diff --git a/.Rbuildignore b/.Rbuildignore index 5e4a3338..0613275f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,4 @@ +^renv$ +^renv\.lock$ ^LICENSE\.md$ ^\.github$ diff --git a/.github/workflows/bookdown-test.yaml b/.github/workflows/bookdown-test.yaml index 5aba1710..fd9df0e4 100644 --- a/.github/workflows/bookdown-test.yaml +++ b/.github/workflows/bookdown-test.yaml @@ -8,7 +8,7 @@ on: - main - master -name: preview bookdown +name: Preview website jobs: build: @@ -16,15 +16,37 @@ jobs: runs-on: ubuntu-latest container: inseefrlab/utilitr:latest steps: - - name: Checkout Repository - if: ${{ github.repository == 'inseefrlab/utilitr' }} - env: - GITHUB_PAT: ${{ secrets.PAT }} - uses: actions/checkout@master - - name: Install Dependencies - if: ${{ github.repository == 'inseefrlab/utilitr' }} + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + ref: ${{ github.event.pull_request.head.ref }} + repository: ${{github.event.pull_request.head.repo.full_name}} + - name: Configure safe repository + run: | + git config --global --add safe.directory /__w/utilitR/utilitR + - name: Set RENV_PATHS_ROOT + shell: bash run: | - Rscript -e "install.packages(c('remotes', 'htmltools', 'sf'))" + echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV + - name: Install and activate renv + run: | + install.packages("yaml") + install.packages("renv") + renv::status() + renv::activate() + shell: Rscript {0} + - name: Get R and OS version + id: get-version + run: | + cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "") + cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "") + shell: Rscript {0} + - name: Restore Renv package cache + uses: actions/cache@v4 + with: + path: ${{ env.RENV_PATHS_ROOT }} + key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }} + restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}- env: GITHUB_PAT: ${{ secrets.PAT }} - name: Render Book diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 49c32c5a..219ea6e6 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -1,82 +1,42 @@ -name: Production de la documentation - - on: + workflow_dispatch: push: - branches: - - main - - master - - test + branches: renv + +name: Quarto Publish jobs: - docker: - if: "!contains(github.event.commits[0].message, '[skip ci]')" + build-deploy: runs-on: ubuntu-latest + permissions: + contents: write steps: - - - name: Checkout - uses: actions/checkout@v2 - - - name: Set up QEMU - if: ${{ github.repository == 'inseefrlab/utilitr' }} - uses: docker/setup-qemu-action@v1 - - - name: Set up Docker Buildx - if: ${{ github.repository == 'inseefrlab/utilitr' }} - uses: docker/setup-buildx-action@v1 - - - name: Login to DockerHub - if: ${{ github.repository == 'inseefrlab/utilitr' }} - uses: docker/login-action@v1 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - - - name: Build and push - if: ${{ github.repository == 'inseefrlab/utilitr' }} - id: docker_build - uses: docker/build-push-action@v2 - env: - GITHUB_PAT: ${{ secrets.PAT }} - with: - push: true - context: . - tags: | - inseefrlab/utilitr:latest - inseefrlab/utilitr:0.9.1 - - - name: Image digest - run: echo ${{ steps.docker_build.outputs.digest }} - website: - name: Render website - if: "!contains(github.event.commits[0].message, '[skip ci]')" - needs: docker - runs-on: ubuntu-latest - container: inseefrlab/utilitr:latest - steps: - - uses: actions/checkout@v4 + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set up Quarto environement + uses: quarto-dev/quarto-actions/setup@v2 + + - name: Install R dependency + run: | + Rscript -e "install.packages('yaml')" + + - name: Install R + uses: r-lib/actions/setup-r@v2 with: - fetch-depth: 0 - ref: ${{ github.event.pull_request.head.ref }} - repository: ${{github.event.pull_request.head.repo.full_name}} + r-version: '4.4.1' + - name: Install dependencies run: | - git config --global --add safe.directory /__w/utilitR/utilitR - Rscript -e "install.packages(c('remotes'))" - Rscript -e "remotes::install_github('rstudio/htmltools')" - Rscript -e "remotes::install_github('r-spatial/sf', dependencies = TRUE)" - env: - GITHUB_PAT: ${{ secrets.PAT }} - - name: Render Book - run: | - ls - git remote -v - git config --global user.email quarto-github-actions-publish@example.com - git config --global user.name "Quarto GHA Workflow Runner" - quarto render --to html - quarto publish gh-pages --no-render --no-browser - - uses: actions/upload-artifact@v2 + sudo ./docker/dependencies.sh + - name: Install R Dependencies + uses: r-lib/actions/setup-renv@v2 + with: + cache-version: 1 + + - name: Render and Publish + uses: quarto-dev/quarto-actions/publish@v2 with: - name: _public - path: _public/ - retention-days: 5 + target: gh-pages + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION deleted file mode 100644 index 679624bb..00000000 --- a/DESCRIPTION +++ /dev/null @@ -1,111 +0,0 @@ -Package: documentationR -Type: Book -Title: Documentation R de l'Insee -Version: 0.8.0 -Description: Ce dépôt comprend les fichiers relatifs à la - documentation R de l'Insee. -Authors@R: c( - person("Lino" , "Galiana" , role = c("aut", "cre"), email = "lino.galiana@insee.fr"), - person("Olivier" , "Meslin" , role = c("aut", "cre"), email = "olivier.meslin@insee.fr"), - person("Gilles" , "Fidani" , role = "ctb", email = "gilles.fidani@insee.fr"), - person("Pierre" , "Lamarche" , role = "ctb", email = "pierre.lamarche@insee.fr"), - person("Gaëlle" , "Genin" , role = "ctb", email = "gaelle.genin@insee.fr"), - person("Romain" , "Lesur" , role = "ctb", email = "romain.lesur@insee.fr"), - person("Pierre-Yves" , "Berrard" , role = "ctb", email = "pierre-yves.berrard@insee.fr"), - person("Cédric" , "Tassart" , role = "ctb", email = "cedric.tassart@insee.fr"), - person("Pascal" , "Mercier" , role = "ctb", email = "pascal.mercier@insee.fr"), - person("Arthur" , "Cazaubiel" , role = "ctb", email = "arthur.cazaubiel@insee.fr"), - person("Arlindo" , "Dos Santos", role = "ctb", email = "arlindo.dos-santos@insee.fr"), - person("Alexis" , "Eidelman" , role = "ctb", email = "alexis.eidelman@travail.gouv.fr"), - person("Claire" , "Legroux" , role = "ctb", email = "claire.legroux@insee.fr"), - person("Lionel" , "Cacheux" , role = "ctb", email = "lionel.cacheux@insee.fr"), - person("Marie-Emmanuelle", "Faure" , role = "ctb", email = "marie-emmanuelle.faure@insee.fr"), - person("Mathias" , "André" , role = "ctb", email = "mathias.andre@insee.fr"), - person("Sylvain" , "Daubrée" , role = "ctb", email = "sylvain.daubree@insee.fr"), - person("Raphaële" , "Adjerad" , role = "ctb", email = "raphaele.adjerad@sante.gouv.fr"), - person("Jean-Daniel" , "Lomenède" , role = "ctb", email = "jean-daniel.lomenede@developpement-durable.gouv.fr"), - person("Géraldine" , "Rochambeau", role = "ctb", email = "geraldine.Rochambeau@justice.gouv.fr"), - person("Milena" , "Suarez Castillo", role = "ctb", email = "milena.suarez-castillo@insee.fr"), - person("Violaine" , "Poirot" , role = "ctb", email = "violaine.poirot@justice.gouv.fr"), - person("Frédérique" , "Cornuau" , role = "ctb", email = "frederique.cornuau@justice.gouv.fr"), - person("Clément" , "Rousset" , role = "ctb", email = "clement.rousset@insee.fr"), - person("Aurélien" , "D'Isanto" , role = "ctb", email = "aurelien.disanto@insee.fr"), - person("Sébastien" , "Li-Thiao-Té", role = "ctb", email = "sebastien.li-thiao-te@travail.gouv.fr"), - person(given = NULL, family = "Institut National de la Statistique et des Études Économiques", role = "cph") - ) -License: Licence Ouverte 2.0 -Encoding: UTF-8 -URL: https://github.com/InseeFrLab/utilitR -VignetteBuilder: knitr -Imports: - base, - utils, - xfun (>= 0.19), - rmarkdown, - bookdown, - pagedown (>= 0.13.11), - data.table, - readr, - openxlsx, - import, - FactoMineR, - factoextra, - corrplot, - tmap, - ggplot2, - cartography, - import, - htmltools (>= 0.5.1), - doremifasolData, - readODS, - kableExtra, - fontawesome, - magick, - magrittr, - sass, - bslib, - downlit, - utilitr, - usethis, - renv, - remotes, - targets, - lintr, - parsedate, - lubridate, - zoo, - dygraphs, - yaml, - knitr, - desc, - dplyr, - MASS, - httr, - jsonlite, - arrow, - parallel, - tools, - stringr, - sf, - units, - rex, - duckdb, - DBI, - scales, - viridis, - readxl, - tibble, - tidyr, - doremifasol, - shiny -Suggests: - cranlogs, - haven, - rprojroot -Remotes: - rstudio/htmltools@v0.5.1, - rstudio/sass, - yihui/xfun, - InseeFrLab/utilitr-template, - hadley/emo, - InseeFrLab/doremifasolData@v0.2.0 diff --git a/Dockerfile b/Dockerfile index e501a492..8b82e01c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,15 +1,12 @@ -FROM inseefrlab/onyxia-rstudio:r4.3.2-2024.02.13 +FROM inseefrlab/onyxia-rstudio:r4.4.1-2024.10.14 # R packages COPY ./DESCRIPTION /tmp/build_image/ -RUN Rscript -e "install.packages(c('xfun','knitr', 'insee', 'OECD', 'htmltools'))" -RUN Rscript -e "remotes::install_deps('/tmp/build_image', dependencies = TRUE, upgrade = FALSE)" -RUN Rscript -e "remotes::install_github('kevinushey/rex')" -RUN Rscript -e "remotes::install_github('inseefrlab/inseelocaldata')" +RUN Rscript -e "install.packages(c('renv','yaml'))" RUN apt-get update \ && apt-get -qq install gnupg - + RUN sh -c 'echo "deb http://http.us.debian.org/debian stable main contrib non-free" >> /etc/apt/sources.list' \ && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138 \ && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0E98404D386FA1D9 \ diff --git a/docker/dependencies.sh b/docker/dependencies.sh new file mode 100755 index 00000000..cb204794 --- /dev/null +++ b/docker/dependencies.sh @@ -0,0 +1,43 @@ +#!/bin/bash + +# Update package lists +apt-get update && apt-get -qq install gnupg + +# Add Debian sources to apt and import necessary GPG keys +sh -c 'echo "deb http://http.us.debian.org/debian stable main contrib non-free" >> /etc/apt/sources.list' +apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138 +apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0E98404D386FA1D9 +apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 605C66F00D6C9793 + +# Update package lists and set debconf selections for mscorefonts installer +apt-get update +echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula select true" | debconf-set-selections + +# Install necessary packages without recommended dependencies +apt-get -qq install --no-install-recommends \ + ttf-mscorefonts-installer \ + fonts-liberation \ + fonts-freefont-ttf \ + libssl-dev + +apt-get -qq install --no-install-recommends \ + imagemagick \ + libmagick++-dev \ + ghostscript \ + libglpk40 + +apt-get -qq install --no-install-recommends \ + libgs-dev \ + librsvg2-dev \ + libwebp-dev \ + jq + +# Clean up apt cache +rm -rf /var/lib/apt/lists/* && rm -rf /src/*.deb + +# Upgrade packages +apt-get upgrade -y + +# Install mc (MinIO Client) +wget https://dl.min.io/client/mc/release/linux-amd64/mc -O /usr/local/bin/mc && \ + chmod +x /usr/local/bin/mc diff --git a/index.qmd b/index.qmd index 8dcb9f15..13270199 100644 --- a/index.qmd +++ b/index.qmd @@ -5,7 +5,7 @@ ::::: {.headline .g-col-lg-9 .g-col-12 .g-col-md-12} :::::: h1 -`utilitR` +utilitR :::::: diff --git a/renv.lock b/renv.lock new file mode 100644 index 00000000..1274a2e4 --- /dev/null +++ b/renv.lock @@ -0,0 +1,3204 @@ +{ + "R": { + "Version": "4.4.1", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://packagemanager.posit.co/cran/latest" + } + ] + }, + "Packages": { + "AsioHeaders": { + "Package": "AsioHeaders", + "Version": "1.22.1-2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "85bf3bd8fa58da21a22d84fd4f4ef0a8" + }, + "DBI": { + "Package": "DBI", + "Version": "1.2.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "methods" + ], + "Hash": "065ae649b05f1ff66bb0c793107508f5" + }, + "DT": { + "Package": "DT", + "Version": "0.33", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "crosstalk", + "htmltools", + "htmlwidgets", + "httpuv", + "jquerylib", + "jsonlite", + "magrittr", + "promises" + ], + "Hash": "64ff3427f559ce3f2597a4fe13255cb6" + }, + "Deriv": { + "Package": "Deriv", + "Version": "4.1.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "methods" + ], + "Hash": "cd52c065c9e687c60c56b51f10f7bcd3" + }, + "FactoMineR": { + "Package": "FactoMineR", + "Version": "2.11", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "DT", + "MASS", + "R", + "car", + "cluster", + "ellipse", + "emmeans", + "flashClust", + "ggplot2", + "ggrepel", + "grDevices", + "graphics", + "lattice", + "leaps", + "multcompView", + "scatterplot3d", + "stats", + "utils" + ], + "Hash": "54fc333adf872599b177a62d5759892a" + }, + "Formula": { + "Package": "Formula", + "Version": "1.2-5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats" + ], + "Hash": "7a29697b75e027767a53fde6c903eca7" + }, + "KernSmooth": { + "Package": "KernSmooth", + "Version": "2.23-24", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats" + ], + "Hash": "9f33a1ee37bbe8919eb2ec4b9f2473a5" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-60.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "stats", + "utils" + ], + "Hash": "2f342c46163b0b54d7b64d1f798e2c78" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.7-0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "grid", + "lattice", + "methods", + "stats", + "utils" + ], + "Hash": "1920b2f11133b12350024297d8a4ff4a" + }, + "MatrixModels": { + "Package": "MatrixModels", + "Version": "0.5-3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "Matrix", + "R", + "methods", + "stats" + ], + "Hash": "0776bf7526869e0286b0463cb72fb211" + }, + "R.methodsS3": { + "Package": "R.methodsS3", + "Version": "1.8.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "278c286fd6e9e75d0c2e8f731ea445c8" + }, + "R.oo": { + "Package": "R.oo", + "Version": "1.26.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "methods", + "utils" + ], + "Hash": "4fed809e53ddb5407b3da3d0f572e591" + }, + "R.utils": { + "Package": "R.utils", + "Version": "2.12.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "R.oo", + "methods", + "tools", + "utils" + ], + "Hash": 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of renv + version <- "1.0.11" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + + `%||%` <- function(x, 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) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) + + } + + 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 + 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 + 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() { + getOption("renv.tests.running", default = FALSE) + } + + 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)) { + + # 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) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + 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(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + # retrieve package database + db <- tryCatch( + as.data.frame( + do.call(utils::available.packages, args), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + 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." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + token <- renv_bootstrap_github_token() + if (nzchar(Sys.which("curl")) && nzchar(token)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + 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 + 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) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # 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 + 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 + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + 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 = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + 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. + ") + 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-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # 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 = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + 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_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_read_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_read_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_read_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 00000000..ffdbb320 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/resources/rmarkdown/chunk07.png b/resources/rmarkdown/chunk07.png index f152943b..e6c063d1 100644 Binary files a/resources/rmarkdown/chunk07.png and b/resources/rmarkdown/chunk07.png differ