}/Dockerfile target: r cache_from: # should speed up the build in CI, where we have a cold cache - - ghcr.io/opensafely-core/base-docker - - ghcr.io/opensafely-core/r + - ghcr.io/opensafely-core/base-docker:${BASE} + - ghcr.io/opensafely-core/r:${MAJOR_VERSION} args: # this makes the image work for later cache_from: usage - BUILDKIT_INLINE_CACHE=1 @@ -15,6 +16,10 @@ services: - BUILD_DATE - REVISION - VERSION + - BASE + - MAJOR_VERSION + - CRAN_DATE + - REPOS init: true platform: linux/amd64 add-package: @@ -28,7 +33,7 @@ services: platform: linux/amd64 rstudio: extends: r - image: rstudio + image: rstudio:${MAJOR_VERSION} build: target: rstudio args: diff --git a/justfile b/justfile index 09d432e..eb9b54d 100644 --- a/justfile +++ b/justfile @@ -5,40 +5,55 @@ export DOCKER_BUILDKIT := "1" export COMPOSE_DOCKER_CLI_BUILD := "1" # build the R image locally -build: +build version: #!/usr/bin/env bash set -euo pipefail + source {{ version }}/env # set build args for prod builds export BUILD_DATE=$(date -u +'%y-%m-%dT%H:%M:%SZ') export GITREF=$(git rev-parse --short HEAD) # build the thing - docker-compose build --pull r + docker-compose --env-file {{ version }}/env build --pull r + if [ "{{ version }}" = "v1" ]; then + # update renv.lock + 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 + # update pkg.lock + cp ${MAJOR_VERSION}/pkg.lock ${MAJOR_VERSION}/pkg.lock.bak + # cannot use docker-compose run as it mangles the output + docker run --platform linux/amd64 --rm r:{{ version }} cat /pkg.lock > ${MAJOR_VERSION}/pkg.lock + fi + # render the packages.md file + {{ just_executable() }} render {{ version }} + +# render the version/packages.md file +render version: + docker run --platform linux/amd64 --env-file {{ version }}/env --entrypoint bash --rm -v "/$PWD:/out" -v "$PWD/scripts:/out/scripts" r:{{ version }} "/out/scripts/render.sh" + # build and add a package and its dependencies to the image -add-package package repos="NULL": - bash ./add-package.sh {{ package }} {{ repos }} +add-package-v1 package repos="NULL": + bash v1/scripts/add-package.sh {{ package }} {{ repos }} # r image containing rstudio-server -build-rstudio: - #!/usr/bin/env bash - set -euo pipefail - - # Set RStudio Server .deb filename - export RSTUDIO_BASE_URL=https://download2.rstudio.org/server/focal/amd64/ - export RSTUDIO_DEB=rstudio-server-2024.09.0-375-amd64.deb - docker-compose build --pull rstudio +build-rstudio version: + docker-compose --env-file {{ version }}/env build --pull rstudio # test the locally built image -test image="r": build - bash ./test.sh "{{ image }}" +test version: + #!/usr/bin/env bash + source {{ version }}/env + bash tests/test.sh {{ version }} # test rstudio-server launches -test-rstudio: _env - bash ./test-rstudio.sh +test-rstudio version: _env + bash tests/test-rstudio.sh {{ version }} _env: #!/bin/bash @@ -47,14 +62,24 @@ _env: echo "HOSTPLATFORM=$(docker info -f '{{{{ lower .ClientInfo.Os }}')" >> .env # lint source code -lint: +lint version: docker pull hadolint/hadolint - docker run --rm -i hadolint/hadolint < Dockerfile + docker run --rm -i hadolint/hadolint < {{ version }}/Dockerfile -publish: - docker tag r ghcr.io/opensafely-core/r:latest - docker push ghcr.io/opensafely-core/r:latest +publish version: + #!/usr/bin/env bash + docker tag r:{{ version }} ghcr.io/opensafely-core/r:{{ version }} + docker push ghcr.io/opensafely-core/r:{{ version }} + if [ "{{ version }}" = "v1" ]; then + docker tag r:{{ version }} ghcr.io/opensafely-core/r:latest + docker push ghcr.io/opensafely-core/r:latest + fi -publish-rstudio: - docker tag rstudio ghcr.io/opensafely-core/rstudio:latest - docker push ghcr.io/opensafely-core/rstudio:latest +publish-rstudio version: + #!/usr/bin/env bash + docker tag rstudio:{{ version }} ghcr.io/opensafely-core/rstudio:{{ version }} + docker push ghcr.io/opensafely-core/rstudio:{{ version }} + if [ "{{ version }}" = "v1" ]; then + docker tag rstudio:{{ version }} ghcr.io/opensafely-core/rstudio:latest + docker push ghcr.io/opensafely-core/rstudio:latest + fi diff --git a/packages-tmp.csv b/packages-tmp.csv deleted file mode 100644 index 413cd4e..0000000 --- a/packages-tmp.csv +++ /dev/null @@ -1,2 +0,0 @@ -"Package","Version" -"Rcpp","1.0.5" diff --git a/packages.csv b/packages.csv deleted file mode 100644 index d28c929..0000000 --- a/packages.csv +++ /dev/null @@ -1,464 +0,0 @@ -"Package","Version" -"abind","1.4-5" -"anytime","0.3.9" -"ape","5.7-1" -"arrow","4.0.0.1" -"ash","1.0-15" -"askpass","1.1" -"assertthat","0.2.1" -"astsa","2.1" -"aweek","1.0.2" -"backports","1.4.1" -"base64enc","0.1-3" -"BayesianTools","0.1.8" -"bayesm","3.1-4" -"bayesplot","1.7.2" -"bayestestR","0.8.2" -"bdsmatrix","1.3-4" -"BH","1.72.0-3" -"binom","1.1-1" -"bit","4.0.4" -"bit64","4.0.5" -"bitops","1.0-6" -"blob","1.2.1" -"boot","1.3-25" -"brglm2","0.7.1" -"bridgesampling","1.0-0" -"brms","2.13.5" -"Brobdingnag","1.2-6" -"broom","0.7.5" -"broom.helpers","1.2.1" -"butcher","0.1.5" -"callr","3.4.3" -"car","3.0-9" -"carData","3.0-4" -"caret","6.0-86" -"caTools","1.18.2" -"cellranger","1.1.0" -"checkmate","2.0.0" -"class","7.3-17" -"classInt","0.4-3" -"cli","3.6.1" -"clipr","0.7.0" -"clue","0.3-61" -"cluster","2.1.0" -"cmprsk","2.2-11" -"cobalt","4.4.0" -"coda","0.19-3" -"codetools","0.2-16" -"colorspace","1.4-1" -"colourpicker","1.0" -"commonmark","1.7" -"conquer","1.0.2" -"consort","1.0.1" -"corpcor","1.6.9" -"corrplot","0.84" -"cowplot","1.0.0" -"coxme","2.2-16" -"cpp11","0.2.7" -"crayon","1.3.4" -"credentials","1.3.0" -"crosstalk","1.1.0.1" -"curl","4.3" -"dagitty","0.3-4" -"data.table","1.13.0" -"date","1.2-39" -"DBI","1.1.0" -"dbplyr","1.4.4" -"dd4d","0.0.0.9000" -"Deriv","4.1.6" -"desc","1.2.0" -"deSolve","1.28" -"detectseparation","0.2" -"dfidx","0.0-4" -"DHARMa","0.4.6" -"digest","0.6.25" -"distributional","0.2.0" -"doBy","4.6.15" -"doParallel","1.0.15" -"dplyr","1.0.2" -"DT","0.15" -"dtplyr","1.0.1" -"dtw","1.23-1" -"dtwclust","5.5.10" -"dummies","1.5.6" -"dygraphs","1.1.1.6" -"e1071","1.7-3" -"egg","0.4.5" -"ellipse","0.5.0" -"ellipsis","0.3.1" -"emmeans","1.7.5" -"emulator","1.2-21" -"enrichwith","0.3.1" -"Epi","2.46" -"epitools","0.5-10.1" -"estimability","1.4.1" -"estimatr","0.30.2" -"etm","1.1.1" -"evaluate","0.14" -"exactRankTests","0.8-31" -"expm","0.999-7" -"fansi","0.4.1" -"farver","2.0.3" -"fastDummies","1.6.3" -"fastmap","1.0.1" -"fastshap","0.0.7" -"fda","5.1.7" -"fds","1.8" -"feather","0.3.5" -"finalfit","1.0.4" -"flexclust","1.4-1" -"flexsurv","1.1.1" -"FNN","1.1.3" -"fontBitstreamVera","0.1.1" -"fontLiberation","0.1.0" -"fontquiver","0.2.1" -"forcats","0.5.0" -"foreach","1.5.0" -"forecast","8.16" -"foreign","0.8-80" -"forestplot","1.10.1" -"forestploter","1.0.0" -"Formula","1.2-3" -"fracdiff","1.5-3" -"fs","1.5.0" -"furrr","0.1.0" -"future","1.18.0" -"fuzzyjoin","0.1.6" -"gap","1.5-1" -"gap.datasets","0.0.5" -"gdtools","0.2.3" -"geepack","1.3.4" -"generics","0.1.0" -"geosphere","1.5-18" -"gert","1.2.0" -"getopt","1.20.3" -"gets","0.29" -"ggalluvial","0.12.3" -"GGally","2.0.0" -"ggdist","2.2.0" -"ggfittext","0.10.0" -"ggfortify","0.4.15" -"gggenes","0.5.0" -"ggh4x","0.2.6" -"ggplot2","3.4.2" -"ggpubr","0.4.0" -"ggrepel","0.9.1" -"ggridges","0.5.2" -"ggsci","2.9" -"ggsignif","0.6.0" -"ggvenn","0.1.9" -"gh","1.2.0" -"gitcreds","0.1.1" -"glmmTMB","1.1.2" -"glmnet","4.1-4" -"globals","0.12.5" -"glue","1.4.2" -"Gmisc","2.0.1" -"gmm","1.8" -"gnm","1.1-1" -"gower","0.2.2" -"gridExtra","2.3" -"gridtext","0.1.5" -"gt","0.2.2" -"gtable","0.3.0" -"gtools","3.8.2" -"gtsummary","1.3.7" -"haven","2.3.1" -"HDInterval","0.2.2" -"hdrcde","3.3" -"here","0.1" -"hexbin","1.28.3" -"highr","0.8" -"Hmisc","4.4-1" -"hms","0.5.3" -"htmlTable","2.0.1" -"htmltools","0.5.0" -"htmlwidgets","1.5.1" -"httpuv","1.5.4" -"httr","1.4.2" -"httr2","0.2.3" -"IDPmisc","1.1.20" -"igraph","1.2.5" -"incidence","1.7.3" -"ini","0.3.1" -"inline","0.3.15" -"insight","0.13.1" -"interactions","1.1.3" -"ipred","0.9-9" -"isoband","0.2.2" -"iterators","1.0.12" -"janitor","2.0.1" -"jpeg","0.1-8.1" -"jsonlite","1.7.0" -"jtools","2.1.2" -"kableExtra","1.3.4" -"kernlab","0.9-29" -"KernSmooth","2.23-17" -"km.ci","0.5-2" -"KMsurv","0.1-5" -"knitr","1.29" -"ks","1.11.7" -"labeling","0.3" -"labelled","2.7.0" -"later","1.1.0.1" -"lattice","0.20-41" -"latticeExtra","0.6-29" -"lava","1.6.8.1" -"lazyeval","0.2.2" -"lcmm","2.0.0" -"lifecycle","1.0.3" -"listenv","0.8.0" -"lme4","1.1-23" -"lmtest","0.9-37" -"lobstr","1.1.1" -"locfit","1.5-9.4" -"loo","2.3.1" -"lpSolveAPI","5.5.2.0-17.7" -"lubridate","1.7.9" -"magick","2.7.3" -"magrittr","1.5" -"maptools","1.0-2" -"markdown","1.1" -"marqLevAlg","2.0.7" -"MASS","7.3-52" -"MatchIt","4.2.0" -"mathjaxr","1.6-0" -"Matrix","1.2-18" -"MatrixModels","0.4-1" -"matrixStats","0.56.0" -"maxstat","0.7-25" -"mclust","5.4.7" -"metadat","1.2-0" -"metafor","3.8-1" -"mets","1.2.9" -"mgcv","1.8-33" -"mice","3.11.0" -"microbenchmark","1.5.0" -"mime","0.9" -"miniUI","0.1.1.1" -"minqa","1.2.4" -"mitools","2.4" -"mlogit","1.1-1" -"mnlogit","1.2.6" -"ModelMetrics","1.2.2.2" -"modelr","0.1.8" -"modelsummary","0.6.6" -"modeltools","0.2-23" -"msm","1.7" -"mstate","0.3.1" -"muhaz","1.2.6.1" -"multcomp","1.4-18" -"multicool","0.1-11" -"munsell","0.5.0" -"mvtnorm","1.1-1" -"naniar","0.6.0" -"NHPoisson","3.3" -"nleqslv","3.3.2" -"nlme","3.1-149" -"nloptr","1.2.2.2" -"nnet","7.3-14" -"numDeriv","2016.8-1.1" -"odbc","1.3.0" -"openssl","1.4.2" -"openxlsx","4.1.5" -"optparse","1.6.6" -"packrat","0.5.0" -"pacman","0.5.1" -"padr","0.6.2" -"pammtools","0.5.8" -"pander","0.6.3" -"parameters","0.12.0" -"parglm","0.1.6" -"patchwork","1.1.1" -"pbapply","1.5-0" -"pbkrtest","0.4-8.6" -"pcaPP","1.9-73" -"pch","2.0" -"pec","2021.10.11" -"performance","0.7.0" -"PerformanceAnalytics","2.0.4" -"PHEindicatormethods","1.3.2" -"pillar","1.4.6" -"pkgbuild","1.1.0" -"pkgconfig","2.0.3" -"pkgload","1.1.0" -"plotly","4.8.0" -"plotrix","3.7-8" -"plyr","1.8.6" -"png","0.1-7" -"polspline","1.1.19" -"polynom","1.4-0" -"praise","1.0.0" -"predtools","0.0.2" -"prettyunits","1.1.1" -"pROC","1.16.2" -"processx","3.4.4" -"prodlim","2019.11.13" -"progress","1.2.2" -"promises","1.1.1" -"proxy","0.4-27" -"ps","1.3.4" -"pscl","1.5.5.1" -"pseudo","1.4.3" -"Publish","2020.12.23" -"purrr","0.3.4" -"qgam","1.3.4" -"quadprog","1.5-8" -"quantmod","0.4.26" -"quantreg","5.61" -"qvcalc","1.0.2" -"R.methodsS3","1.8.1" -"R.oo","1.25.0" -"R.utils","2.12.0" -"R6","2.4.1" -"rainbow","3.6" -"randomForest","4.6-14" -"randomForestExplainer","0.10.1" -"randtoolbox","2.0.2" -"ranger","0.13.1" -"rappdirs","0.3.1" -"rbibutils","2.0" -"RColorBrewer","1.1-2" -"RConics","1.1.1" -"Rcpp","1.0.5" -"RcppArmadillo","0.9.900.3.0" -"RcppEigen","0.3.3.7.0" -"RcppParallel","5.0.2" -"RcppProgress","0.4.2" -"RcppRoll","0.3.0" -"RcppThread","2.1.3" -"RCurl","1.98-1.2" -"Rdpack","2.1.1" -"rdrobust","2.1.1" -"readr","1.3.1" -"readxl","1.3.1" -"recipes","0.1.15" -"registry","0.5-1" -"relimp","1.0-5" -"relsurv","2.2-3" -"rematch","1.0.1" -"remotes","2.2.0" -"renv","0.16.0" -"repr","1.1.0" -"reprex","0.3.0" -"reshape","0.8.8" -"reshape2","1.4.4" -"rgdal","1.5-16" -"rgeos","0.5-3" -"rio","0.5.16" -"riskRegression","2021.10.10" -"rlang","1.1.1" -"rmarkdown","2.3" -"rms","6.2-0" -"rngWELL","0.10-7" -"ROI","1.0-0" -"ROI.plugin.lpsolve","1.0-0" -"rpart","4.1-15" -"rpart.plot","3.1.1" -"rprojroot","1.3-2" -"rsample","1.0.0" -"rsconnect","0.8.16" -"RSpectra","0.16-1" -"rstan","2.21.2" -"rstantools","2.1.1" -"rstatix","0.6.0" -"rstudioapi","0.11" -"rvest","0.3.6" -"sandwich","2.5-1" -"sass","0.3.0" -"scales","1.2.1" -"SCCS","1.2" -"segmented","1.4-1" -"selectr","0.4-2" -"sf","0.9-5" -"shades","1.4.0" -"shape","1.4.6" -"shapviz","0.8.0" -"shiny","1.5.0" -"shinyjs","1.1" -"shinystan","2.5.0" -"shinythemes","1.1.2" -"skimr","2.1.2" -"slam","0.1-48" -"slider","0.3.0" -"snakecase","0.11.0" -"sourcetools","0.1.7" -"sp","1.4-2" -"SparseM","1.78" -"splines2","0.4.1" -"SQUAREM","2020.5" -"StanHeaders","2.21.0-6" -"statmod","1.4.34" -"stringdist","0.9.10" -"stringi","1.4.6" -"stringr","1.4.0" -"survey","4.1-1" -"survival","3.2-3" -"survminer","0.4.8" -"survMisc","0.5.5" -"svglite","1.2.3.2" -"sweep","0.2.5" -"sys","3.4" -"systemfonts","0.3.2" -"tables","0.9.6" -"testthat","2.3.2" -"TH.data","1.1-0" -"threejs","0.3.3" -"tibble","3.0.3" -"tictoc","1.0" -"tidyquant","1.0.9" -"tidyr","1.1.2" -"tidyselect","1.1.0" -"tidyverse","1.3.0" -"timeDate","3043.102" -"timereg","2.0.1" -"timetk","2.7.0" -"tinytex","0.25" -"TMB","1.9.10" -"tmvtnorm","1.5" -"tseries","0.10-58" -"tsfeatures","1.1.1" -"tsModel","0.6" -"TTR","0.24.4" -"twopartm","0.1.0" -"units","0.6-7" -"UpSetR","1.4.0" -"urca","1.3-4" -"usethis","2.0.1" -"utf8","1.1.4" -"V8","3.2.0" -"vcd","1.4-9" -"vctrs","0.6.2" -"VGAM","1.1-6" -"viridis","0.5.1" -"viridisLite","0.3.0" -"visdat","0.5.3" -"warp","0.2.1" -"webshot","0.5.2" -"WeightIt","0.13.1" -"whisker","0.4" -"withr","2.5.0" -"xfun","0.16" -"xgboost","1.7.5.1" -"XML","3.99-0.6" -"xml2","1.3.2" -"xtable","1.8-4" -"xts","0.12-0" -"yaml","2.2.1" -"zip","2.1.1" -"zoo","1.8-8" -"base","4.0.5" -"compiler","4.0.5" -"datasets","4.0.5" -"graphics","4.0.5" -"grDevices","4.0.5" -"grid","4.0.5" -"methods","4.0.5" -"parallel","4.0.5" -"splines","4.0.5" -"stats","4.0.5" -"stats4","4.0.5" -"tcltk","4.0.5" -"tools","4.0.5" -"utils","4.0.5" diff --git a/scripts/build.R b/scripts/build.R new file mode 100644 index 0000000..7903778 --- /dev/null +++ b/scripts/build.R @@ -0,0 +1,35 @@ +REPOS <- Sys.getenv("REPOS") +CRAN_DATE <- Sys.getenv("CRAN_DATE") + +# Set HTTPUserAgent so that PPPM serves binary R packages for Linux +options(HTTPUserAgent = sprintf( + "R/%s R (%s)", getRversion(), + paste( + getRversion(), + R.version["platform"], + R.version["arch"], + R.version["os"] + ) +)) + +install.packages("pak", repos = c(CRAN = REPOS), destdir = "/cache") +pak::repo_add(CRAN = paste0("RSPM@", CRAN_DATE)) +options(pkg.sysreqs = FALSE) + +# Read in input list +input <- utils::read.csv("/tmp/packages.csv", header = TRUE) +# Obtain list of non-CRAN CRAN-like repositories, and add them to pak +repos <- unique(input[[2]]) +repos <- repos[repos != ""] +nrepos <- length(repos) +names(repos) <- LETTERS[1:nrepos] +pak::repo_add(.list = repos) + +# Include pak in packages list, and remove any duplicates +pkgs <- unique(c("pak", input[[1]])) + +# Create pkg.lock file +pak::lockfile_create(pkgs, lockfile = "/pkg.lock") + +# Install the packages based upon the lockfile +pak::lockfile_install("/pkg.lock") diff --git a/copy-symlink.sh b/scripts/copy-symlink.sh similarity index 100% rename from copy-symlink.sh rename to scripts/copy-symlink.sh diff --git a/scripts/packages.Rmd b/scripts/packages.Rmd new file mode 100644 index 0000000..7829926 --- /dev/null +++ b/scripts/packages.Rmd @@ -0,0 +1,56 @@ +--- +title: "Package Versions for `r Sys.getenv('MAJOR_VERSION')`" +output: + github_document: + html_preview: false +--- + +This r:`r Sys.getenv('MAJOR_VERSION')` OpenSAFELY image is based on Ubuntu `r Sys.getenv('BASE')` with R `r getRversion()`. + +## 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. + +```{r, echo=FALSE, results='asis', warning=FALSE} +if (Sys.getenv("MAJOR_VERSION") == "v1") { +suppressMessages(library(dplyr)) +renvlock <- jsonlite::fromJSON(paste0("/out/", Sys.getenv("MAJOR_VERSION"), "/renv.lock")) +pkgs <- renvlock[["Packages"]] +pkgs <- data.frame(Reduce(rbind, pkgs)) +pkgs <- pkgs %>% dplyr::select(Package, Version, Repository) +pkgs <- pkgs %>% + mutate( + Url = case_when( + Repository == "RSPM" | Repository == "CRAN" ~ paste0(""), + Repository != "RSPM" | Repository != "CRAN" ~ paste0("<", Repository, "/", Package, ">") + ) + ) +pkgs <- pkgs %>% + dplyr::select(Package, Version, Url) %>% + mutate(Package = as.character(Package), Version = as.character(Version)) %>% + arrange(Package, .locale = "en") +knitr::kable(pkgs, row.names = FALSE) +} +if (Sys.getenv("MAJOR_VERSION") == "v2") { +suppressMessages(library(dplyr)) +pkglock <- jsonlite::fromJSON(paste0("/out/", Sys.getenv("MAJOR_VERSION"), "/pkg.lock")) +pkgs <- pkglock[["packages"]] +metadataremoterepos <- pkgs$metadata$RemoteRepos +pkgs <- pkgs %>% dplyr::select(package, version, sources, repotype) +pkgs <- pkgs %>% mutate(metadataremoterepos = metadataremoterepos) +pkgs <- pkgs %>% + mutate( + url = case_when( + repotype == "cran" ~ paste0(""), + repotype == "cranlike" ~ paste0("<", sub("/bin/linux/noble/4.4/", "", metadataremoterepos), "/", package, ">") + ) + ) +pkgs <- pkgs %>% + dplyr::select(package, version, url) %>% + arrange(package, .locale = "en") +pkgs <- pkgs %>% rename(Package = package, Version = version, Url = url) +knitr::kable(pkgs, row.names = FALSE) +} +``` diff --git a/scripts/render.sh b/scripts/render.sh new file mode 100644 index 0000000..0fce6b9 --- /dev/null +++ b/scripts/render.sh @@ -0,0 +1,6 @@ +#!/usr/bin/env bash +set -euo pipefail + +echo "BASE=$BASE" >> /usr/lib/R/etc/Renviron.site +echo "MAJOR_VERSION=$MAJOR_VERSION" >> /usr/lib/R/etc/Renviron.site +R -q -e "rmarkdown::render('/out/scripts/packages.Rmd', output_dir = paste0('/out/', \"$MAJOR_VERSION\"))" diff --git a/test.sh b/test.sh deleted file mode 100755 index 1adea57..0000000 --- a/test.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env bash -set -eu -IMAGE=${1:-ghcr.io/opensafely-core/r} -python3 -c 'import json; print("\n".join(json.load(open("renv.lock"))["Packages"]))' | xargs -I {} echo "if (!library({}, warn.conflicts = FALSE, logical.return = TRUE)) {stop(\"Package {} failed to load, please investigate\")}" > .tests.R -docker run --platform linux/amd64 --rm -v "$PWD:/tests/" "$IMAGE" /tests/.tests.R diff --git a/tests/test-loading-base.R b/tests/test-loading-base.R new file mode 100644 index 0000000..ba94327 --- /dev/null +++ b/tests/test-loading-base.R @@ -0,0 +1,12 @@ +options(warn = -1) +basepkgs <- c("base", "compiler", "datasets", "grDevices", "graphics", "grid", "methods", "parallel", "splines", "stats", "stats4", "tcltk", "tools", "utils") + +for (i in 1:length(basepkgs)) { + suppressMessages({ + if (!library(basepkgs[i], logical.return = TRUE, character.only = TRUE)) { + stop(paste("Package", basepkgs[i], "failed to load, please investigate")) + } + }) +} + +print("All base R packages successfully loaded.") diff --git a/tests/test-loading-packages.R b/tests/test-loading-packages.R new file mode 100644 index 0000000..08a40ba --- /dev/null +++ b/tests/test-loading-packages.R @@ -0,0 +1,19 @@ +options(warn = -1) +Sys.setenv('_R_S3_METHOD_REGISTRATION_NOTE_OVERWRITES_'=0) +pkgs <- installed.packages()[, 1] +pkgs <- pkgs[!pkgs %in% c("base", "compiler", "datasets", "grDevices", "graphics", "grid", "methods", "parallel", "splines", "stats", "stats4", "tcltk", "tools", "utils")] +pkgs <- unname(pkgs) +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")) + } + dtch <- paste0("package:", package) + detach(dtch, force = TRUE, unload = TRUE, character.only = TRUE) + }) +} + +print("All non-base R packages successfully loaded and unloaded.") diff --git a/test-rstudio.sh b/tests/test-rstudio.sh similarity index 65% rename from test-rstudio.sh rename to tests/test-rstudio.sh index 25c64dd..4f92941 100755 --- a/test-rstudio.sh +++ b/tests/test-rstudio.sh @@ -1,11 +1,13 @@ #!/bin/bash set -euo pipefail +MAJOR_VERSION="$1" + trap "docker compose kill > /dev/null 2>&1 || true" EXIT -docker compose up -d --wait rstudio +docker compose --env-file ${MAJOR_VERSION}/env up -d --wait --wait-timeout 30 rstudio -status_code=$(curl --write-out '%{http_code}' --silent --output /dev/null -L --retry 3 --max-time 10 http://localhost:8787) +status_code=$(curl --write-out '%{http_code}' --silent --output /dev/null -L --retry 10 --max-time 30 --keepalive-time 30 http://localhost:8787) if [[ "$status_code" -ne 200 ]] ; then echo "200 response not received from http://localhost:8787" exit 1 diff --git a/tests/test.sh b/tests/test.sh new file mode 100755 index 0000000..8d23f8b --- /dev/null +++ b/tests/test.sh @@ -0,0 +1,24 @@ +#!/usr/bin/env bash +set -eu +MAJOR_VERSION=${1} + +if [ "${MAJOR_VERSION}" = "v1" ]; then + # Test all R packages can be loaded + python3 -c "import json; print('\n'.join(json.load(open(\"./$MAJOR_VERSION/renv.lock\"))['Packages']))" | xargs -I {} echo "if (!library({}, warn.conflicts = FALSE, logical.return = TRUE)) {stop(\"Package {} failed to load, please investigate\")}" > .tests.R + docker run --platform linux/amd64 --rm -v "$PWD:/tests/" r:${MAJOR_VERSION} /tests/.tests.R +elif [ "${MAJOR_VERSION}" = "v2" ]; then + # Test all R packages can be attached then detached + docker run --platform linux/amd64 --env-file ${MAJOR_VERSION}/env --rm -v "${PWD}:/tests" r:"${MAJOR_VERSION}" /tests/tests/test-loading-packages.R +fi + +# Check that a basic Rcpp call runs successfully +docker compose --env-file ${MAJOR_VERSION}/env run --rm r -e "if (is.numeric(Rcpp::evalCpp('2 + 2'))) {print('Rcpp test passed')}" + +# Check number of packages +docker compose --env-file ${MAJOR_VERSION}/env run --rm r -e "print(paste('Total number of R packages:', nrow(installed.packages())))" + +# Check capabilities of arrow package +docker compose --env-file ${MAJOR_VERSION}/env run --rm r -e "arrow::arrow_info()" + +# Test loading the 14 base packages +docker run --platform linux/amd64 --env-file ${MAJOR_VERSION}/env --rm -v "${PWD}:/tests" r:"${MAJOR_VERSION}" /tests/tests/test-loading-base.R diff --git a/20.04-library-changes.txt b/v1/20.04-library-changes.txt similarity index 100% rename from 20.04-library-changes.txt rename to v1/20.04-library-changes.txt diff --git a/Dockerfile b/v1/Dockerfile similarity index 91% rename from Dockerfile rename to v1/Dockerfile index 3e47ec3..36db5b4 100644 --- a/Dockerfile +++ b/v1/Dockerfile @@ -5,10 +5,10 @@ # create base image with those installed to save installing them twice. FROM ghcr.io/opensafely-core/base-action:20.04 as base-r -COPY dependencies.txt /root/dependencies.txt +COPY v1/dependencies.txt /root/dependencies.txt # add cran repo for R packages and install -RUN --mount=type=cache,target=/var/cache/apt \ +RUN --mount=type=cache,target=/var/cache/apt,id=apt-2004 \ echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" > /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 /root/dependencies.txt @@ -23,8 +23,8 @@ ENV RENV_PATHS_LIBRARY=/renv/lib \ FROM base-r as builder # install build time dependencies -COPY build-dependencies.txt /root/build-dependencies.txt -RUN --mount=type=cache,target=/var/cache/apt /root/docker-apt-install.sh /root/build-dependencies.txt +COPY v1/build-dependencies.txt /root/build-dependencies.txt +RUN --mount=type=cache,target=/var/cache/apt,id=apt-2004 /root/docker-apt-install.sh /root/build-dependencies.txt RUN mkdir -p /cache /renv/lib @@ -41,13 +41,13 @@ WORKDIR /renv RUN --mount=type=cache,target=/cache,id=/cache-2004 R -e 'install.packages("renv", destdir="/cache"); renv::init(bare = TRUE)' # use renv to install packages -COPY renv.lock /renv/renv.lock +COPY v1/renv.lock /renv/renv.lock RUN --mount=type=cache,target=/cache,id=/cache-2004 R -e 'renv::restore()' # renv uses symlinks to the the build cache to populate the lib directory. As # our cache is mounted only at build (so we can do fast rebuilds), we need to # change the symlinks into full copies, to store them in the image. -COPY copy-symlink.sh /tmp/copy-symlink.sh +COPY scripts/copy-symlink.sh /tmp/copy-symlink.sh RUN --mount=type=cache,target=/cache,id=/cache-2004 bash /tmp/copy-symlink.sh /renv/lib @@ -108,7 +108,7 @@ FROM r as rstudio # Install rstudio-server (and a few dependencies) COPY rstudio/rstudio-dependencies.txt /root/rstudio-dependencies.txt -RUN --mount=type=cache,target=/var/cache/apt /root/docker-apt-install.sh /root/rstudio-dependencies.txt &&\ +RUN --mount=type=cache,target=/var/cache/apt,id=apt-2004 /root/docker-apt-install.sh /root/rstudio-dependencies.txt &&\ test -f /var/cache/apt/"${RSTUDIO_DEB}" ||\ /usr/lib/apt/apt-helper download-file "${RSTUDIO_BASE_URL}${RSTUDIO_DEB}" /var/cache/apt/"${RSTUDIO_DEB}" &&\ apt-get install --no-install-recommends -y /var/cache/apt/"${RSTUDIO_DEB}" diff --git a/build-dependencies.txt b/v1/build-dependencies.txt similarity index 100% rename from build-dependencies.txt rename to v1/build-dependencies.txt diff --git a/dependencies.txt b/v1/dependencies.txt similarity index 100% rename from dependencies.txt rename to v1/dependencies.txt diff --git a/v1/env b/v1/env new file mode 100644 index 0000000..8c08231 --- /dev/null +++ b/v1/env @@ -0,0 +1,4 @@ +MAJOR_VERSION=v1 +BASE=20.04 +RSTUDIO_BASE_URL=https://download2.rstudio.org/server/focal/amd64/ +RSTUDIO_DEB=rstudio-server-2024.09.0-375-amd64.deb diff --git a/v1/packages.md b/v1/packages.md new file mode 100644 index 0000000..df6e49e --- /dev/null +++ b/v1/packages.md @@ -0,0 +1,465 @@ +Package Versions for v1 +================ + +This r:v1 OpenSAFELY image is based on Ubuntu 20.04 with R 4.0.5. + +## 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 | 1.4-5 | | +| anytime | 0.3.9 | | +| ape | 5.7-1 | | +| arrow | 4.0.0.1 | | +| ash | 1.0-15 | | +| askpass | 1.1 | | +| assertthat | 0.2.1 | | +| astsa | 2.1 | | +| aweek | 1.0.2 | | +| backports | 1.4.1 | | +| base64enc | 0.1-3 | | +| BayesianTools | 0.1.8 | | +| bayesm | 3.1-4 | | +| bayesplot | 1.7.2 | | +| bayestestR | 0.8.2 | | +| bdsmatrix | 1.3-4 | | +| BH | 1.72.0-3 | | +| binom | 1.1-1 | | +| bit | 4.0.4 | | +| bit64 | 4.0.5 | | +| bitops | 1.0-6 | | +| blob | 1.2.1 | | +| boot | 1.3-25 | | +| brglm2 | 0.7.1 | | +| bridgesampling | 1.0-0 | | +| brms | 2.13.5 | | +| Brobdingnag | 1.2-6 | | +| broom | 0.7.5 | | +| broom.helpers | 1.2.1 | | +| butcher | 0.1.5 | | +| callr | 3.4.3 | | +| car | 3.0-9 | | +| carData | 3.0-4 | | +| caret | 6.0-86 | | +| caTools | 1.18.2 | | +| cellranger | 1.1.0 | | +| checkmate | 2.0.0 | | +| class | 7.3-17 | | +| classInt | 0.4-3 | | +| cli | 3.6.1 | | +| clipr | 0.7.0 | | +| clue | 0.3-61 | | +| cluster | 2.1.0 | | +| cmprsk | 2.2-11 | | +| cobalt | 4.4.0 | | +| coda | 0.19-3 | | +| codetools | 0.2-16 | | +| colorspace | 1.4-1 | | +| colourpicker | 1.0 | | +| commonmark | 1.7 | | +| conquer | 1.0.2 | | +| consort | 1.0.1 | | +| corpcor | 1.6.9 | | +| corrplot | 0.84 | | +| cowplot | 1.0.0 | | +| coxme | 2.2-16 | | +| cpp11 | 0.2.7 | | +| crayon | 1.3.4 | | +| credentials | 1.3.0 | | +| crosstalk | 1.1.0.1 | | +| curl | 4.3 | | +| dagitty | 0.3-4 | | +| data.table | 1.13.0 | | +| date | 1.2-39 | | +| DBI | 1.1.0 | | +| dbplyr | 1.4.4 | | +| dd4d | 0.0.0.9000 | | +| Deriv | 4.1.6 | | +| desc | 1.2.0 | | +| deSolve | 1.28 | | +| detectseparation | 0.2 | | +| dfidx | 0.0-4 | | +| DHARMa | 0.4.6 | | +| digest | 0.6.25 | | +| distributional | 0.2.0 | | +| doBy | 4.6.15 | | +| doParallel | 1.0.15 | | +| dplyr | 1.0.2 | | +| DT | 0.15 | | +| dtplyr | 1.0.1 | | +| dtw | 1.23-1 | | +| dtwclust | 5.5.10 | | +| dummies | 1.5.6 | | +| dygraphs | 1.1.1.6 | | +| e1071 | 1.7-3 | | +| egg | 0.4.5 | | +| ellipse | 0.5.0 | | +| ellipsis | 0.3.1 | | +| emmeans | 1.7.5 | | +| emulator | 1.2-21 | | +| enrichwith | 0.3.1 | | +| Epi | 2.46 | | +| epitools | 0.5-10.1 | | +| estimability | 1.4.1 | | +| estimatr | 0.30.2 | | +| etm | 1.1.1 | | +| evaluate | 0.14 | | +| exactRankTests | 0.8-31 | | +| expm | 0.999-7 | | +| fansi | 0.4.1 | | +| farver | 2.0.3 | | +| fastDummies | 1.6.3 | | +| fastmap | 1.0.1 | | +| fastshap | 0.0.7 | | +| fda | 5.1.7 | | +| fds | 1.8 | | +| feather | 0.3.5 | | +| finalfit | 1.0.4 | | +| flexclust | 1.4-1 | | +| flexsurv | 1.1.1 | | +| FNN | 1.1.3 | | +| fontBitstreamVera | 0.1.1 | | +| fontLiberation | 0.1.0 | | +| fontquiver | 0.2.1 | | +| forcats | 0.5.0 | | +| foreach | 1.5.0 | | +| forecast | 8.16 | | +| foreign | 0.8-80 | | +| forestplot | 1.10.1 | | +| forestploter | 1.0.0 | | +| Formula | 1.2-3 | | +| fracdiff | 1.5-3 | | +| fs | 1.5.0 | | +| furrr | 0.1.0 | | +| future | 1.18.0 | | +| fuzzyjoin | 0.1.6 | | +| gap | 1.5-1 | | +| gap.datasets | 0.0.5 | | +| gdtools | 0.2.3 | | +| geepack | 1.3.4 | | +| generics | 0.1.0 | | +| geosphere | 1.5-18 | | +| gert | 1.2.0 | | +| getopt | 1.20.3 | | +| gets | 0.29 | | +| ggalluvial | 0.12.3 | | +| GGally | 2.0.0 | | +| ggdist | 2.2.0 | | +| ggfittext | 0.10.0 | | +| ggfortify | 0.4.15 | | +| gggenes | 0.5.0 | | +| ggh4x | 0.2.6 | | +| ggplot2 | 3.4.2 | | +| ggpubr | 0.4.0 | | +| ggrepel | 0.9.1 | | +| ggridges | 0.5.2 | | +| ggsci | 2.9 | | +| ggsignif | 0.6.0 | | +| ggvenn | 0.1.9 | | +| gh | 1.2.0 | | +| gitcreds | 0.1.1 | | +| glmmTMB | 1.1.2 | | +| glmnet | 4.1-4 | | +| globals | 0.12.5 | | +| glue | 1.4.2 | | +| Gmisc | 2.0.1 | | +| gmm | 1.8 | | +| gnm | 1.1-1 | | +| gower | 0.2.2 | | +| gridExtra | 2.3 | | +| gridtext | 0.1.5 | | +| gt | 0.2.2 | | +| gtable | 0.3.0 | | +| gtools | 3.8.2 | | +| gtsummary | 1.3.7 | | +| haven | 2.3.1 | | +| HDInterval | 0.2.2 | | +| hdrcde | 3.3 | | +| here | 0.1 | | +| hexbin | 1.28.3 | | +| highr | 0.8 | | +| Hmisc | 4.4-1 | | +| hms | 0.5.3 | | +| htmlTable | 2.0.1 | | +| htmltools | 0.5.0 | | +| htmlwidgets | 1.5.1 | | +| httpuv | 1.5.4 | | +| httr | 1.4.2 | | +| httr2 | 0.2.3 | | +| IDPmisc | 1.1.20 | | +| igraph | 1.2.5 | | +| incidence | 1.7.3 | | +| ini | 0.3.1 | | +| inline | 0.3.15 | | +| insight | 0.13.1 | | +| interactions | 1.1.3 | | +| ipred | 0.9-9 | | +| isoband | 0.2.2 | | +| iterators | 1.0.12 | | +| janitor | 2.0.1 | | +| jpeg | 0.1-8.1 | | +| jsonlite | 1.7.0 | | +| jtools | 2.1.2 | | +| kableExtra | 1.3.4 | | +| kernlab | 0.9-29 | | +| KernSmooth | 2.23-17 | | +| km.ci | 0.5-2 | | +| KMsurv | 0.1-5 | | +| knitr | 1.29 | | +| ks | 1.11.7 | | +| labeling | 0.3 | | +| labelled | 2.7.0 | | +| later | 1.1.0.1 | | +| lattice | 0.20-41 | | +| latticeExtra | 0.6-29 | | +| lava | 1.6.8.1 | | +| lazyeval | 0.2.2 | | +| lcmm | 2.0.0 | | +| lifecycle | 1.0.3 | | +| listenv | 0.8.0 | | +| lme4 | 1.1-23 | | +| lmtest | 0.9-37 | | +| lobstr | 1.1.1 | | +| locfit | 1.5-9.4 | | +| loo | 2.3.1 | | +| lpSolveAPI | 5.5.2.0-17.7 | | +| lubridate | 1.7.9 | | +| magick | 2.7.3 | | +| magrittr | 1.5 | | +| maptools | 1.0-2 | | +| markdown | 1.1 | | +| marqLevAlg | 2.0.7 | | +| MASS | 7.3-52 | | +| MatchIt | 4.2.0 | | +| mathjaxr | 1.6-0 | | +| Matrix | 1.2-18 | | +| MatrixModels | 0.4-1 | | +| matrixStats | 0.56.0 | | +| maxstat | 0.7-25 | | +| mclust | 5.4.7 | | +| metadat | 1.2-0 | | +| metafor | 3.8-1 | | +| mets | 1.2.9 | | +| mgcv | 1.8-33 | | +| mice | 3.11.0 | | +| microbenchmark | 1.5.0 | | +| mime | 0.9 | | +| miniUI | 0.1.1.1 | | +| minqa | 1.2.4 | | +| mitools | 2.4 | | +| mlogit | 1.1-1 | | +| mnlogit | 1.2.6 | | +| ModelMetrics | 1.2.2.2 | | +| modelr | 0.1.8 | | +| modelsummary | 0.6.6 | | +| modeltools | 0.2-23 | | +| msm | 1.7 | | +| mstate | 0.3.1 | | +| muhaz | 1.2.6.1 | | +| multcomp | 1.4-18 | | +| multicool | 0.1-11 | | +| munsell | 0.5.0 | | +| mvtnorm | 1.1-1 | | +| naniar | 0.6.0 | | +| NHPoisson | 3.3 | | +| nleqslv | 3.3.2 | | +| nlme | 3.1-149 | | +| nloptr | 1.2.2.2 | | +| nnet | 7.3-14 | | +| numDeriv | 2016.8-1.1 | | +| odbc | 1.3.0 | | +| openssl | 1.4.2 | | +| openxlsx | 4.1.5 | | +| optparse | 1.6.6 | | +| packrat | 0.5.0 | | +| pacman | 0.5.1 | | +| padr | 0.6.2 | | +| pammtools | 0.5.8 | | +| pander | 0.6.3 | | +| parameters | 0.12.0 | | +| parglm | 0.1.6 | | +| patchwork | 1.1.1 | | +| pbapply | 1.5-0 | | +| pbkrtest | 0.4-8.6 | | +| pcaPP | 1.9-73 | | +| pch | 2.0 | | +| pec | 2021.10.11 | | +| performance | 0.7.0 | | +| PerformanceAnalytics | 2.0.4 | | +| PHEindicatormethods | 1.3.2 | | +| pillar | 1.4.6 | | +| pkgbuild | 1.1.0 | | +| pkgconfig | 2.0.3 | | +| pkgload | 1.1.0 | | +| plotly | 4.8.0 | | +| plotrix | 3.7-8 | | +| plyr | 1.8.6 | | +| png | 0.1-7 | | +| polspline | 1.1.19 | | +| polynom | 1.4-0 | | +| praise | 1.0.0 | | +| predtools | 0.0.2 | | +| prettyunits | 1.1.1 | | +| pROC | 1.16.2 | | +| processx | 3.4.4 | | +| prodlim | 2019.11.13 | | +| progress | 1.2.2 | | +| promises | 1.1.1 | | +| proxy | 0.4-27 | | +| ps | 1.3.4 | | +| pscl | 1.5.5.1 | | +| pseudo | 1.4.3 | | +| Publish | 2020.12.23 | | +| purrr | 0.3.4 | | +| qgam | 1.3.4 | | +| quadprog | 1.5-8 | | +| quantmod | 0.4.26 | | +| quantreg | 5.61 | | +| qvcalc | 1.0.2 | | +| R.methodsS3 | 1.8.1 | | +| R.oo | 1.25.0 | | +| R.utils | 2.12.0 | | +| R6 | 2.4.1 | | +| rainbow | 3.6 | | +| randomForest | 4.6-14 | | +| randomForestExplainer | 0.10.1 | | +| randtoolbox | 2.0.2 | | +| ranger | 0.13.1 | | +| rappdirs | 0.3.1 | | +| rbibutils | 2.0 | | +| RColorBrewer | 1.1-2 | | +| RConics | 1.1.1 | | +| Rcpp | 1.0.5 | | +| RcppArmadillo | 0.9.900.3.0 | | +| RcppEigen | 0.3.3.7.0 | | +| RcppParallel | 5.0.2 | | +| RcppProgress | 0.4.2 | | +| RcppRoll | 0.3.0 | | +| RcppThread | 2.1.3 | | +| RCurl | 1.98-1.2 | | +| Rdpack | 2.1.1 | | +| rdrobust | 2.1.1 | | +| readr | 1.3.1 | | +| readxl | 1.3.1 | | +| recipes | 0.1.15 | | +| registry | 0.5-1 | | +| relimp | 1.0-5 | | +| relsurv | 2.2-3 | | +| rematch | 1.0.1 | | +| remotes | 2.2.0 | | +| renv | 0.16.0 | | +| repr | 1.1.0 | | +| reprex | 0.3.0 | | +| reshape | 0.8.8 | | +| reshape2 | 1.4.4 | | +| rgdal | 1.5-16 | | +| rgeos | 0.5-3 | | +| rio | 0.5.16 | | +| riskRegression | 2021.10.10 | | +| rlang | 1.1.1 | | +| rmarkdown | 2.3 | | +| rms | 6.2-0 | | +| rngWELL | 0.10-7 | | +| ROI | 1.0-0 | | +| ROI.plugin.lpsolve | 1.0-0 | | +| rpart | 4.1-15 | | +| rpart.plot | 3.1.1 | | +| rprojroot | 1.3-2 | | +| rsample | 1.0.0 | | +| rsconnect | 0.8.16 | | +| RSpectra | 0.16-1 | | +| rstan | 2.21.2 | | +| rstantools | 2.1.1 | | +| rstatix | 0.6.0 | | +| rstudioapi | 0.11 | | +| rvest | 0.3.6 | | +| sandwich | 2.5-1 | | +| sass | 0.3.0 | | +| scales | 1.2.1 | | +| SCCS | 1.2 | | +| segmented | 1.4-1 | | +| selectr | 0.4-2 | | +| sf | 0.9-5 | | +| shades | 1.4.0 | | +| shape | 1.4.6 | | +| shapviz | 0.8.0 | | +| shiny | 1.5.0 | | +| shinyjs | 1.1 | | +| shinystan | 2.5.0 | | +| shinythemes | 1.1.2 | | +| skimr | 2.1.2 | | +| slam | 0.1-48 | | +| slider | 0.3.0 | | +| snakecase | 0.11.0 | | +| sourcetools | 0.1.7 | | +| sp | 1.4-2 | | +| SparseM | 1.78 | | +| splines2 | 0.4.1 | | +| SQUAREM | 2020.5 | | +| StanHeaders | 2.21.0-6 | | +| statmod | 1.4.34 | | +| stringdist | 0.9.10 | | +| stringi | 1.4.6 | | +| stringr | 1.4.0 | | +| survey | 4.1-1 | | +| survival | 3.2-3 | | +| survminer | 0.4.8 | | +| survMisc | 0.5.5 | | +| svglite | 1.2.3.2 | | +| sweep | 0.2.5 | | +| sys | 3.4 | | +| systemfonts | 0.3.2 | | +| tables | 0.9.6 | | +| testthat | 2.3.2 | | +| TH.data | 1.1-0 | | +| threejs | 0.3.3 | | +| tibble | 3.0.3 | | +| tictoc | 1.0 | | +| tidyquant | 1.0.9 | | +| tidyr | 1.1.2 | | +| tidyselect | 1.1.0 | | +| tidyverse | 1.3.0 | | +| timeDate | 3043.102 | | +| timereg | 2.0.1 | | +| timetk | 2.7.0 | | +| tinytex | 0.25 | | +| TMB | 1.9.10 | | +| tmvtnorm | 1.5 | | +| tseries | 0.10-58 | | +| tsfeatures | 1.1.1 | | +| tsModel | 0.6 | | +| TTR | 0.24.4 | | +| twopartm | 0.1.0 | | +| units | 0.6-7 | | +| UpSetR | 1.4.0 | | +| urca | 1.3-4 | | +| usethis | 2.0.1 | | +| utf8 | 1.1.4 | | +| V8 | 3.2.0 | | +| vcd | 1.4-9 | | +| vctrs | 0.6.2 | | +| VGAM | 1.1-6 | | +| viridis | 0.5.1 | | +| viridisLite | 0.3.0 | | +| visdat | 0.5.3 | | +| warp | 0.2.1 | | +| webshot | 0.5.2 | | +| WeightIt | 0.13.1 | | +| whisker | 0.4 | | +| withr | 2.5.0 | | +| xfun | 0.16 | | +| xgboost | 1.7.5.1 | | +| XML | 3.99-0.6 | | +| xml2 | 1.3.2 | | +| xtable | 1.8-4 | | +| xts | 0.12-0 | | +| yaml | 2.2.1 | | +| zip | 2.1.1 | | +| zoo | 1.8-8 | | diff --git a/renv.lock b/v1/renv.lock similarity index 100% rename from renv.lock rename to v1/renv.lock diff --git a/add-package.sh b/v1/scripts/add-package.sh similarity index 64% rename from add-package.sh rename to v1/scripts/add-package.sh index b617a85..df60337 100755 --- a/add-package.sh +++ b/v1/scripts/add-package.sh @@ -1,6 +1,7 @@ #!/usr/bin/env bash set -euo pipefail -test -n "$1" || { echo "You must specify a package name. If you want a specific version, append @VERSION"; exit 1; } +export MAJOR_VERSION=v1 +test -n "$2" || { echo "You must specify a package name. If you want a specific version, append @VERSION"; exit 1; } export PACKAGE="$1" if [ "$2" != "NULL" ]; then @@ -13,7 +14,7 @@ export IMAGE_TAG IMAGE=${IMAGE:-r} echo "Attempting to build and install $PACKAGE" -if ! docker-compose build add-package; then +if ! docker-compose --env-file ${MAJOR_VERSION}/env build add-package; then echo "Building $PACKAGE failed." echo "You may need to add build dependencies (e.g. -dev packages) to build-dependencies.txt" echo "Alternatively, you may need to install an older version of $PACKAGE. Please see the Trouble shooting section of the README." @@ -21,19 +22,16 @@ if ! docker-compose build add-package; then fi # update renv.lock -cp renv.lock renv.lock.bak +cp ${MAJOR_VERSION}/renv.lock ${MAJOR_VERSION}/renv.lock.bak # cannot use docker-compose run as it mangles the output -docker run --platform linux/amd64 --rm "$IMAGE_TAG" cat /renv/renv.lock > renv.lock +docker run --platform linux/amd64 --rm "$IMAGE_TAG" cat /renv/renv.lock > ${MAJOR_VERSION}/renv.lock -echo "$PACKAGE and its dependencies built and cached, renv.lock updated." +echo "$PACKAGE and its dependencies built and cached, ${MAJOR_VERSION}/renv.lock updated." echo "Rebuilding R image with new renv.lock file." -if ! just build; then +if ! just build ${MAJOR_VERSION}; then echo "Building the image with the new package failed" exit 1 fi -just test "$IMAGE" - -# update packages.csv for backwards compat with current docs -docker run --platform linux/amd64 "$IMAGE" -e 'write.csv(installed.packages()[, c("Package","Version")], row.names=FALSE, file="/dev/stdout")' 2>/dev/null > packages.csv +just test ${MAJOR_VERSION} diff --git a/squash.sh b/v1/scripts/squash.sh similarity index 100% rename from squash.sh rename to v1/scripts/squash.sh diff --git a/v2/Dockerfile b/v2/Dockerfile new file mode 100644 index 0000000..31032f5 --- /dev/null +++ b/v2/Dockerfile @@ -0,0 +1,89 @@ +# syntax=docker/dockerfile:1.11 +# enable docker linting +# check=error=true +# +################################################# +FROM ghcr.io/opensafely-core/base-action:24.04 AS base-r +ARG MAJOR_VERSION=v2 + +# add cran repo for R packages and install +RUN --mount=type=cache,target=/var/cache/apt,id=apt-2404,sharing=locked \ + --mount=type=cache,target=/var/lib/apt,id=apt-2404,sharing=locked \ + --mount=type=bind,source=${MAJOR_VERSION}/dependencies.txt,target=/tmp/dependencies.txt < /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 +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-2404,sharing=locked \ + --mount=type=bind,source=scripts/,target=/tmp/scripts/ \ + --mount=type=bind,source=${MAJOR_VERSION}/packages.csv,target=/tmp/packages.csv \ + Rscript /tmp/scripts/build.R + + +################################################ +# +# Finally, build the actual image from the base-r image +FROM base-r AS r + +# Some static metadata for this specific image, as defined by: +# https://github.com/opencontainers/image-spec/blob/master/annotations.md#pre-defined-annotation-keys +# The org.opensafely.action label is used by the jobrunner to indicate this is +# an approved action image to run. +LABEL org.opencontainers.image.title="r" \ + org.opencontainers.image.description="R action for opensafely.org" \ + org.opencontainers.image.source="https://github.com/opensafely-core/r-docker" \ + org.opensafely.action="r" \ + org.opensafely.version="${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 + + +################################################# +# +# Add rstudio-server to r image - creating rstudio image +ARG RSTUDIO_BASE_URL="default-arg-to-silence-docker" +ARG RSTUDIO_DEB="default-arg-to-silence-docker" +FROM r AS rstudio + +# Install rstudio-server (and a few dependencies) +COPY rstudio/rstudio-dependencies.txt /root/rstudio-dependencies.txt +RUN --mount=type=cache,target=/var/cache/apt,id=apt-2404,sharing=locked \ + --mount=type=cache,target=/var/lib/apt,id=apt-2404,sharing=locked \ + --mount=type=bind,source=rstudio/rstudio-dependencies.txt,target=/tmp/rstudio-dependencies.txt <> /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/v2/dependencies.txt b/v2/dependencies.txt new file mode 100644 index 0000000..21d2d01 --- /dev/null +++ b/v2/dependencies.txt @@ -0,0 +1,58 @@ +## Core systemdependencies +tzdata +r-base-core=4.4.2-1.2404.0 +r-base-dev=4.4.2-1.2404.0 + +## 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 +# +# There is usually a package in the form of $PACKAGEVERSION in the tree which is the +# one we actually need. This will need doing once for every version of base Ubuntu +# image we use for an R version. + +# igraph: documented dependency is libglpk-dev +libglpk40 + +# sf +libgdal34t64 + +# magick: documented dependency is libmagick++-dev +libmagick++-6.q16-9t64 + +# V8, via daggity: documented dependency is libnode-dev +libnode109 diff --git a/v2/env b/v2/env new file mode 100644 index 0000000..c1fe145 --- /dev/null +++ b/v2/env @@ -0,0 +1,6 @@ +MAJOR_VERSION=v2 +BASE=24.04 +RSTUDIO_BASE_URL=https://download2.rstudio.org/server/jammy/amd64/ +RSTUDIO_DEB=rstudio-server-2024.12.0-467-amd64.deb +CRAN_DATE=2024-12-18 +REPOS=https://packagemanager.posit.co/cran/__linux__/noble/${CRAN_DATE} diff --git a/v2/packages.csv b/v2/packages.csv new file mode 100644 index 0000000..f43286c --- /dev/null +++ b/v2/packages.csv @@ -0,0 +1,173 @@ +Package,Repo +arrow, +AsioHeaders, +astsa, +BayesianTools, +bayesm, +BH, +binom, +blob, +brglm2, +brms, +broom, +broom.helpers, +butcher, +caret, +caTools, +cmprsk, +cobalt, +consort, +corrr, +cowplot, +coxme, +cpp11, +dagitty, +data.table, +DBI, +dbplyr, +dd4d,https://opensafely-core.r-universe.dev/bin/linux/noble/4.4/ +deSolve, +detectseparation, +DiagrammeR, +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, +httpgd, +incidence, +infer, +interactions, +interp, +janitor, +jsonlite, +kableExtra, +knitr, +labelled, +languageserver, +latticeExtra, +lcmm, +lintr, +lme4, +lubridate, +magick, +magrittr, +MASS, +MatchIt, +matrixStats, +metafor, +mgcv, +mice, +mlogit, +modelsummary, +multcomp, +mvtnorm, +naniar, +NHPoisson, +nlme, +optparse, +pammtools, +parallel, +parameters, +parglm, +parsnip, +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, +rms, +rpart.plot, +sandwich, +SCCS, +segmented, +sf, +shapviz, +shiny, +sjPlot, +skimr, +speedglm, +splines2, +stringi, +stringr, +styler, +survey, +survminer, +svglite, +sweep, +targets, +tictoc, +tidycmprsk, +tidymodels, +tidypredict, +tidyr, +tidyselect, +tidyverse, +timetk, +TrialEmulation, +tsModel, +twopartm, +vcd, +VGAM, +WeightIt, +xml2, +xts, +zip, +zoo, diff --git a/v2/packages.md b/v2/packages.md new file mode 100644 index 0000000..3ae1be1 --- /dev/null +++ b/v2/packages.md @@ -0,0 +1,542 @@ +Package Versions for v2 +================ + +This r:v2 OpenSAFELY image is based on Ubuntu 24.04 with R 4.4.2. + +## 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 | 0.3.10 | | +| ape | 5.8-1 | | +| arrow | 18.1.0 | | +| ash | 1.0-15 | | +| AsioHeaders | 1.22.1-2 | | +| askpass | 1.2.1 | | +| assertthat | 0.2.1 | | +| astsa | 2.1 | | +| aweek | 1.0.3 | | +| backports | 1.5.0 | | +| base64enc | 0.1-3 | | +| base64url | 1.4 | | +| BayesianTools | 0.1.8 | | +| bayesm | 3.1-6 | | +| bayesplot | 1.11.1 | | +| bayestestR | 0.15.0 | | +| bbmle | 1.0.25.1 | | +| bdsmatrix | 1.3-7 | | +| BH | 1.87.0-1 | | +| bigD | 0.3.0 | | +| biglm | 0.9-3 | | +| binom | 1.1-1.1 | | +| bit | 4.5.0.1 | | +| bit64 | 4.5.2 | | +| bitops | 1.0-9 | | +| blob | 1.2.4 | | +| boot | 1.3-31 | | +| brew | 1.0-10 | | +| brglm2 | 0.9.2 | | +| bridgesampling | 1.1-2 | | +| brms | 2.22.0 | | +| Brobdingnag | 1.2-9 | | +| broom | 1.0.7 | | +| broom.helpers | 1.17.0 | | +| broom.mixed | 0.2.9.6 | | +| bslib | 0.8.0 | | +| butcher | 0.3.4 | | +| ca | 0.71.1 | | +| cachem | 1.1.0 | | +| callr | 3.7.6 | | +| car | 3.1-3 | | +| carData | 3.0-5 | | +| cards | 0.4.0 | | +| caret | 7.0-1 | | +| caTools | 1.18.3 | | +| cellranger | 1.1.0 | | +| checkmate | 2.3.2 | | +| chk | 0.9.2 | | +| class | 7.3-22 | | +| classInt | 0.4-10 | | +| cli | 3.6.3 | | +| clipr | 0.8.0 | | +| clock | 0.7.1 | | +| clue | 0.3-66 | | +| cluster | 2.1.8 | | +| cmprsk | 2.2-12 | | +| cobalt | 4.5.5 | | +| coda | 0.19-4.1 | | +| codetools | 0.2-20 | | +| collections | 0.3.7 | | +| colorspace | 2.1-1 | | +| commonmark | 1.9.2 | | +| conflicted | 1.2.0 | | +| consort | 1.2.2 | | +| corpcor | 1.6.10 | | +| corrplot | 0.95 | | +| corrr | 0.4.4 | | +| cowplot | 1.1.3 | | +| coxme | 2.2-22 | | +| cpp11 | 0.5.1 | | +| crayon | 1.5.3 | | +| crosstalk | 1.2.1 | | +| curl | 6.0.1 | | +| cyclocomp | 1.1.1 | | +| dagitty | 0.3-4 | | +| data.table | 1.16.4 | | +| datawizard | 0.13.0 | | +| date | 1.2-42 | | +| DBI | 1.2.3 | | +| dbplyr | 2.5.0 | | +| dd4d | 0.0.0.9000 | | +| deldir | 2.0-4 | | +| Deriv | 4.1.6 | | +| desc | 1.4.3 | | +| deSolve | 1.40 | | +| detectseparation | 0.3 | | +| dfidx | 0.1-0 | | +| DHARMa | 0.4.7 | | +| diagram | 1.6.5 | | +| DiagrammeR | 1.0.11 | | +| dials | 1.3.0 | | +| DiceDesign | 1.10 | | +| digest | 0.6.37 | | +| distributional | 0.5.0 | | +| doBy | 4.6.24 | | +| doFuture | 1.0.1 | | +| doParallel | 1.0.17 | | +| dplyr | 1.1.4 | | +| DT | 0.33 | | +| dtplyr | 1.3.1 | | +| dtw | 1.23-1 | | +| dtwclust | 6.0.0 | | +| duckdb | 1.1.3-1 | | +| e1071 | 1.7-16 | | +| effectsize | 1.0.0 | | +| egg | 0.4.5 | | +| ellipse | 0.5.0 | | +| emmeans | 1.10.6 | | +| emulator | 1.2-24 | | +| enrichwith | 0.3.1 | | +| Epi | 2.58 | | +| epitools | 0.5-10.1 | | +| estimability | 1.5.1 | | +| estimatr | 1.0.4 | | +| etm | 1.1.1 | | +| evaluate | 1.0.1 | | +| exactRankTests | 0.8-35 | | +| expm | 1.0-0 | | +| fansi | 1.0.6 | | +| farver | 2.1.2 | | +| fastDummies | 1.7.4 | | +| fastGHQuad | 1.0.1 | | +| fastmap | 1.2.0 | | +| fastshap | 0.1.1 | | +| fda | 6.2.0 | | +| fds | 1.8 | | +| finalfit | 1.0.8 | | +| flexclust | 1.4-2 | | +| 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 | 1.0.0 | | +| foreach | 1.5.2 | | +| forecast | 8.23.0 | | +| foreign | 0.8-87 | | +| forestplot | 3.1.6 | | +| forestploter | 1.1.2 | | +| Formula | 1.2-5 | | +| formula.tools | 1.7.1 | | +| fracdiff | 1.5-3 | | +| fs | 1.6.5 | | +| furrr | 0.3.1 | | +| future | 1.34.0 | | +| future.apply | 1.11.3 | | +| fuzzyjoin | 0.1.6 | | +| gap | 1.6 | | +| gap.datasets | 0.0.6 | | +| gargle | 1.5.2 | | +| gclus | 1.3.2 | | +| geepack | 1.3.12 | | +| generics | 0.1.3 | | +| geosphere | 1.5-20 | | +| getopt | 1.20.4 | | +| gets | 0.38 | | +| ggalluvial | 0.12.5 | | +| GGally | 2.2.1 | | +| ggdist | 3.3.2 | | +| ggeffects | 2.0.0 | | +| ggfittext | 0.10.2 | | +| ggfortify | 0.4.17 | | +| gggenes | 0.5.1 | | +| ggh4x | 0.3.0 | | +| ggplot2 | 3.5.1 | | +| ggpubr | 0.6.0 | | +| ggrepel | 0.9.6 | | +| ggridges | 0.5.6 | | +| ggsci | 3.2.0 | | +| ggsignif | 0.6.4 | | +| ggstats | 0.7.0 | | +| ggtext | 0.1.2 | | +| ggvenn | 0.1.10 | | +| gh | 1.4.1 | | +| gitcreds | 0.1.2 | | +| glmmTMB | 1.1.10 | | +| glmnet | 4.1-8 | | +| globals | 0.16.3 | | +| glue | 1.8.0 | | +| Gmisc | 3.0.3 | | +| gmm | 1.8 | | +| gnm | 1.1-5 | | +| googledrive | 2.1.1 | | +| googlesheets4 | 1.1.1 | | +| gower | 1.0.2 | | +| GPfit | 1.0-8 | | +| gridExtra | 2.3 | | +| gridtext | 0.1.5 | | +| gt | 0.11.1 | | +| gtable | 0.3.6 | | +| gtsummary | 2.0.4 | | +| hardhat | 1.4.0 | | +| haven | 2.5.4 | | +| HDInterval | 0.2.4 | | +| hdrcde | 3.4 | | +| here | 1.0.1 | | +| hexbin | 1.28.5 | | +| highr | 0.11 | | +| Hmisc | 5.2-1 | | +| hms | 1.1.3 | | +| htmlTable | 2.4.3 | | +| htmltools | 0.5.8.1 | | +| htmlwidgets | 1.6.4 | | +| httpgd | 2.0.2 | | +| httpuv | 1.6.15 | | +| httr | 1.4.7 | | +| httr2 | 1.0.7 | | +| IDPmisc | 1.1.21 | | +| ids | 1.0.1 | | +| igraph | 2.1.2 | | +| incidence | 1.7.5 | | +| infer | 1.0.7 | | +| ini | 0.3.1 | | +| inline | 0.3.20 | | +| insight | 1.0.0 | | +| interactions | 1.2.0 | | +| interp | 1.1-6 | | +| ipred | 0.9-15 | | +| isoband | 0.2.7 | | +| iterators | 1.0.14 | | +| janitor | 2.2.0 | | +| jomo | 2.7-6 | | +| jpeg | 0.1-10 | | +| jquerylib | 0.1.4 | | +| jsonlite | 1.8.9 | | +| jtools | 2.3.0 | | +| juicyjuice | 0.1.0 | | +| kableExtra | 1.4.0 | | +| kernlab | 0.9-33 | | +| KernSmooth | 2.23-24 | | +| km.ci | 0.5-6 | | +| KMsurv | 0.1-5 | | +| knitr | 1.49 | | +| ks | 1.14.3 | | +| labeling | 0.4.3 | | +| labelled | 2.13.0 | | +| languageserver | 0.3.16 | | +| later | 1.4.1 | | +| lattice | 0.22-6 | | +| latticeExtra | 0.6-30 | | +| lava | 1.8.0 | | +| lazyeval | 0.2.2 | | +| lcmm | 2.1.0 | | +| lhs | 1.2.0 | | +| lifecycle | 1.0.4 | | +| lintr | 3.1.2 | | +| listenv | 0.9.1 | | +| lme4 | 1.1-35.5 | | +| lmtest | 0.9-40 | | +| lobstr | 1.1.2 | | +| locfit | 1.5-9.10 | | +| loo | 2.8.0 | | +| lpSolveAPI | 5.5.2.0-17.12 | | +| lubridate | 1.9.4 | | +| magick | 2.8.5 | | +| magrittr | 2.0.3 | | +| markdown | 1.13 | | +| marqLevAlg | 2.0.8 | | +| MASS | 7.3-61 | | +| MatchIt | 4.6.0 | | +| mathjaxr | 1.6-0 | | +| Matrix | 1.7-1 | | +| MatrixModels | 0.5-3 | | +| matrixStats | 1.4.1 | | +| maxstat | 0.7-25 | | +| mclust | 6.1.1 | | +| memoise | 2.0.1 | | +| metadat | 1.2-0 | | +| metafor | 4.6-0 | | +| mets | 1.3.4 | | +| mgcv | 1.9-1 | | +| mice | 3.17.0 | | +| microbenchmark | 1.5.0 | | +| mime | 0.12 | | +| minqa | 1.2.8 | | +| mitml | 0.4-5 | | +| mitools | 2.4 | | +| mlogit | 1.1-1 | | +| modeldata | 1.4.0 | | +| modelenv | 0.2.0 | | +| ModelMetrics | 1.2.2.2 | | +| modelr | 0.1.11 | | +| modelsummary | 2.2.0 | | +| modeltools | 0.2-23 | | +| msm | 1.8.2 | | +| mstate | 0.3.3 | | +| muhaz | 1.2.6.4 | | +| multcomp | 1.4-26 | | +| multicool | 1.0.1 | | +| munsell | 0.5.1 | | +| mvtnorm | 1.3-2 | | +| naniar | 1.1.0 | | +| NHPoisson | 3.3 | | +| nleqslv | 3.3.5 | | +| nlme | 3.1-166 | | +| nloptr | 2.1.1 | | +| nnet | 7.3-19 | | +| norm | 1.0-11.1 | | +| numDeriv | 2016.8-1.1 | | +| openssl | 2.3.0 | | +| operator.tools | 1.6.3 | | +| optparse | 1.7.5 | | +| ordinal | 2023.12-4.1 | | +| padr | 0.6.3 | | +| pak | 0.8.0 | | +| pammtools | 0.5.93 | | +| pan | 1.9 | | +| pander | 0.6.5 | | +| parallelly | 1.40.1 | | +| parameters | 0.24.0 | | +| parglm | 0.1.7 | | +| parsnip | 1.2.1 | | +| patchwork | 1.3.0 | | +| pbapply | 1.7-2 | | +| pbkrtest | 0.5.3 | | +| pcaPP | 2.0-5 | | +| pch | 2.1 | | +| pec | 2023.04.12 | | +| performance | 0.12.4 | | +| PerformanceAnalytics | 2.0.8 | | +| permute | 0.9-7 | | +| PHEindicatormethods | 2.1.0 | | +| pillar | 1.10.0 | | +| pkgbuild | 1.4.5 | | +| pkgconfig | 2.0.3 | | +| pkgload | 1.4.0 | | +| plotly | 4.10.4 | | +| plotrix | 3.8-4 | | +| plyr | 1.8.9 | | +| png | 0.1-8 | | +| polspline | 1.1.25 | | +| polynom | 1.4-1 | | +| posterior | 1.6.0 | | +| pracma | 2.4.4 | | +| predtools | 0.0.3 | | +| prettyunits | 1.2.0 | | +| pROC | 1.18.5 | | +| processx | 3.8.4 | | +| prodlim | 2024.06.25 | | +| progress | 1.2.3 | | +| progressr | 0.15.1 | | +| promises | 1.3.2 | | +| proxy | 0.4-27 | | +| ps | 1.8.1 | | +| pscl | 1.5.9 | | +| pseudo | 1.4.3 | | +| Publish | 2023.01.17 | | +| purrr | 1.0.2 | | +| qap | 0.1-2 | | +| qgam | 1.3.4 | | +| quadprog | 1.5-8 | | +| quantmod | 0.4.26 | | +| quantreg | 5.99.1 | | +| QuickJSR | 1.4.0 | | +| qvcalc | 1.0.3 | | +| R.cache | 0.16.0 | | +| R.methodsS3 | 1.8.2 | | +| R.oo | 1.27.0 | | +| R.utils | 2.12.3 | | +| R6 | 2.5.1 | | +| ragg | 1.3.3 | | +| rainbow | 3.8 | | +| randomForest | 4.7-1.2 | | +| randomForestExplainer | 0.10.1 | | +| randtoolbox | 2.0.5 | | +| ranger | 0.17.0 | | +| rappdirs | 0.3.3 | | +| rbibutils | 2.3 | | +| RColorBrewer | 1.1-3 | | +| RConics | 1.1.1 | | +| Rcpp | 1.0.13-1 | | +| RcppArmadillo | 14.2.2-1 | | +| RcppEigen | 0.3.4.0.2 | | +| RcppParallel | 5.1.9 | | +| RcppProgress | 0.4.2 | | +| RcppRoll | 0.3.1 | | +| RcppThread | 2.1.7 | | +| RCurl | 1.98-1.16 | | +| Rdpack | 2.6.2 | | +| rdrobust | 2.2 | | +| reactable | 0.4.4 | | +| reactR | 0.6.1 | | +| readr | 2.1.5 | | +| readxl | 1.4.3 | | +| recipes | 1.1.0 | | +| reformulas | 0.4.0 | | +| registry | 0.5-1 | | +| relimp | 1.0-5 | | +| relsurv | 2.2-9 | | +| rematch | 2.0.0 | | +| rematch2 | 2.1.2 | | +| remotes | 2.5.0 | | +| repr | 1.1.7 | | +| reprex | 2.1.1 | | +| reshape2 | 1.4.4 | | +| rex | 1.2.1 | | +| riskRegression | 2023.12.21 | | +| rlang | 1.1.4 | | +| rmarkdown | 2.29 | | +| rms | 6.9-0 | | +| rngWELL | 0.10-10 | | +| ROI | 1.0-1 | | +| ROI.plugin.lpsolve | 1.0-2 | | +| roxygen2 | 7.3.2 | | +| rpart | 4.1.23 | | +| rpart.plot | 3.1.2 | | +| rprojroot | 2.0.4 | | +| rsample | 1.2.1 | | +| RSpectra | 0.16-2 | | +| rstan | 2.32.6 | | +| rstantools | 2.4.0 | | +| rstatix | 0.7.2 | | +| rstpm2 | 1.6.6 | | +| rstudioapi | 0.17.1 | | +| rvest | 1.0.4 | | +| s2 | 1.1.7 | | +| sandwich | 3.1-1 | | +| sass | 0.4.9 | | +| scales | 1.3.0 | | +| SCCS | 1.7 | | +| secretbase | 1.0.3 | | +| segmented | 2.1-3 | | +| selectr | 0.4-2 | | +| seriation | 1.5.7 | | +| sf | 1.0-19 | | +| sfd | 0.1.0 | | +| shades | 1.4.0 | | +| shape | 1.4.6.1 | | +| shapviz | 0.9.6 | | +| shiny | 1.10.0 | | +| shinyjs | 2.1.0 | | +| sjlabelled | 1.2.0 | | +| sjmisc | 2.8.10 | | +| sjPlot | 2.8.17 | | +| sjstats | 0.19.0 | | +| skimr | 2.1.5 | | +| slam | 0.1-55 | | +| slider | 0.3.2 | | +| snakecase | 0.11.1 | | +| sourcetools | 0.1.7-1 | | +| sp | 2.1-4 | | +| SparseM | 1.84-2 | | +| speedglm | 0.3-5 | | +| splines2 | 0.5.3 | | +| SQUAREM | 2021.1 | | +| StanHeaders | 2.32.10 | | +| statmod | 1.5.0 | | +| stringdist | 0.9.14 | | +| stringi | 1.8.4 | | +| stringr | 1.5.1 | | +| styler | 1.10.3 | | +| survey | 4.4-2 | | +| survival | 3.8-3 | | +| survminer | 0.5.0 | | +| survMisc | 0.5.6 | | +| svglite | 2.1.3 | | +| sweep | 0.2.5 | | +| sys | 3.4.3 | | +| systemfonts | 1.1.0 | | +| tables | 0.9.31 | | +| targets | 1.9.1 | | +| tensorA | 0.36.2.1 | | +| textshaping | 0.4.1 | | +| TH.data | 1.1-2 | | +| tibble | 3.2.1 | | +| tictoc | 1.2.1 | | +| tidycmprsk | 1.1.0 | | +| tidymodels | 1.2.0 | | +| tidypredict | 0.5 | | +| tidyquant | 1.0.9 | | +| tidyr | 1.3.1 | | +| tidyselect | 1.2.1 | | +| tidyverse | 2.0.0 | | +| timechange | 0.3.0 | | +| timeDate | 4041.110 | | +| timereg | 2.0.6 | | +| timetk | 2.9.0 | | +| tinytable | 0.6.1 | | +| tinytex | 0.54 | | +| TMB | 1.9.15 | | +| tmvtnorm | 1.6 | | +| TrialEmulation | 0.0.4.0 | | +| tseries | 0.10-58 | | +| tsfeatures | 1.1.1 | | +| tsModel | 0.6-2 | | +| TSP | 1.2-4 | | +| TTR | 0.24.4 | | +| tune | 1.2.1 | | +| twopartm | 0.1.0 | | +| tzdb | 0.4.0 | | +| ucminf | 1.2.2 | | +| unigd | 0.1.2 | | +| units | 0.8-5 | | +| UpSetR | 1.4.0 | | +| urca | 1.3-4 | | +| utf8 | 1.2.4 | | +| 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