From 900d3eaf923a7b27ed5a4ace73cfaace9e3a600a Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Nov 2023 11:59:41 +0000 Subject: [PATCH] Remove R 4.1 a it causing dependencies issues. We want to use purrr >= 1.0.0 --- .Rprofile | 2 +- .devcontainer/4.1/devcontainer.json | 95 -- .github/workflows/r-renv-lock.yml | 1 - DESCRIPTION | 6 +- renv/profiles/4.1/renv.lock | 1254 -------------------------- renv/profiles/4.1/renv/.gitignore | 7 - renv/profiles/4.1/renv/settings.json | 21 - 7 files changed, 4 insertions(+), 1382 deletions(-) delete mode 100644 .devcontainer/4.1/devcontainer.json delete mode 100644 renv/profiles/4.1/renv.lock delete mode 100644 renv/profiles/4.1/renv/.gitignore delete mode 100644 renv/profiles/4.1/renv/settings.json diff --git a/.Rprofile b/.Rprofile index a94c4d6f..062e3271 100644 --- a/.Rprofile +++ b/.Rprofile @@ -27,7 +27,7 @@ Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE) if (!Sys.getenv("RENV_AUTOLOADER_ENABLED") %in% c("false", "FALSE")) { .renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") if (!file.exists("./renv/profile")) { - if (.renv_profile %in% c("4.1", "4.2", "4.3")) { + if (.renv_profile %in% c("4.2", "4.3")) { message("Set renv profile to `", .renv_profile, "`") Sys.setenv("RENV_PROFILE" = .renv_profile) } else { diff --git a/.devcontainer/4.1/devcontainer.json b/.devcontainer/4.1/devcontainer.json deleted file mode 100644 index e60b4fd9..00000000 --- a/.devcontainer/4.1/devcontainer.json +++ /dev/null @@ -1,95 +0,0 @@ -{ - // https://containers.dev/implementors/json_reference/ - "name": "sdtm.oak (RStudio) container", - "image": "ghcr.io/pharmaverse/sdtm.oak-4.1:latest", - // Install Dev Container Features. More info: https://containers.dev/features - "containerEnv": { - "ROOT": "true", - "PASSWORD": "rstudio", - "DISABLE_AUTH": "true", - "RENV_AUTOLOADER_ENABLED": "false" - }, - "features": { - "./ca-cert": {}, - "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { - "version": "none", - "vscodeRSupport": "full", - "installRadian": true, - "installVscDebugger": true - }, - "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, - "ghcr.io/devcontainers/features/common-utils:2": { - "installZsh": true, - "configureZshAsDefaultShell": false, - "installOhMyZsh": true, - "username": "rstudio", - "upgradePackages": false - }, - "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {} - }, - "overrideFeatureInstallOrder": [ - "./ca-cert", - "./arm64-repos", - "ghcr.io/devcontainers/features/common-utils", - "ghcr.io/rocker-org/devcontainer-features/renv-cache", - "ghcr.io/rocker-org/devcontainer-features/r-rig", - "ghcr.io/mikaello/devcontainer-features/modern-shell-utils" - ], - "init": true, - "overrideCommand": false, - - "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", - - "postAttachCommand": "rstudio || true", - - "customizations": { - "codespaces": { - "repositories": { - "pharmaverse/mint": { - "permissions": "write-all" - }, - "pharmaverse/raw.synthetic.data": { - "permissions": "write-all" - } - } - }, - "vscode": { - "settings": { - "r.rterm.linux": "/usr/local/bin/radian", - "r.bracketedPaste": true, - "editor.bracketPairColorization.enabled": true, - "editor.guides.bracketPairs": "active" - }, - "extensions": [ - "vsls-contrib.codetour", - "GitHub.copilot", - "GitHub.copilot-chat", - // R extensions - "ikuyadeu.r", - "REditorSupport.r-lsp", - // Extra extension - "streetsidesoftware.code-spell-checker", - "eamodio.gitlens", - "cweijan.vscode-office", - "donjayamanne.githistory", - "GitHub.vscode-github-actions", - "GitHub.vscode-pull-request-github", - "GitHub.remotehub", - "alefragnani.Bookmarks", - "vscode-icons-team.vscode-icons" - ] - } - }, - - // RStudio ports - "forwardPorts": [8787], - "portsAttributes": { - "8787": { - "label": "Rstudio", - "requireLocalPort": true, - "onAutoForward": "openBrowser" - } - }, - // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root - "remoteUser": "rstudio" -} diff --git a/.github/workflows/r-renv-lock.yml b/.github/workflows/r-renv-lock.yml index fd5015d4..d07747e0 100644 --- a/.github/workflows/r-renv-lock.yml +++ b/.github/workflows/r-renv-lock.yml @@ -22,7 +22,6 @@ jobs: fail-fast: false matrix: config: - - {os: ubuntu-20.04, r: '4.1', repos: 'https://packagemanager.posit.co/cran/2022-03-10/'} - {os: ubuntu-20.04, r: '4.2', repos: 'https://packagemanager.posit.co/cran/2023-03-15/'} - {os: ubuntu-20.04, r: '4.3', repos: 'https://packagemanager.posit.co/cran/2023-04-20/'} diff --git a/DESCRIPTION b/DESCRIPTION index 4509f099..d115078b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,11 +19,11 @@ Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) RoxygenNote: 7.2.3 -Depends: R (>= 4.1) +Depends: R (>= 4.2) Imports: admiraldev, - dplyr, - purrr, + dplyr (>= 1.0.0), + purrr (>= 1.0.0), rlang (>= 1.0.0), stringr, tibble diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock deleted file mode 100644 index 5b858691..00000000 --- a/renv/profiles/4.1/renv.lock +++ /dev/null @@ -1,1254 +0,0 @@ -{ - 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