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@@ -24,3 +24,4 @@ | |
| ^data-raw$ | ||
| ^CRAN-SUBMISSION$ | ||
| ^cran-comments\.md$ | ||
| ^.devcontainer$ | ||
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| @@ -1,15 +1,48 @@ | ||
| # Set renv profile base on R version. | ||
| if ((Sys.getenv("GITHUB_ACTIONS") == "") && (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) { | ||
| renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") | ||
| if (file.exists("./renv/profile")) { | ||
| message("Using renv profile from `renv/profile` file.") | ||
| } else if (renv_profile %in% c("4.1", "4.2", "4.3")) { | ||
| message("Set renv profile to `", renv_profile, "`") | ||
| Sys.setenv("RENV_PROFILE" = renv_profile) | ||
| .get_dependencies <- function(project_dir) { | ||
|
|
||
| admdev_loc <- find.package("admiraldev", lib.loc = .libPaths(), quiet = TRUE) | ||
| adm_dev_suggests <- if(length(admdev_loc) != 0) { | ||
| renv:::renv_dependencies_discover_description(admdev_loc, fields = c("Depends", "Imports", "LinkingTo", "Suggests")) | ||
| } else { | ||
| data.frame(Packages = character(0)) | ||
| } | ||
| suggests_packages <- renv:::renv_dependencies_discover_description(project_dir, fields = "Suggests") | ||
|
|
||
| packages <- names( | ||
| renv:::renv_package_dependencies( | ||
| unique(c( | ||
| project_dir, | ||
| adm_dev_suggests[["Package"]], | ||
| suggests_packages[["Package"]], | ||
| c("staged.dependencies", "renv", "styler") | ||
| )) | ||
| ) | ||
| ) | ||
| packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm", getwd()))] | ||
| } | ||
|
|
||
| options(renv.snapshot.filter = .get_dependencies) | ||
|
|
||
| .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")) { | ||
| message("Set renv profile to `", .renv_profile, "`") | ||
| Sys.setenv("RENV_PROFILE" = .renv_profile) | ||
| } else { | ||
| message("This repository do not contains the renv profile for your R version.") | ||
| } | ||
| source("renv/activate.R") | ||
| } else { | ||
| options(repos = c(CRAN = "https://cran.rstudio.com")) | ||
| message( | ||
| "Using renv profile from `renv/profile` file.\n", | ||
| "The `", readLines("./renv/profile"), "` profile will be used." | ||
| ) | ||
| } | ||
|
|
||
| if (Sys.getenv("GITHUB_ACTIONS") != "") { | ||
| options(repos = c(CRAN = "https://packagemanager.posit.co/cran/latest")) | ||
| Sys.setenv("RENV_AUTOLOADER_ENABLED" = FALSE) | ||
| } | ||
| Sys.setenv("RENV_CONFIG_SANDBOX_ENABLED" = FALSE) | ||
| Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE) | ||
| source("renv/activate.R") |
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| @@ -0,0 +1,76 @@ | ||
| { | ||
| // https://containers.dev/implementors/json_reference/ | ||
| "name": "Admiral R-4.1 (RStudio) container", | ||
| "image": "ghcr.io/pharmaverse/admiralci-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": { | ||
| "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": {} | ||
| }, | ||
| "init": true, | ||
| "overrideCommand": false, | ||
|
|
||
| "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", | ||
|
|
||
| "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"", | ||
|
|
||
| "customizations": { | ||
| "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" | ||
| } |
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|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| { | ||
| // https://containers.dev/implementors/json_reference/ | ||
| "name": "Admiral R-4.2 (RStudio) container", | ||
| "image": "ghcr.io/pharmaverse/admiralci-4.2:latest", | ||
| // Install Dev Container Features. More info: https://containers.dev/features | ||
| "containerEnv": { | ||
| "ROOT": "true", | ||
| "PASSWORD": "rstudio", | ||
| "DISABLE_AUTH": "true", | ||
| "RENV_AUTOLOADER_ENABLED": "false" | ||
| }, | ||
| "features": { | ||
| "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": {} | ||
| }, | ||
| "init": true, | ||
| "overrideCommand": false, | ||
|
|
||
| "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", | ||
|
|
||
| "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"", | ||
|
|
||
| "customizations": { | ||
| "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" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| { | ||
| // https://containers.dev/implementors/json_reference/ | ||
| "name": "Admiral R-4.3 (RStudio) container", | ||
| "image": "ghcr.io/pharmaverse/admiralci-4.3:latest", | ||
| // Install Dev Container Features. More info: https://containers.dev/features | ||
| "containerEnv": { | ||
| "ROOT": "true", | ||
| "PASSWORD": "rstudio", | ||
| "DISABLE_AUTH": "true", | ||
| "RENV_AUTOLOADER_ENABLED": "false" | ||
| }, | ||
| "features": { | ||
| "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": {} | ||
| }, | ||
| "init": true, | ||
| "overrideCommand": false, | ||
|
|
||
| "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", | ||
|
|
||
| "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"", | ||
|
|
||
| "customizations": { | ||
| "vscode": { | ||
| "settings": { | ||
| "r.rterm.linux": "/usr/local/bin/radian", | ||
| "r.bracketedPaste": true, | ||
| "editor.bracketPairColorization.enabled": true, | ||
| "editor.guides.bracketPairs": "active" | ||
| }, | ||
| "extensions": [ | ||
| "vsls-contrib.codetour", | ||
| "GitHub.copilot", | ||
| "GitHub.copilot-chat", | ||
| // R extensions | ||
| "ikuyadeu.r", | ||
| "REditorSupport.r-lsp", | ||
| // Extra extension | ||
| "streetsidesoftware.code-spell-checker", | ||
| "eamodio.gitlens", | ||
| "cweijan.vscode-office", | ||
| "donjayamanne.githistory", | ||
| "GitHub.vscode-github-actions", | ||
| "GitHub.vscode-pull-request-github", | ||
| "GitHub.remotehub", | ||
| "alefragnani.Bookmarks", | ||
| "vscode-icons-team.vscode-icons" | ||
| ] | ||
| } | ||
| }, | ||
|
|
||
| // RStudio ports | ||
| "forwardPorts": [8787], | ||
| "portsAttributes": { | ||
| "8787": { | ||
| "label": "Rstudio", | ||
| "requireLocalPort": true, | ||
| "onAutoForward": "openBrowser" | ||
| } | ||
| }, | ||
| // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root | ||
| "remoteUser": "rstudio" | ||
| } |
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| @@ -0,0 +1,5 @@ | ||
| #!/bin/bash | ||
|
|
||
| R -q -e 'renv::restore(lockfile = file.path("renv", "profiles", paste(R.version$major, substr(R.version$minor, 1, 1), sep = "."), "renv.lock")); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = ".", verbose = 1), verbose = 1);' | ||
|
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| jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json |
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|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| { | ||
| "save_workspace": "never", | ||
| "always_save_history": false, | ||
| "reuse_sessions_for_project_links": true, | ||
| "posix_terminal_shell": "bash", | ||
| "initial_working_directory": "/workspaces", | ||
| "show_hidden_files": true | ||
| } |
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