diff --git a/.Rbuildignore b/.Rbuildignore index bde08966..94d45520 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -32,4 +32,5 @@ ^admiralvaccine\.Rcheck$ ^admiralvaccine.*\.tar\.gz$ ^admiralvaccine.*\.tgz$ +^\.devcontainer$ ^doc$ diff --git a/.Rprofile b/.Rprofile index 3ac58f50..6d46e675 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,5 +1,47 @@ -if (Sys.getenv("GITHUB_ACTIONS") == "" || (Sys.getenv("GITHUB_ACTIONS") == "true" && getRversion()$major == 3 && getRversion()$minor == 6)) { - source("renv/activate.R") +# Set renv profile base on R version. +.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", "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.") + } } 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") diff --git a/.devcontainer/4.1/devcontainer.json b/.devcontainer/4.1/devcontainer.json new file mode 100644 index 00000000..ab6ddfee --- /dev/null +++ b/.devcontainer/4.1/devcontainer.json @@ -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}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'", + + "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" +} diff --git a/.devcontainer/4.2/devcontainer.json b/.devcontainer/4.2/devcontainer.json new file mode 100644 index 00000000..decbcca5 --- /dev/null +++ b/.devcontainer/4.2/devcontainer.json @@ -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}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'", + + "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" +} diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..3f47589f --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -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.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'", + + "customizations": { + "vscode": { + "settings": { + "r.rterm.linux": "/usr/local/bin/radian", + "r.bracketedPaste": true, + "editor.bracketPairColorization.enabled": true, + "editor.guides.bracketPairs": "active" + }, + "extensions": [ + "vsls-contrib.codetour", + "GitHub.copilot", + "GitHub.copilot-chat", + // R extensions + "ikuyadeu.r", + "REditorSupport.r-lsp", + // Extra extension + "streetsidesoftware.code-spell-checker", + "eamodio.gitlens", + "cweijan.vscode-office", + "donjayamanne.githistory", + "GitHub.vscode-github-actions", + "GitHub.vscode-pull-request-github", + "GitHub.remotehub", + "alefragnani.Bookmarks", + "vscode-icons-team.vscode-icons" + ] + } + }, + + // RStudio ports + "forwardPorts": [8787], + "portsAttributes": { + "8787": { + "label": "Rstudio", + "requireLocalPort": true, + "onAutoForward": "openBrowser" + } + }, + // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root + "remoteUser": "rstudio" +} diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh new file mode 100644 index 00000000..8dfe4e23 --- /dev/null +++ b/.devcontainer/postCreateCommand.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +# move script rstudio into /usr/bin +sudo cp "$(pwd)/.devcontainer/rstudio.sh" /usr/bin/rstudio +sudo chmod +x /usr/bin/rstudio + +# Restore renv and install staged dependencies +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);' + +# Define rstudio default working directory +jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json diff --git a/.devcontainer/rstudio-prefs.json b/.devcontainer/rstudio-prefs.json new file mode 100644 index 00000000..2d5cce84 --- /dev/null +++ b/.devcontainer/rstudio-prefs.json @@ -0,0 +1,8 @@ +{ + "save_workspace": "never", + "always_save_history": false, + "reuse_sessions_for_project_links": true, + "posix_terminal_shell": "bash", + "initial_working_directory": "/workspaces", + "show_hidden_files": true +} diff --git a/.devcontainer/rstudio.sh b/.devcontainer/rstudio.sh new file mode 100644 index 00000000..053a247b --- /dev/null +++ b/.devcontainer/rstudio.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +$BROWSER "https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}" + +exit 1 diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml index 7294cd56..663dd223 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -13,7 +13,6 @@ on: push: branches: - main - - devel - pre-release - test # 'pull_request' events are triggered when PRs are @@ -21,7 +20,6 @@ on: pull_request: branches: - main - - devel - pre-release - test # 'release' events are triggered when... @@ -37,7 +35,7 @@ concurrency: env: R_VERSION: "4.1" - + jobs: get_r_version: name: Get R version @@ -81,6 +79,8 @@ jobs: name: Check uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main if: github.event_name == 'pull_request' + with: + error-on: warning # TODO: find a way to ignore specific notes docs: name: Documentation uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main @@ -91,7 +91,7 @@ jobs: # Whether to skip multiversion docs # Note that if you have multiple versions of docs, # your URL links are likely to break due to path changes - skip-multiversion-docs: false + skip-multiversion-docs: true linter: name: Lint uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main @@ -130,4 +130,4 @@ jobs: if: github.event_name == 'pull_request' needs: get_r_version with: - r-version: "${{ needs.get_r_version.outputs.r-version }}" + r-version: "${{ needs.get_r_version.outputs.r-version }}" \ No newline at end of file diff --git a/renv.lock b/renv.lock index b6e48a22..5801ed10 100644 --- a/renv.lock +++ b/renv.lock @@ -1,390 +1,368 @@ { "R": { - "Version": "4.0.5", + "Version": "4.1.3", "Repositories": [ { "Name": "CRAN", - "URL": "https://cloud.r-project.org" + "URL": "https://packagemanager.posit.co/cran/latest" }, { - "Name": "MRAN", - "URL": "https://cran.microsoft.com/snapshot/2021-03-31" + "Name": "RSPM", + "URL": "https://packagemanager.posit.co/cran/2022-03-10" } ] }, "Packages": { - "BH": { - "Package": "BH", - "Version": "1.75.0-0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "e4c04affc2cac20c8fec18385cd14691", - "Requirements": [] - }, "DT": { "Package": "DT", - "Version": "0.17", + "Version": "0.21", "Source": "Repository", - "Repository": "CRAN", - "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0", + "Repository": "RSPM", "Requirements": [ "crosstalk", "htmltools", "htmlwidgets", + "jquerylib", "jsonlite", "magrittr", "promises" - ] - }, - "KernSmooth": { - "Package": "KernSmooth", - "Version": "2.23-18", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "9e703ad8bf0e99f3691f05da32dfe68b", - "Requirements": [] - }, - "MASS": { - "Package": "MASS", - "Version": "7.3-53.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "4ef21dd0348b9abb7f8bd1d77e4cd0c3", - "Requirements": [] - }, - "Matrix": { - "Package": "Matrix", - "Version": "1.3-2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "ff280503079ad8623d3c4b1519b24ea2", - "Requirements": [ - "lattice" - ] + ], + "Hash": "45fa28dbf288cd606e13ca35d3d72437" }, "R.cache": { "Package": "R.cache", - "Version": "0.16.0", + "Version": "0.15.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "fe539ca3f8efb7410c3ae2cf5fe6c0f8", + "Repository": "RSPM", "Requirements": [ + "R", "R.methodsS3", "R.oo", "R.utils", - "digest" - ] + "digest", + "utils" + ], + "Hash": "e92a8ea8388c47c82ed8aa435ed3be50" }, "R.methodsS3": { "Package": "R.methodsS3", "Version": "1.8.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4bf6453323755202d5909697b6f7c109", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "4bf6453323755202d5909697b6f7c109" }, "R.oo": { "Package": "R.oo", "Version": "1.24.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "5709328352717e2f0a9c012be8a97554", + "Repository": "RSPM", "Requirements": [ - "R.methodsS3" - ] + "R", + "R.methodsS3", + "methods", + "utils" + ], + "Hash": "5709328352717e2f0a9c012be8a97554" }, "R.utils": { "Package": "R.utils", - "Version": "2.12.0", + "Version": "2.11.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "d31333e10f14027e1cbbc6f266512806", + "Repository": "RSPM", "Requirements": [ + "R", "R.methodsS3", - "R.oo" - ] + "R.oo", + "methods", + "tools", + "utils" + ], + "Hash": "a7ecb8e60815c7a18648e84cd121b23a" }, "R6": { "Package": "R6", - "Version": "2.5.0", + "Version": "2.5.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b203113193e70978a696b2809525649d", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "470851b6d5d0ac559e9d01bb352b4021" }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.6", + "Version": "1.0.8", "Source": "Repository", - "Repository": "CRAN", - "Hash": "dbb5e436998a7eba5a9d682060533338", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "methods", + "utils" + ], + "Hash": "22b546dd7e337f6c0c58a39983a496bc" }, "askpass": { "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "e8a22846fff485f0be3770c2da758713", + "Repository": "RSPM", "Requirements": [ "sys" - ] - }, - "assertthat": { - "Package": "assertthat", - "Version": "0.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "50c838a310445e954bc13f26f26a6ecf", - "Requirements": [] + ], + "Hash": "e8a22846fff485f0be3770c2da758713" }, "backports": { "Package": "backports", - "Version": "1.2.1", + "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "644043219fc24e190c2f620c1a380a69", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "c39fbec8a30d23e721980b8afb31984c" }, "base64enc": { "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "543776ae6848fde2f48ff3816d0628bc", - "Requirements": [] - }, - "boot": { - "Package": "boot", - "Version": "1.3-27", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "d9778c960792721e8433daaf3db8f16a", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "543776ae6848fde2f48ff3816d0628bc" }, "brew": { "Package": "brew", - "Version": "1.0-6", + "Version": "1.0-7", "Source": "Repository", - "Repository": "CRAN", - "Hash": "92a5f887f9ae3035ac7afde22ba73ee9", - "Requirements": [] + "Repository": "RSPM", + "Hash": "38875ea52350ff4b4c03849fc69736c8" }, "brio": { "Package": "brio", "Version": "1.1.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "976cf154dfb043c012d87cddd8bca363", - "Requirements": [] + "Repository": "RSPM", + "Hash": "976cf154dfb043c012d87cddd8bca363" }, "bslib": { "Package": "bslib", - "Version": "0.4.0", + "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "be5ee090716ce1671be6cd5d7c34d091", + "Repository": "RSPM", "Requirements": [ - "cachem", + "R", + "grDevices", "htmltools", "jquerylib", "jsonlite", - "memoise", "rlang", "sass" - ] + ], + "Hash": "56ae7e1987b340186a8a5a157c2ec358" }, "cachem": { "Package": "cachem", - "Version": "1.0.4", + "Version": "1.0.6", "Source": "Repository", - "Repository": "CRAN", - "Hash": "2703a46dcabfb902f10060b2bca9f708", + "Repository": "RSPM", "Requirements": [ "fastmap", "rlang" - ] + ], + "Hash": "648c5b3d71e6a37e3043617489a0a0e9" }, "callr": { "Package": "callr", - "Version": "3.7.2", + "Version": "3.7.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "358689cac9fe93b1bb3a19088d2dbed8", + "Repository": "RSPM", "Requirements": [ + "R", "R6", - "processx" - ] + "processx", + "utils" + ], + "Hash": "9b2191ede20fa29828139b9900922e51" }, "cellranger": { "Package": "cellranger", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "f61dbaec772ccd2e17705c1e872e9e7c", + "Repository": "RSPM", "Requirements": [ + "R", "rematch", "tibble" - ] - }, - "class": { - "Package": "class", - "Version": "7.3-18", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "15ef288688a6919417ade6251deea2b3", - "Requirements": [ - "MASS" - ] + ], + "Hash": "f61dbaec772ccd2e17705c1e872e9e7c" }, "cli": { "Package": "cli", "Version": "3.4.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0d297d01734d2bcea40197bd4971a764", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "0d297d01734d2bcea40197bd4971a764" }, "clipr": { "Package": "clipr", - "Version": "0.7.1", + "Version": "0.8.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "ebaa97ac99cc2daf04e77eecc7b781d7", - "Requirements": [] - }, - "cluster": { - "Package": "cluster", - "Version": "2.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "5ea8f54741ff907e2c0b5efabc9de729", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" }, "codetools": { "Package": "codetools", "Version": "0.2-18", "Source": "Repository", "Repository": "CRAN", - "Hash": "019388fc48e48b3da0d3a76ff94608a8", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "019388fc48e48b3da0d3a76ff94608a8" + }, + "collections": { + "Package": "collections", + "Version": "0.3.5", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "92537c684a3d2eaa6bd8f65c28ef97f0" }, "commonmark": { "Package": "commonmark", - "Version": "1.7", + "Version": "1.8.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0f22be39ec1d141fd03683c06f3a6e67", - "Requirements": [] + "Repository": "RSPM", + "Hash": "2ba81b120c1655ab696c935ef33ea716" }, "covr": { "Package": "covr", "Version": "3.5.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6d80a9fc3c0c8473153b54fa54719dfd", + "Repository": "RSPM", "Requirements": [ + "R", "crayon", "digest", "httr", "jsonlite", + "methods", "rex", + "stats", + "utils", "withr", "yaml" - ] + ], + "Hash": "6d80a9fc3c0c8473153b54fa54719dfd" }, "cpp11": { "Package": "cpp11", "Version": "0.4.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "ed588261931ee3be2c700d22e94a29ab", - "Requirements": [] + "Repository": "RSPM", + "Hash": "ed588261931ee3be2c700d22e94a29ab" }, "crayon": { "Package": "crayon", - "Version": "1.4.1", + "Version": "1.5.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "e75525c55c70e5f4f78c9960a4b402e9", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "grDevices", + "methods", + "utils" + ], + "Hash": "741c2e098e98afe3dc26a7b0e5489f4e" }, "credentials": { "Package": "credentials", - "Version": "1.3.0", + "Version": "1.3.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a96728288c75a814c900af9da84387be", + "Repository": "RSPM", "Requirements": [ "askpass", "curl", "jsonlite", "openssl", "sys" - ] + ], + "Hash": "93762d0a34d78e6a025efdbfb5c6bb41" }, "crosstalk": { "Package": "crosstalk", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "2b06f9e415a62b6762e4b8098d2aecbc", + "Repository": "RSPM", "Requirements": [ "R6", "htmltools", "jsonlite", "lazyeval" - ] + ], + "Hash": "6aa54f69598c32177e920eb3402e8293" }, "curl": { "Package": "curl", - "Version": "4.3", + "Version": "4.3.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "2b7d10581cc730804e9ed178c8374bd6", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "022c42d49c28e95d69ca60446dbabf88" }, "cyclocomp": { "Package": "cyclocomp", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "53cbed70a2f7472d48fb6aef08442f25", + "Repository": "RSPM", "Requirements": [ "callr", "crayon", "desc", "remotes", "withr" - ] + ], + "Hash": "53cbed70a2f7472d48fb6aef08442f25" }, "desc": { "Package": "desc", "Version": "1.4.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", + "Repository": "RSPM", "Requirements": [ + "R", "R6", "cli", - "rprojroot" - ] + "rprojroot", + "utils" + ], + "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21" }, "devtools": { "Package": "devtools", - "Version": "2.3.2", + "Version": "2.4.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "415656f50722f5b6e6bcf80855ce11b9", + "Repository": "RSPM", "Requirements": [ - "DT", + "R", "callr", "cli", - "covr", "desc", "ellipsis", + "fs", "httr", - "jsonlite", + "lifecycle", "memoise", "pkgbuild", "pkgload", @@ -395,46 +373,59 @@ "rstudioapi", "rversions", "sessioninfo", + "stats", "testthat", + "tools", "usethis", + "utils", "withr" - ] + ], + "Hash": "fc35e13bb582e5fe6f63f3d647a4cbe5" }, "diffdf": { "Package": "diffdf", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "9ddedef46959baad2080047a1b0117fe", + "Repository": "RSPM", "Requirements": [ + "R", "tibble" - ] + ], + "Hash": "9ddedef46959baad2080047a1b0117fe" }, "diffobj": { "Package": "diffobj", - "Version": "0.3.4", + "Version": "0.3.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "feb5b7455eba422a2c110bb89852e6a3", + "Repository": "RSPM", "Requirements": [ - "crayon" - ] + "R", + "crayon", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8" }, "digest": { "Package": "digest", - "Version": "0.6.27", + "Version": "0.6.29", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a0cbe758a531d054b537d16dff4d58a1", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "cf6b206a045a684728c3267ef7596190" }, "downlit": { "Package": "downlit", - "Version": "0.4.2", + "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "79bf3f66590752ffbba20f8d2da94c7c", + "Repository": "RSPM", "Requirements": [ + "R", "brio", "desc", "digest", @@ -443,93 +434,113 @@ "memoise", "rlang", "vctrs", - "withr", "yaml" - ] + ], + "Hash": "ba63dc9ab5a31f3209892437e40c5f60" }, "dplyr": { "Package": "dplyr", - "Version": "1.0.5", + "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "d0d76c11ec807eb3f000eba4e3eb0f68", + "Repository": "RSPM", "Requirements": [ + "R", "R6", - "ellipsis", + "cli", "generics", "glue", "lifecycle", "magrittr", + "methods", + "pillar", "rlang", "tibble", "tidyselect", + "utils", "vctrs" - ] + ], + "Hash": "eb5742d256a0d9306d85ea68756d8187" }, "ellipsis": { "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077", + "Repository": "RSPM", "Requirements": [ + "R", "rlang" - ] + ], + "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" }, "evaluate": { "Package": "evaluate", - "Version": "0.17", + "Version": "0.15", "Source": "Repository", - "Repository": "CRAN", - "Hash": "9171b012a55a1ef53f1442b1d798a3b4", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "methods" + ], + "Hash": "699a7a93d08c962d9f8950b2d7a227f1" }, "fansi": { "Package": "fansi", - "Version": "0.4.2", + "Version": "1.0.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "fea074fb67fe4c25d47ad09087da847d", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "grDevices", + "utils" + ], + "Hash": "f28149c2d7a1342a834b314e95e67260" }, "fastmap": { "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", - "Requirements": [] + "Repository": "RSPM", + "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" }, - "foreign": { - "Package": "foreign", - "Version": "0.8-81", + "fontawesome": { + "Package": "fontawesome", + "Version": "0.2.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "74628ea7a3be5ee8a7b5bb0a8e84882e", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "htmltools", + "rlang" + ], + "Hash": "55624ed409e46c5f358b2c060be87f67" }, "fs": { "Package": "fs", "Version": "1.5.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "7c89603d81793f0d5486d91ab1fc6f1d", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "methods" + ], + "Hash": "7c89603d81793f0d5486d91ab1fc6f1d" }, "generics": { "Package": "generics", - "Version": "0.1.0", + "Version": "0.1.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4d243a9c10b00589889fe32314ffd902", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "methods" + ], + "Hash": "177475892cf4a55865868527654a7741" }, "gert": { "Package": "gert", - "Version": "1.9.1", + "Version": "1.5.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "9a091a6d2fb91e43afd4337e2dcef2e7", + "Repository": "RSPM", "Requirements": [ "askpass", "credentials", @@ -537,366 +548,362 @@ "rstudioapi", "sys", "zip" - ] + ], + "Hash": "8fddce7cbd59467106266a6e93e253b4" }, "gh": { "Package": "gh", - "Version": "1.3.1", + "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b6a12054ee13dce0f6696c019c10e539", + "Repository": "RSPM", "Requirements": [ "cli", "gitcreds", "httr", "ini", "jsonlite" - ] + ], + "Hash": "38c2580abbda249bd6afeec00d14f531" }, "git2r": { "Package": "git2r", - "Version": "0.28.0", + "Version": "0.29.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "f64fd34026f6025de71a4354800e6d79", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "graphics", + "utils" + ], + "Hash": "b114135c4749076bd5ef74a5827b6f62" }, "gitcreds": { "Package": "gitcreds", "Version": "0.1.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "f3aefccc1cc50de6338146b62f115de8", - "Requirements": [] + "Repository": "RSPM", + "Hash": "f3aefccc1cc50de6338146b62f115de8" }, "glue": { "Package": "glue", "Version": "1.6.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "methods" + ], + "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e" }, "highr": { "Package": "highr", - "Version": "0.8", + "Version": "0.9", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4dc5bb88961e347a0f4d8aad597cbfac", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "xfun" + ], + "Hash": "8eb36c8125038e648e5d111c0d7b2ed4" }, "hms": { "Package": "hms", - "Version": "1.0.0", + "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "bf552cdd96f5969873afdac7311c7d0d", + "Repository": "RSPM", "Requirements": [ "ellipsis", "lifecycle", + "methods", "pkgconfig", "rlang", "vctrs" - ] + ], + "Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca" }, "htmltools": { "Package": "htmltools", - "Version": "0.5.3", + "Version": "0.5.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6496090a9e00f8354b811d1a2d47b566", + "Repository": "RSPM", "Requirements": [ + "R", "base64enc", "digest", "fastmap", - "rlang" - ] + "grDevices", + "rlang", + "utils" + ], + "Hash": "526c484233f42522278ab06fb185cb26" }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.5.3", + "Version": "1.5.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6fdaa86d0700f8b3e92ee3c445a5a10d", + "Repository": "RSPM", "Requirements": [ + "grDevices", "htmltools", "jsonlite", "yaml" - ] + ], + "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb" }, "httpuv": { "Package": "httpuv", - "Version": "1.5.5", + "Version": "1.6.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b9d5d39be2150cf86538b8488334b8f8", + "Repository": "RSPM", "Requirements": [ - "BH", + "R", "R6", "Rcpp", "later", - "promises" - ] + "promises", + "utils" + ], + "Hash": "97fe71f0a4a1c9890e6c2128afa04bc0" }, "httr": { "Package": "httr", "Version": "1.4.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a525aba14184fec243f9eaec62fbed43", + "Repository": "RSPM", "Requirements": [ + "R", "R6", "curl", "jsonlite", "mime", "openssl" - ] + ], + "Hash": "a525aba14184fec243f9eaec62fbed43" }, "hunspell": { "Package": "hunspell", "Version": "3.0.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "3987784c19192ad0f2261c456d936df1", + "Repository": "RSPM", "Requirements": [ + "R", "Rcpp", "digest" - ] + ], + "Hash": "3987784c19192ad0f2261c456d936df1" }, "ini": { "Package": "ini", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6154ec2223172bce8162d4153cda21f7", - "Requirements": [] + "Repository": "RSPM", + "Hash": "6154ec2223172bce8162d4153cda21f7" }, "jquerylib": { "Package": "jquerylib", "Version": "0.1.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "5aab57a3bd297eee1c1d862735972182", + "Repository": "RSPM", "Requirements": [ "htmltools" - ] + ], + "Hash": "5aab57a3bd297eee1c1d862735972182" }, "jsonlite": { "Package": "jsonlite", - "Version": "1.7.2", + "Version": "1.8.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "98138e0994d41508c7a6b84a0600cfcb", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "methods" + ], + "Hash": "d07e729b27b372429d42d24d503613a0" }, "knitr": { "Package": "knitr", "Version": "1.40", "Source": "Repository", - "Repository": "CRAN", - "Hash": "caea8b0f899a0b1738444b9bc47067e7", + "Repository": "RSPM", "Requirements": [ + "R", "evaluate", "highr", + "methods", "stringr", + "tools", "xfun", "yaml" - ] + ], + "Hash": "caea8b0f899a0b1738444b9bc47067e7" + }, + "languageserver": { + "Package": "languageserver", + "Version": "0.3.12", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R6", + "callr", + "collections", + "fs", + "jsonlite", + "lintr", + "parallel", + "roxygen2", + "stringi", + "styler", + "tools", + "utils", + "xml2", + "xmlparsedata" + ], + "Hash": "f62ed8b09fd56cd70291bd077bc52c4b" }, "later": { "Package": "later", - "Version": "1.1.0.1", + "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "d0a62b247165aabf397fded504660d8a", + "Repository": "RSPM", "Requirements": [ - "BH", "Rcpp", "rlang" - ] - }, - "lattice": { - "Package": "lattice", - "Version": "0.20-41", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "fbd9285028b0263d76d18c95ae51a53d", - "Requirements": [] + ], + "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e" }, "lazyeval": { "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "d908914ae53b04d4c0c0fd72ecc35370", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "d908914ae53b04d4c0c0fd72ecc35370" }, "lifecycle": { "Package": "lifecycle", "Version": "1.0.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "001cecbeac1cff9301bdc3775ee46a86", + "Repository": "RSPM", "Requirements": [ + "R", "cli", "glue", "rlang" - ] + ], + "Hash": "001cecbeac1cff9301bdc3775ee46a86" }, "lintr": { "Package": "lintr", - "Version": "2.0.1", + "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "023cecbdc0a32f86ad3cb1734c018d2e", + "Repository": "RSPM", "Requirements": [ + "R", + "backports", "codetools", "crayon", "cyclocomp", "digest", - "httr", + "glue", "jsonlite", "knitr", "rex", - "rstudioapi", - "testthat", + "stats", + "utils", "xml2", "xmlparsedata" - ] + ], + "Hash": "b21ebd652d940f099915221f3328ab7b" }, "lubridate": { "Package": "lubridate", - "Version": "1.7.10", + "Version": "1.8.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "1ebfdc8a3cfe8fe19184f5481972b092", + "Repository": "RSPM", "Requirements": [ - "Rcpp", - "generics" - ] + "R", + "cpp11", + "generics", + "methods" + ], + "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a" }, "magrittr": { "Package": "magrittr", - "Version": "2.0.3", + "Version": "2.0.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "7ce2733a9826b3aeb1775d56fd305472", - "Requirements": [] - }, - "markdown": { - "Package": "markdown", - "Version": "1.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "61e4a10781dd00d7d81dd06ca9b94e95", - "Requirements": [ - "mime", - "xfun" - ] + "Repository": "RSPM", + "Hash": "cdc87ecd81934679d1557633d8e1fe51" }, "memoise": { "Package": "memoise", - "Version": "2.0.0", + "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a0bc51650201a56d00a4798523cc91b3", + "Repository": "RSPM", "Requirements": [ "cachem", "rlang" - ] - }, - "mgcv": { - "Package": "mgcv", - "Version": "1.8-34", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "bd4a6c4b600f58651d60d381b0e9a397", - "Requirements": [ - "Matrix", - "nlme" - ] + ], + "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" }, "mime": { "Package": "mime", - "Version": "0.10", + "Version": "0.12", "Source": "Repository", - "Repository": "CRAN", - "Hash": "26fa77e707223e1ce042b2b5d09993dc", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "tools" + ], + "Hash": "18e9c28c1d3ca1560ce30658b22ce104" }, "miniUI": { "Package": "miniUI", "Version": "0.1.1.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "fec5f52652d60615fdb3957b3d74324a", + "Repository": "RSPM", "Requirements": [ "htmltools", - "shiny" - ] - }, - "mockery": { - "Package": "mockery", - "Version": "0.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "313fa6504824ba5aab9308412135fb5f", - "Requirements": [ - "testthat" - ] - }, - "nlme": { - "Package": "nlme", - "Version": "3.1-152", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "35de1ce639f20b5e10f7f46260730c65", - "Requirements": [ - "lattice" - ] - }, - "nnet": { - "Package": "nnet", - "Version": "7.3-15", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "b67ac021b3fb3a4b69d0d3c2bc049e9f", - "Requirements": [] + "shiny", + "utils" + ], + "Hash": "fec5f52652d60615fdb3957b3d74324a" }, "openssl": { "Package": "openssl", - "Version": "2.0.4", + "Version": "2.0.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "e86c5ffeb8474a9e03d75f5d2919683e", + "Repository": "RSPM", "Requirements": [ "askpass" - ] + ], + "Hash": "cf4329aac12c2c44089974559c18e446" }, "pillar": { "Package": "pillar", - "Version": "1.5.1", + "Version": "1.9.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "24622aa4a0d3de3463c34513edca99b2", + "Repository": "RSPM", "Requirements": [ "cli", - "crayon", - "ellipsis", "fansi", + "glue", "lifecycle", "rlang", "utf8", + "utils", "vctrs" - ] + ], + "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.2.0", + "Version": "1.3.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "725fcc30222d4d11ec68efb8ff11a9af", + "Repository": "RSPM", "Requirements": [ + "R", "R6", "callr", "cli", @@ -905,23 +912,26 @@ "prettyunits", "rprojroot", "withr" - ] + ], + "Hash": "66d2adfed274daf81ccfe77d974c3b9b" }, "pkgconfig": { "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "01f28d4278f15c76cddbea05899c5d6f", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "01f28d4278f15c76cddbea05899c5d6f" }, "pkgdown": { "Package": "pkgdown", - "Version": "2.0.6", + "Version": "2.0.7", "Source": "Repository", - "Repository": "CRAN", - "Hash": "f958d0b2a5dabc5ffd414f062b1ffbe7", + "Repository": "RSPM", "Requirements": [ + "R", "bslib", "callr", "cli", @@ -942,375 +952,396 @@ "withr", "xml2", "yaml" - ] + ], + "Hash": "16fa15449c930bf3a7761d3c68f8abf9" }, "pkgload": { "Package": "pkgload", - "Version": "1.2.0", + "Version": "1.2.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "cb57de933545960a86f03513e4bd2911", + "Repository": "RSPM", "Requirements": [ "cli", "crayon", "desc", - "pkgbuild", + "methods", "rlang", "rprojroot", "rstudioapi", + "utils", "withr" - ] + ], + "Hash": "7533cd805940821bf23eaf3c8d4c1735" }, "praise": { "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a555924add98c99d2f411e37e7d25e9f", - "Requirements": [] + "Repository": "RSPM", + "Hash": "a555924add98c99d2f411e37e7d25e9f" }, "prettyunits": { "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", - "Requirements": [] + "Repository": "RSPM", + "Hash": "95ef9167b75dde9d2ccc3c7528393e7e" }, "processx": { "Package": "processx", - "Version": "3.8.0", + "Version": "3.6.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a33ee2d9bf07564efb888ad98410da84", + "Repository": "RSPM", "Requirements": [ + "R", "R6", - "ps" - ] + "ps", + "utils" + ], + "Hash": "a11891e28c1f1e5ddd773ba1b8c07cf6" }, "progress": { "Package": "progress", "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061", + "Repository": "RSPM", "Requirements": [ "R6", "crayon", "hms", "prettyunits" - ] + ], + "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061" }, "promises": { "Package": "promises", "Version": "1.2.0.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4ab2c43adb4d4699cf3690acd378d75d", + "Repository": "RSPM", "Requirements": [ "R6", "Rcpp", "later", "magrittr", - "rlang" - ] + "rlang", + "stats" + ], + "Hash": "4ab2c43adb4d4699cf3690acd378d75d" }, "ps": { "Package": "ps", "Version": "1.6.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "32620e2001c1dce1af49c49dccbb9420", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "32620e2001c1dce1af49c49dccbb9420" }, "purrr": { "Package": "purrr", "Version": "0.3.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "97def703420c8ab10d8f0e6c72101e02", + "Repository": "RSPM", "Requirements": [ + "R", "magrittr", "rlang" - ] + ], + "Hash": "97def703420c8ab10d8f0e6c72101e02" }, "ragg": { "Package": "ragg", - "Version": "1.2.4", + "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0db17bd5a1d4abfec76487b6f5dd957b", + "Repository": "RSPM", "Requirements": [ "systemfonts", "textshaping" - ] + ], + "Hash": "14932bb6f2739c771ca4ceaba6b4248e" }, "rappdirs": { "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "5e3c5dc0b071b21fa128676560dbe94d", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "5e3c5dc0b071b21fa128676560dbe94d" }, "rcmdcheck": { "Package": "rcmdcheck", - "Version": "1.3.3", + "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "ed95895886dab6d2a584da45503555da", + "Repository": "RSPM", "Requirements": [ "R6", "callr", "cli", - "crayon", + "curl", "desc", "digest", "pkgbuild", "prettyunits", "rprojroot", "sessioninfo", + "utils", "withr", "xopen" - ] + ], + "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" }, "readxl": { "Package": "readxl", "Version": "1.3.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "63537c483c2dbec8d9e3183b3735254a", + "Repository": "RSPM", "Requirements": [ "Rcpp", "cellranger", "progress", - "tibble" - ] + "tibble", + "utils" + ], + "Hash": "63537c483c2dbec8d9e3183b3735254a" }, "rematch": { "Package": "rematch", "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c66b930d20bb6d858cd18e1cebcfae5c", - "Requirements": [] + "Repository": "RSPM", + "Hash": "c66b930d20bb6d858cd18e1cebcfae5c" }, "rematch2": { "Package": "rematch2", "Version": "2.1.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "76c9e04c712a05848ae7a23d2f170a40", + "Repository": "RSPM", "Requirements": [ "tibble" - ] + ], + "Hash": "76c9e04c712a05848ae7a23d2f170a40" }, "remotes": { "Package": "remotes", - "Version": "2.2.0", + "Version": "2.4.2.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "430a0908aee75b1fcba0e62857cab0ce", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "63d15047eb239f95160112bcadc4fcb9" }, "renv": { "Package": "renv", - "Version": "0.16.0", + "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c9e8442ab69bc21c9697ecf856c1e6c7", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "c321cd99d56443dbffd1c9e673c0c1a2" }, "rex": { "Package": "rex", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "093584b944440c5cd07a696b3c8e0e4c", + "Repository": "RSPM", "Requirements": [ "lazyeval" - ] + ], + "Hash": "ae34cd56890607370665bee5bd17812f" }, "rlang": { "Package": "rlang", - "Version": "1.0.6", + "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4ed1f8336c8d52c3e750adcdc57228a7", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "dc079ccd156cde8647360f473c1fa718" }, "rmarkdown": { "Package": "rmarkdown", "Version": "2.17", "Source": "Repository", - "Repository": "CRAN", - "Hash": "e97c8be593e010f93520e8215c0f9189", + "Repository": "RSPM", "Requirements": [ + "R", "bslib", "evaluate", "htmltools", "jquerylib", "jsonlite", "knitr", + "methods", "stringr", "tinytex", + "tools", + "utils", "xfun", "yaml" - ] + ], + "Hash": "e97c8be593e010f93520e8215c0f9189" }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.1", + "Version": "7.2.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "da1f278262e563c835345872f2fef537", + "Repository": "RSPM", "Requirements": [ + "R", "R6", "brew", "cli", "commonmark", "cpp11", "desc", - "digest", "knitr", + "methods", "pkgload", "purrr", "rlang", "stringi", "stringr", + "utils", "withr", "xml2" - ] - }, - "rpart": { - "Package": "rpart", - "Version": "4.1-15", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "9787c1fcb680e655d062e7611cadf78e", - "Requirements": [] + ], + "Hash": "7b153c746193b143c14baa072bae4e27" }, "rprojroot": { "Package": "rprojroot", "Version": "2.0.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "249d8cd1e74a8f6a26194a91b47f21d1", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "249d8cd1e74a8f6a26194a91b47f21d1" }, "rstudioapi": { "Package": "rstudioapi", "Version": "0.13", "Source": "Repository", - "Repository": "CRAN", - "Hash": "06c85365a03fdaf699966cc1d3cf53ea", - "Requirements": [] + "Repository": "RSPM", + "Hash": "06c85365a03fdaf699966cc1d3cf53ea" }, "rversions": { "Package": "rversions", - "Version": "2.0.2", + "Version": "2.1.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0ec41191f744d0f5afad8c6f35cc36e4", + "Repository": "RSPM", "Requirements": [ "curl", + "utils", "xml2" - ] + ], + "Hash": "f88fab00907b312f8b23ec13e2d437cb" }, "sass": { "Package": "sass", - "Version": "0.4.2", + "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "1b191143d7d3444d504277843f3a95fe", + "Repository": "RSPM", "Requirements": [ "R6", "fs", "htmltools", "rappdirs", "rlang" - ] + ], + "Hash": "50cf822feb64bb3977bda0b7091be623" }, "sessioninfo": { "Package": "sessioninfo", - "Version": "1.1.1", + "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "308013098befe37484df72c39cf90d6e", + "Repository": "RSPM", "Requirements": [ + "R", "cli", - "withr" - ] + "tools", + "utils" + ], + "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f" }, "shiny": { "Package": "shiny", - "Version": "1.6.0", + "Version": "1.7.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6e3b6ae7fe02b5859e4bb277f218b8ae", + "Repository": "RSPM", "Requirements": [ + "R", "R6", "bslib", "cachem", "commonmark", "crayon", - "digest", "ellipsis", "fastmap", + "fontawesome", "glue", + "grDevices", "htmltools", "httpuv", "jsonlite", "later", "lifecycle", + "methods", "mime", "promises", "rlang", "sourcetools", + "tools", + "utils", "withr", "xtable" - ] + ], + "Hash": "00344c227c7bd0ab5d78052c5d736c44" }, "sourcetools": { "Package": "sourcetools", "Version": "0.1.7", "Source": "Repository", - "Repository": "CRAN", - "Hash": "947e4e02a79effa5d512473e10f41797", - "Requirements": [] - }, - "spatial": { - "Package": "spatial", - "Version": "7.3-13", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "8d0918547149f72e78ae942ccd1fdbc7", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "947e4e02a79effa5d512473e10f41797" }, "spelling": { "Package": "spelling", "Version": "2.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b8c899a5c83f0d897286550481c91798", + "Repository": "RSPM", "Requirements": [ "commonmark", "hunspell", "knitr", "xml2" - ] + ], + "Hash": "b8c899a5c83f0d897286550481c91798" }, "staged.dependencies": { "Package": "staged.dependencies", - "Version": "0.2.7", + "Version": "0.3.1", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", - "RemoteRepo": "staged.dependencies", "RemoteUsername": "openpharma", - "RemoteRef": "HEAD", - "RemoteSha": "669f45a95d8772899551ad51fc3b38a3b5a1056a", - "Hash": "348648f944ce5dbcbdc2b120c9ba3a3c", + "RemoteRepo": "staged.dependencies", + "RemoteRef": "main", + "RemoteSha": "1ab184a029bef8839a57bb6acd1c5c919cf1fd89", "Requirements": [ "desc", "devtools", @@ -1321,91 +1352,92 @@ "glue", "httr", "jsonlite", + "methods", "rcmdcheck", "remotes", "rlang", + "stats", "tidyr", + "utils", "withr", "yaml" - ] + ], + "Hash": "ea298f9fb221a8c7ca4c9e55e9c29b48" }, "stringi": { "Package": "stringi", - "Version": "1.5.3", + "Version": "1.7.6", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a063ebea753c92910a4cca7b18bc1f05", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "stats", + "tools", + "utils" + ], + "Hash": "bba431031d30789535745a9627ac9271" }, "stringr": { "Package": "stringr", "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0759e6b6c0957edb1311028a49a35e76", + "Repository": "RSPM", "Requirements": [ + "R", "glue", "magrittr", "stringi" - ] + ], + "Hash": "0759e6b6c0957edb1311028a49a35e76" }, "styler": { "Package": "styler", - "Version": "1.8.0", + "Version": "1.9.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c855e70eb69b3dd8883660b7110e0c44", + "Repository": "RSPM", "Requirements": [ + "R", "R.cache", "cli", "magrittr", "purrr", "rlang", "rprojroot", + "tools", "vctrs", "withr" - ] - }, - "survival": { - "Package": "survival", - "Version": "3.2-10", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "6b7453cd9bb32b12577c78d54eeea56a", - "Requirements": [ - "Matrix" - ] + ], + "Hash": "ed8c90822b7da46beee603f263a85fe0" }, "sys": { "Package": "sys", "Version": "3.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b227d13e29222b4574486cfcbde077fa", - "Requirements": [] + "Repository": "RSPM", + "Hash": "b227d13e29222b4574486cfcbde077fa" }, "systemfonts": { "Package": "systemfonts", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "90b28393209827327de889f49935140a", + "Repository": "RSPM", "Requirements": [ + "R", "cpp11" - ] + ], + "Hash": "90b28393209827327de889f49935140a" }, "testthat": { "Package": "testthat", - "Version": "3.0.2", + "Version": "3.1.7", "Source": "Repository", - "Repository": "CRAN", - "Hash": "495e0434d9305716b6a87031570ce109", + "Repository": "RSPM", "Requirements": [ + "R", "R6", "brio", "callr", "cli", - "crayon", "desc", "digest", "ellipsis", @@ -1413,50 +1445,56 @@ "jsonlite", "lifecycle", "magrittr", + "methods", "pkgload", "praise", "processx", "ps", "rlang", + "utils", "waldo", "withr" - ] + ], + "Hash": "7eb5fd202a61d2fb78af5869b6c08998" }, "textshaping": { "Package": "textshaping", "Version": "0.3.6", "Source": "Repository", - "Repository": "CRAN", - "Hash": "1ab6223d3670fac7143202cb6a2d43d5", + "Repository": "RSPM", "Requirements": [ + "R", "cpp11", "systemfonts" - ] + ], + "Hash": "1ab6223d3670fac7143202cb6a2d43d5" }, "tibble": { "Package": "tibble", - "Version": "3.1.0", + "Version": "3.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4d894a114dbd4ecafeda5074e7c538e6", + "Repository": "RSPM", "Requirements": [ - "ellipsis", + "R", "fansi", "lifecycle", "magrittr", + "methods", "pillar", "pkgconfig", "rlang", + "utils", "vctrs" - ] + ], + "Hash": "37695ff125982007d42a59ad10982ff2" }, "tidyr": { "Package": "tidyr", - "Version": "1.1.3", + "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "450d7dfaedde58e28586b854eeece4fa", + "Repository": "RSPM", "Requirements": [ + "R", "cpp11", "dplyr", "ellipsis", @@ -1467,40 +1505,44 @@ "rlang", "tibble", "tidyselect", + "utils", "vctrs" - ] + ], + "Hash": "d8b95b7fee945d7da6888cf7eb71a49c" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.1.0", + "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6ea435c354e8448819627cf686f66e0a", + "Repository": "RSPM", "Requirements": [ - "ellipsis", + "R", + "cli", "glue", - "purrr", + "lifecycle", "rlang", - "vctrs" - ] + "vctrs", + "withr" + ], + "Hash": "79540e5fcd9e0435af547d885f184fd5" }, "tinytex": { "Package": "tinytex", - "Version": "0.42", + "Version": "0.37", "Source": "Repository", - "Repository": "CRAN", - "Hash": "7629c6c1540835d5248e6e7df265fa74", + "Repository": "RSPM", "Requirements": [ "xfun" - ] + ], + "Hash": "a80abeb527a977e4bef21873d29222dd" }, "usethis": { "Package": "usethis", - "Version": "2.1.6", + "Version": "2.1.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a67a22c201832b12c036cc059f1d137d", + "Repository": "RSPM", "Requirements": [ + "R", "cli", "clipr", "crayon", @@ -1517,134 +1559,143 @@ "rlang", "rprojroot", "rstudioapi", + "stats", + "utils", "whisker", "withr", "yaml" - ] + ], + "Hash": "c499f488e6dd7718accffaee5bc5a79b" }, "utf8": { "Package": "utf8", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c3ad47dc6da0751f18ed53c4613e3ac7", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "c9c462b759a5cc844ae25b5942654d13" }, "vctrs": { "Package": "vctrs", - "Version": "0.5.0", + "Version": "0.6.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "001fd6a5ebfff8316baf9fb2b5516dc9", + "Repository": "RSPM", "Requirements": [ + "R", "cli", "glue", "lifecycle", "rlang" - ] - }, - "visNetwork": { - "Package": "visNetwork", - "Version": "2.0.9", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "12545f2acf49d1d346d075580122d89c", - "Requirements": [ - "htmltools", - "htmlwidgets", - "jsonlite", - "magrittr" - ] + ], + "Hash": "7e877404388794361277be95d8445de8" }, "waldo": { "Package": "waldo", - "Version": "0.2.5", + "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "20c45f1d511a3f730b7b469f4d11e104", + "Repository": "RSPM", "Requirements": [ "cli", "diffobj", "fansi", "glue", + "methods", "rematch2", "rlang", "tibble" - ] + ], + "Hash": "035fba89d0c86e2113120f93301b98ad" }, "whisker": { "Package": "whisker", "Version": "0.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "ca970b96d894e90397ed20637a0c1bbe", - "Requirements": [] + "Repository": "RSPM", + "Hash": "ca970b96d894e90397ed20637a0c1bbe" }, "withr": { "Package": "withr", "Version": "2.5.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c0e49a9760983e81e55cdd9be92e7182", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats" + ], + "Hash": "c0e49a9760983e81e55cdd9be92e7182" }, "xfun": { "Package": "xfun", "Version": "0.34", "Source": "Repository", - "Repository": "CRAN", - "Hash": "9eba2411b0b1f879797141bd24df7407", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "stats", + "tools" + ], + "Hash": "9eba2411b0b1f879797141bd24df7407" }, "xml2": { "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "40682ed6a969ea5abfd351eb67833adc", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "methods" + ], + "Hash": "40682ed6a969ea5abfd351eb67833adc" }, "xmlparsedata": { "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "45e4bf3c46476896e821fc0a408fb4fc", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "45e4bf3c46476896e821fc0a408fb4fc" }, "xopen": { "Package": "xopen", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6c85f015dee9cc7710ddd20f86881f58", + "Repository": "RSPM", "Requirements": [ + "R", "processx" - ] + ], + "Hash": "6c85f015dee9cc7710ddd20f86881f58" }, "xtable": { "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" }, "yaml": { "Package": "yaml", - "Version": "2.2.1", + "Version": "2.3.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "2826c5d9efb0a88f657c7a679c7106db", - "Requirements": [] + "Repository": "RSPM", + "Hash": "458bb38374d73bf83b1bb85e353da200" }, "zip": { "Package": "zip", - "Version": "2.2.2", + "Version": "2.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88", - "Requirements": [] + "Repository": "RSPM", + "Hash": "c7eef2996ac270a18c2715c997a727c5" } } } diff --git a/renv/.gitignore b/renv/.gitignore index 6ae4167d..2649d0a0 100644 --- a/renv/.gitignore +++ b/renv/.gitignore @@ -5,3 +5,4 @@ local/ lock/ python/ staging/ +profile diff --git a/renv/activate.R b/renv/activate.R index 019b5a66..cc742fc9 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,8 @@ local({ # the requested version of renv - version <- "0.16.0" + version <- "1.0.0" + attr(version, "sha") <- NULL # the project directory project <- getwd() @@ -60,21 +61,75 @@ local({ # load bootstrap tools `%||%` <- function(x, y) { - if (is.environment(x) || length(x)) x else y + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix } bootstrap <- function(version, library) { + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + # attempt to download renv - tarball <- tryCatch(renv_bootstrap_download(version), error = identity) - if (inherits(tarball, "error")) - stop("failed to download renv ", version) + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) # now attempt to install - status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) - if (inherits(status, "error")) - stop("failed to install renv ", version) + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + return(invisible()) } renv_bootstrap_tests_running <- function() { @@ -83,28 +138,32 @@ local({ renv_bootstrap_repos <- function() { + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + # check for repos override repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) - if (!is.na(repos)) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + return(repos) + } + # check for lockfile repositories repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) if (!inherits(repos, "error") && length(repos)) return(repos) - # if we're testing, re-use the test repositories - if (renv_bootstrap_tests_running()) - return(getOption("renv.tests.repos")) - # retrieve current repos repos <- getOption("repos") # ensure @CRAN@ entries are resolved - repos[repos == "@CRAN@"] <- getOption( - "renv.repos.cran", - "https://cloud.r-project.org" - ) + repos[repos == "@CRAN@"] <- cran # add in renv.bootstrap.repos if set default <- c(FALLBACK = "https://cloud.r-project.org") @@ -143,33 +202,34 @@ local({ renv_bootstrap_download <- function(version) { - # if the renv version number has 4 components, assume it must - # be retrieved via github - nv <- numeric_version(version) - components <- unclass(nv)[[1]] - - # if this appears to be a development version of 'renv', we'll - # try to restore from github - dev <- length(components) == 4L - - # begin collecting different methods for finding renv - methods <- c( - renv_bootstrap_download_tarball, - if (dev) - renv_bootstrap_download_github - else c( - renv_bootstrap_download_cran_latest, - renv_bootstrap_download_cran_archive + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) ) - ) + + } for (method in methods) { - path <- tryCatch(method(version), error = identity) + path <- tryCatch(method(), error = identity) if (is.character(path) && file.exists(path)) return(path) } - stop("failed to download renv ", version) + stop("All download methods failed") } @@ -233,8 +293,6 @@ local({ type <- spec$type repos <- spec$repos - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - baseurl <- utils::contrib.url(repos = repos, type = type) ext <- if (identical(type, "source")) ".tar.gz" @@ -251,13 +309,10 @@ local({ condition = identity ) - if (inherits(status, "condition")) { - message("FAILED") + if (inherits(status, "condition")) return(FALSE) - } # report success and return - message("OK (downloaded ", type, ")") destfile } @@ -314,8 +369,6 @@ local({ urls <- file.path(repos, "src/contrib/Archive/renv", name) destfile <- file.path(tempdir(), name) - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - for (url in urls) { status <- tryCatch( @@ -323,14 +376,11 @@ local({ condition = identity ) - if (identical(status, 0L)) { - message("OK") + if (identical(status, 0L)) return(destfile) - } } - message("FAILED") return(FALSE) } @@ -344,8 +394,7 @@ local({ return() # allow directories - info <- file.info(tarball, extra_cols = FALSE) - if (identical(info$isdir, TRUE)) { + if (dir.exists(tarball)) { name <- sprintf("renv_%s.tar.gz", version) tarball <- file.path(tarball, name) } @@ -354,7 +403,7 @@ local({ if (!file.exists(tarball)) { # let the user know we weren't able to honour their request - fmt <- "* RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." msg <- sprintf(fmt, tarball) warning(msg) @@ -363,10 +412,7 @@ local({ } - fmt <- "* Bootstrapping with tarball at path '%s'." - msg <- sprintf(fmt, tarball) - message(msg) - + catf("- Using local tarball '%s'.", tarball) tarball } @@ -393,8 +439,6 @@ local({ on.exit(do.call(base::options, saved), add = TRUE) } - message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) - url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) name <- sprintf("renv_%s.tar.gz", version) destfile <- file.path(tempdir(), name) @@ -404,26 +448,105 @@ local({ condition = identity ) - if (!identical(status, 0L)) { - message("FAILED") + if (!identical(status, 0L)) return(FALSE) - } - message("OK") + renv_bootstrap_download_augment(destfile) + return(destfile) } + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a ‘gzip’ magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + renv_bootstrap_install <- function(version, tarball, library) { # attempt to install it into project library - message("* Installing renv ", version, " ... ", appendLF = FALSE) dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { # invoke using system2 so we can capture and report output bin <- R.home("bin") exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" - r <- file.path(bin, exe) + R <- file.path(bin, exe) args <- c( "--vanilla", "CMD", "INSTALL", "--no-multiarch", @@ -431,19 +554,7 @@ local({ shQuote(path.expand(tarball)) ) - output <- system2(r, args, stdout = TRUE, stderr = TRUE) - message("Done!") - - # check for successful install - status <- attr(output, "status") - if (is.numeric(status) && !identical(status, 0L)) { - header <- "Error installing renv:" - lines <- paste(rep.int("=", nchar(header)), collapse = "") - text <- c(header, lines, output) - writeLines(text, con = stderr()) - } - - status + system2(R, args, stdout = TRUE, stderr = TRUE) } @@ -653,34 +764,60 @@ local({ } - renv_bootstrap_validate_version <- function(version) { + renv_bootstrap_validate_version <- function(version, description = NULL) { - loadedversion <- utils::packageDescription("renv", fields = "Version") - if (version == loadedversion) - return(TRUE) + # resolve description file + description <- description %||% { + path <- getNamespaceInfo("renv", "path") + packageDescription("renv", lib.loc = dirname(path)) + } - # assume four-component versions are from GitHub; three-component - # versions are from CRAN - components <- strsplit(loadedversion, "[.-]")[[1]] - remote <- if (length(components) == 4L) - paste("rstudio/renv", loadedversion, sep = "@") + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) else - paste("renv", loadedversion, sep = "@") + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + remote <- if (!is.null(description[["RemoteSha"]])) { + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + } else { + paste("renv", description[["Version"]], sep = "@") + } + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = description[["RemoteSha"]] + ) fmt <- paste( "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", + "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", + "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", sep = "\n" ) - - msg <- sprintf(fmt, loadedversion, version, remote) - warning(msg, call. = FALSE) + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) FALSE } + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + renv_bootstrap_hash_text <- function(text) { hashfile <- tempfile("renv-hash-") @@ -700,6 +837,12 @@ local({ # warn if the version of renv loaded does not match renv_bootstrap_validate_version(version) + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warning) + # load the project renv::load(project) @@ -839,14 +982,66 @@ local({ } + renv_bootstrap_version_friendly <- function(version, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf("[sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = " ") + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + + renv_bootstrap_in_rstudio <- function() { + commandArgs()[[1]] == "RStudio" + } renv_json_read <- function(file = NULL, text = NULL) { + jlerr <- NULL + # if jsonlite is loaded, use that instead - if ("jsonlite" %in% loadedNamespaces()) - renv_json_read_jsonlite(file, text) + if ("jsonlite" %in% loadedNamespaces()) { + + json <- catch(renv_json_read_jsonlite(file, text)) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- catch(renv_json_read_default(file, text)) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) else - renv_json_read_default(file, text) + stop(json) } @@ -964,31 +1159,23 @@ local({ if (renv_bootstrap_load(project, libpath, version)) return(TRUE) - # load failed; inform user we're about to bootstrap - prefix <- paste("# Bootstrapping renv", version) - postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "") - header <- paste(prefix, postfix) - message(header) - - # perform bootstrap - bootstrap(version, libpath) - - # exit early if we're just testing bootstrap - if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) - return(TRUE) + if (renv_bootstrap_in_rstudio()) { + setHook("rstudio.sessionInit", function(...) { + renv_bootstrap_run(version, libpath) - # try again to load - if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { - message("* Successfully installed and loaded renv ", version, ".") - return(renv::load()) + # Work around buglet in RStudio if hook uses readline + tryCatch( + { + tools <- as.environment("tools:rstudio") + tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE) + }, + error = function(cnd) {} + ) + }) + } else { + renv_bootstrap_run(version, libpath) } - # failed to download or load renv; warn the user - msg <- c( - "Failed to find an renv installation: the project will not be loaded.", - "Use `renv::activate()` to re-initialize the project." - ) - - warning(paste(msg, collapse = "\n"), call. = FALSE) + invisible() }) diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 0f3ac2c8..5801ed10 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -4,7 +4,7 @@ "Repositories": [ { "Name": "CRAN", - "URL": "https://cloud.r-project.org" + "URL": "https://packagemanager.posit.co/cran/latest" }, { "Name": "RSPM", @@ -179,7 +179,7 @@ "Package": "callr", "Version": "3.7.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -188,11 +188,23 @@ ], "Hash": "9b2191ede20fa29828139b9900922e51" }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "rematch", + "tibble" + ], + "Hash": "f61dbaec772ccd2e17705c1e872e9e7c" + }, "cli": { "Package": "cli", "Version": "3.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "utils" @@ -219,6 +231,13 @@ ], "Hash": "019388fc48e48b3da0d3a76ff94608a8" }, + "collections": { + "Package": "collections", + "Version": "0.3.5", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "92537c684a3d2eaa6bd8f65c28ef97f0" + }, "commonmark": { "Package": "commonmark", "Version": "1.8.0", @@ -250,7 +269,7 @@ "Package": "cpp11", "Version": "0.4.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ed588261931ee3be2c700d22e94a29ab" }, "crayon": { @@ -320,7 +339,7 @@ "Package": "desc", "Version": "1.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -423,7 +442,7 @@ "Package": "dplyr", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -704,7 +723,7 @@ "Package": "knitr", "Version": "1.40", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "evaluate", @@ -717,6 +736,30 @@ ], "Hash": "caea8b0f899a0b1738444b9bc47067e7" }, + "languageserver": { + "Package": "languageserver", + "Version": "0.3.12", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R6", + "callr", + "collections", + "fs", + "jsonlite", + "lintr", + "parallel", + "roxygen2", + "stringi", + "styler", + "tools", + "utils", + "xml2", + "xmlparsedata" + ], + "Hash": "f62ed8b09fd56cd70291bd077bc52c4b" + }, "later": { "Package": "later", "Version": "1.3.0", @@ -742,7 +785,7 @@ "Package": "lifecycle", "Version": "1.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "cli", @@ -755,7 +798,7 @@ "Package": "lintr", "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "backports", @@ -841,7 +884,7 @@ "Package": "pillar", "Version": "1.9.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "cli", "fansi", @@ -886,7 +929,7 @@ "Package": "pkgdown", "Version": "2.0.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "bslib", @@ -948,7 +991,7 @@ "Package": "processx", "Version": "3.6.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -957,6 +1000,19 @@ ], "Hash": "a11891e28c1f1e5ddd773ba1b8c07cf6" }, + "progress": { + "Package": "progress", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R6", + "crayon", + "hms", + "prettyunits" + ], + "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061" + }, "promises": { "Package": "promises", "Version": "1.2.0.1", @@ -1038,6 +1094,27 @@ ], "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" }, + "readxl": { + "Package": "readxl", + "Version": "1.3.1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Rcpp", + "cellranger", + "progress", + "tibble", + "utils" + ], + "Hash": "63537c483c2dbec8d9e3183b3735254a" + }, + "rematch": { + "Package": "rematch", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c66b930d20bb6d858cd18e1cebcfae5c" + }, "rematch2": { "Package": "rematch2", "Version": "2.1.2", @@ -1050,7 +1127,7 @@ }, "remotes": { "Package": "remotes", - "Version": "2.4.2", + "Version": "2.4.2.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1060,17 +1137,17 @@ "tools", "utils" ], - "Hash": "227045be9aee47e6dda9bb38ac870d67" + "Hash": "63d15047eb239f95160112bcadc4fcb9" }, "renv": { "Package": "renv", - "Version": "0.17.0", + "Version": "1.0.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "utils" ], - "Hash": "ce3065fc1a0b64a859f55ac3998d6927" + "Hash": "c321cd99d56443dbffd1c9e673c0c1a2" }, "rex": { "Package": "rex", @@ -1086,7 +1163,7 @@ "Package": "rlang", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "utils" @@ -1097,7 +1174,7 @@ "Package": "rmarkdown", "Version": "2.17", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "bslib", @@ -1120,7 +1197,7 @@ "Package": "roxygen2", "Version": "7.2.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -1257,14 +1334,14 @@ }, "staged.dependencies": { "Package": "staged.dependencies", - "Version": "0.2.8", + "Version": "0.3.1", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteUsername": "openpharma", "RemoteRepo": "staged.dependencies", "RemoteRef": "main", - "RemoteSha": "ce7c112ba3d75cf48e4dd6310b3140ab0ec3b486", + "RemoteSha": "1ab184a029bef8839a57bb6acd1c5c919cf1fd89", "Requirements": [ "desc", "devtools", @@ -1285,7 +1362,7 @@ "withr", "yaml" ], - "Hash": "89f2e1d1009601f58f64b7092abcc0d7" + "Hash": "ea298f9fb221a8c7ca4c9e55e9c29b48" }, "stringi": { "Package": "stringi", @@ -1317,7 +1394,7 @@ "Package": "styler", "Version": "1.9.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R.cache", @@ -1354,7 +1431,7 @@ "Package": "testthat", "Version": "3.1.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -1396,7 +1473,7 @@ "Package": "tibble", "Version": "3.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "fansi", @@ -1437,7 +1514,7 @@ "Package": "tidyselect", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "cli", @@ -1504,7 +1581,7 @@ "Package": "vctrs", "Version": "0.6.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "cli", @@ -1518,7 +1595,7 @@ "Package": "waldo", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "cli", "diffobj", @@ -1555,7 +1632,7 @@ "Package": "xfun", "Version": "0.34", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "stats", "tools" diff --git a/renv/profiles/4.1/renv/settings.dcf b/renv/profiles/4.1/renv/settings.dcf deleted file mode 100644 index fd205f80..00000000 --- a/renv/profiles/4.1/renv/settings.dcf +++ /dev/null @@ -1,10 +0,0 @@ -bioconductor.version: -external.libraries: -ignored.packages: admiral, admiraldev, admiral.test, admiralci -package.dependency.fields: Imports, Depends, LinkingTo -r.version: -snapshot.type: implicit -use.cache: TRUE -vcs.ignore.cellar: TRUE -vcs.ignore.library: TRUE -vcs.ignore.local: TRUE diff --git a/renv/profiles/4.1/renv/settings.json b/renv/profiles/4.1/renv/settings.json new file mode 100644 index 00000000..0c8943c5 --- /dev/null +++ b/renv/profiles/4.1/renv/settings.json @@ -0,0 +1,24 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [ + "admiral", + "admiraldev", + "admiralci", + "pharmaversesdtm" + ], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "custom", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index 0bb8fc56..7661270b 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -4,7 +4,7 @@ "Repositories": [ { "Name": "CRAN", - "URL": "https://cloud.r-project.org" + "URL": "https://packagemanager.posit.co/cran/latest" }, { "Name": "RSPM", @@ -192,6 +192,18 @@ ], "Hash": "9b2191ede20fa29828139b9900922e51" }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "rematch", + "tibble" + ], + "Hash": "f61dbaec772ccd2e17705c1e872e9e7c" + }, "cli": { "Package": "cli", "Version": "3.6.0", @@ -223,6 +235,13 @@ ], "Hash": "c089a619a7fae175d149d89164f8c7d8" }, + "collections": { + "Package": "collections", + "Version": "0.3.7", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "90a0eda114ab0bef170ddbf5ef0cd93f" + }, "commonmark": { "Package": "commonmark", "Version": "1.8.1", @@ -429,7 +448,7 @@ "Package": "dplyr", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -749,6 +768,30 @@ ], "Hash": "8329a9bcc82943c8069104d4be3ee22d" }, + "languageserver": { + "Package": "languageserver", + "Version": "0.3.15", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R6", + "callr", + "collections", + "fs", + "jsonlite", + "lintr", + "parallel", + "roxygen2", + "stringi", + "styler", + "tools", + "utils", + "xml2", + "xmlparsedata" + ], + "Hash": "fbea0dd12b4f5dedbe3654e4b9cbbddc" + }, "later": { "Package": "later", "Version": "1.3.0", @@ -876,7 +919,7 @@ "Package": "pillar", "Version": "1.9.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "cli", "fansi", @@ -1007,6 +1050,19 @@ ], "Hash": "e9d21e79848e02e524bea6f5bd53e7e4" }, + "progress": { + "Package": "progress", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R6", + "crayon", + "hms", + "prettyunits" + ], + "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061" + }, "promises": { "Package": "promises", "Version": "1.2.0.1", @@ -1091,6 +1147,28 @@ ], "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" }, + "readxl": { + "Package": "readxl", + "Version": "1.4.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "cellranger", + "cpp11", + "progress", + "tibble", + "utils" + ], + "Hash": "2e6020b1399d95f947ed867045e9ca17" + }, + "rematch": { + "Package": "rematch", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c66b930d20bb6d858cd18e1cebcfae5c" + }, "rematch2": { "Package": "rematch2", "Version": "2.1.2", @@ -1103,7 +1181,7 @@ }, "remotes": { "Package": "remotes", - "Version": "2.4.2", + "Version": "2.4.2.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1113,17 +1191,17 @@ "tools", "utils" ], - "Hash": "227045be9aee47e6dda9bb38ac870d67" + "Hash": "63d15047eb239f95160112bcadc4fcb9" }, "renv": { "Package": "renv", - "Version": "0.17.0", + "Version": "1.0.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "utils" ], - "Hash": "ce3065fc1a0b64a859f55ac3998d6927" + "Hash": "c321cd99d56443dbffd1c9e673c0c1a2" }, "rex": { "Package": "rex", @@ -1173,7 +1251,7 @@ "Package": "roxygen2", "Version": "7.2.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -1310,14 +1388,14 @@ }, "staged.dependencies": { "Package": "staged.dependencies", - "Version": "0.2.8", + "Version": "0.3.1", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteUsername": "openpharma", "RemoteRepo": "staged.dependencies", "RemoteRef": "main", - "RemoteSha": "ce7c112ba3d75cf48e4dd6310b3140ab0ec3b486", + "RemoteSha": "1ab184a029bef8839a57bb6acd1c5c919cf1fd89", "Requirements": [ "desc", "devtools", @@ -1338,7 +1416,7 @@ "withr", "yaml" ], - "Hash": "89f2e1d1009601f58f64b7092abcc0d7" + "Hash": "ea298f9fb221a8c7ca4c9e55e9c29b48" }, "stringi": { "Package": "stringi", @@ -1587,7 +1665,7 @@ "Package": "vctrs", "Version": "0.6.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "cli", diff --git a/renv/profiles/4.2/renv/settings.dcf b/renv/profiles/4.2/renv/settings.dcf deleted file mode 100644 index fd205f80..00000000 --- a/renv/profiles/4.2/renv/settings.dcf +++ /dev/null @@ -1,10 +0,0 @@ -bioconductor.version: -external.libraries: -ignored.packages: admiral, admiraldev, admiral.test, admiralci -package.dependency.fields: Imports, Depends, LinkingTo -r.version: -snapshot.type: implicit -use.cache: TRUE -vcs.ignore.cellar: TRUE -vcs.ignore.library: TRUE -vcs.ignore.local: TRUE diff --git a/renv/profiles/4.2/renv/settings.json b/renv/profiles/4.2/renv/settings.json new file mode 100644 index 00000000..0c8943c5 --- /dev/null +++ b/renv/profiles/4.2/renv/settings.json @@ -0,0 +1,24 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [ + "admiral", + "admiraldev", + "admiralci", + "pharmaversesdtm" + ], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "custom", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/renv/profiles/4.3/renv.lock b/renv/profiles/4.3/renv.lock index b875a5b8..1ce40dba 100644 --- a/renv/profiles/4.3/renv.lock +++ b/renv/profiles/4.3/renv.lock @@ -1,10 +1,10 @@ { "R": { - "Version": "4.3.0", + "Version": "4.3.1", "Repositories": [ { "Name": "CRAN", - "URL": "https://cloud.r-project.org" + "URL": "https://packagemanager.posit.co/cran/latest" }, { "Name": "RSPM", @@ -192,6 +192,18 @@ ], "Hash": "9b2191ede20fa29828139b9900922e51" }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "rematch", + "tibble" + ], + "Hash": "f61dbaec772ccd2e17705c1e872e9e7c" + }, "cli": { "Package": "cli", "Version": "3.6.1", @@ -223,6 +235,13 @@ ], "Hash": "c089a619a7fae175d149d89164f8c7d8" }, + "collections": { + "Package": "collections", + "Version": "0.3.7", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "90a0eda114ab0bef170ddbf5ef0cd93f" + }, "commonmark": { "Package": "commonmark", "Version": "1.9.0", @@ -748,6 +767,30 @@ ], "Hash": "8329a9bcc82943c8069104d4be3ee22d" }, + "languageserver": { + "Package": "languageserver", + "Version": "0.3.15", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R6", + "callr", + "collections", + "fs", + "jsonlite", + "lintr", + "parallel", + "roxygen2", + "stringi", + "styler", + "tools", + "utils", + "xml2", + "xmlparsedata" + ], + "Hash": "fbea0dd12b4f5dedbe3654e4b9cbbddc" + }, "later": { "Package": "later", "Version": "1.3.0", @@ -1006,6 +1049,19 @@ ], "Hash": "e9d21e79848e02e524bea6f5bd53e7e4" }, + "progress": { + "Package": "progress", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R6", + "crayon", + "hms", + "prettyunits" + ], + "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061" + }, "promises": { "Package": "promises", "Version": "1.2.0.1", @@ -1090,6 +1146,28 @@ ], "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" }, + "readxl": { + "Package": "readxl", + "Version": "1.4.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "cellranger", + "cpp11", + "progress", + "tibble", + "utils" + ], + "Hash": "2e6020b1399d95f947ed867045e9ca17" + }, + "rematch": { + "Package": "rematch", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c66b930d20bb6d858cd18e1cebcfae5c" + }, "rematch2": { "Package": "rematch2", "Version": "2.1.2", @@ -1102,7 +1180,7 @@ }, "remotes": { "Package": "remotes", - "Version": "2.4.2", + "Version": "2.4.2.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1112,17 +1190,17 @@ "tools", "utils" ], - "Hash": "227045be9aee47e6dda9bb38ac870d67" + "Hash": "63d15047eb239f95160112bcadc4fcb9" }, "renv": { "Package": "renv", - "Version": "0.17.0", + "Version": "1.0.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "utils" ], - "Hash": "ce3065fc1a0b64a859f55ac3998d6927" + "Hash": "c321cd99d56443dbffd1c9e673c0c1a2" }, "rex": { "Package": "rex", @@ -1173,7 +1251,7 @@ "Package": "roxygen2", "Version": "7.2.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -1310,14 +1388,14 @@ }, "staged.dependencies": { "Package": "staged.dependencies", - "Version": "0.2.8", + "Version": "0.3.1", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteUsername": "openpharma", "RemoteRepo": "staged.dependencies", "RemoteRef": "main", - "RemoteSha": "ce7c112ba3d75cf48e4dd6310b3140ab0ec3b486", + "RemoteSha": "1ab184a029bef8839a57bb6acd1c5c919cf1fd89", "Requirements": [ "desc", "devtools", @@ -1338,7 +1416,7 @@ "withr", "yaml" ], - "Hash": "89f2e1d1009601f58f64b7092abcc0d7" + "Hash": "ea298f9fb221a8c7ca4c9e55e9c29b48" }, "stringi": { "Package": "stringi", diff --git a/renv/profiles/4.3/renv/settings.dcf b/renv/profiles/4.3/renv/settings.dcf deleted file mode 100644 index fd205f80..00000000 --- a/renv/profiles/4.3/renv/settings.dcf +++ /dev/null @@ -1,10 +0,0 @@ -bioconductor.version: -external.libraries: -ignored.packages: admiral, admiraldev, admiral.test, admiralci -package.dependency.fields: Imports, Depends, LinkingTo -r.version: -snapshot.type: implicit -use.cache: TRUE -vcs.ignore.cellar: TRUE -vcs.ignore.library: TRUE -vcs.ignore.local: TRUE diff --git a/renv/profiles/4.3/renv/settings.json b/renv/profiles/4.3/renv/settings.json new file mode 100644 index 00000000..0c8943c5 --- /dev/null +++ b/renv/profiles/4.3/renv/settings.json @@ -0,0 +1,24 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [ + "admiral", + "admiraldev", + "admiralci", + "pharmaversesdtm" + ], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "custom", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/renv/settings.dcf b/renv/settings.dcf deleted file mode 100644 index 0c5119c7..00000000 --- a/renv/settings.dcf +++ /dev/null @@ -1,6 +0,0 @@ -ignored.packages: -package.dependency.fields: Imports, Depends, LinkingTo -r.version: -snapshot.type: implicit -use.cache: TRUE -vcs.ignore.library: TRUE diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 00000000..0c8943c5 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,24 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [ + "admiral", + "admiraldev", + "admiralci", + "pharmaversesdtm" + ], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "custom", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +}