diff --git a/DESCRIPTION b/DESCRIPTION index a8552dc..c15a811 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -36,7 +36,6 @@ Imports: brms, car, condMVNorm, - drake, emmeans, ggridges, glmmTMB, @@ -46,6 +45,7 @@ Imports: mvtnorm, performance, rmarkdown, + targets, tikzDevice, visNetwork Suggests: diff --git a/renv.lock b/renv.lock index 6fd66f9..189847b 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.1.0", + "Version": "4.2.1", "Repositories": [ { "Name": "CRAN", @@ -11,1571 +11,2754 @@ "Packages": { "BH": { "Package": "BH", - "Version": "1.75.0-0", + "Version": "1.78.0-0", "Source": "Repository", "Repository": "CRAN", - "Hash": "e4c04affc2cac20c8fec18385cd14691" + "Hash": "4e348572ffcaa2fb1e610e7a941f6f3a", + "Requirements": [] }, "Brobdingnag": { "Package": "Brobdingnag", - "Version": "1.2-6", + "Version": "1.2-7", "Source": "Repository", "Repository": "CRAN", - "Hash": "365629a3ac7243df8ed6ac88a606d9fe" + "Hash": "f73a31c1c5104baa9073c21f7967853f", + "Requirements": [] }, "DBI": { "Package": "DBI", - 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version <- "0.13.2" + version <- "0.15.5" # the project directory project <- getwd() + # 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) + + # 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 + + }) + + if (!enabled) + return(FALSE) + # avoid recursion - if (!is.na(Sys.getenv("RENV_R_INITIALIZING", unset = NA))) + 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 - Sys.setenv("RENV_R_INITIALIZING" = "true") - on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), add = TRUE) + 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) @@ -22,21 +54,15 @@ local({ # mask 'utils' packages, will come first on the search path library(utils, lib.loc = .Library) - # check to see if renv has already been loaded - if ("renv" %in% loadedNamespaces()) { - - # if renv has already been loaded, and it's the requested version of renv, - # nothing to do - spec <- .getNamespaceInfo(.getNamespace("renv"), "spec") - if (identical(spec[["version"]], version)) - return(invisible(TRUE)) - - # otherwise, unload and attempt to load the correct version of renv + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) unloadNamespace("renv") - } - # load bootstrap tools + `%||%` <- function(x, y) { + if (is.environment(x) || length(x)) x else y + } + bootstrap <- function(version, library) { # attempt to download renv @@ -62,6 +88,11 @@ local({ if (!is.na(repos)) 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")) @@ -86,6 +117,30 @@ local({ } + 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) { # if the renv version number has 4 components, assume it must @@ -93,16 +148,20 @@ local({ nv <- numeric_version(version) components <- unclass(nv)[[1]] - methods <- if (length(components) == 4L) { - list( + # 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 { - list( + else c( renv_bootstrap_download_cran_latest, renv_bootstrap_download_cran_archive ) - } + ) for (method in methods) { path <- tryCatch(method(version), error = identity) @@ -239,6 +298,42 @@ local({ } + 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 + info <- file.info(tarball, extra_cols = FALSE) + if (identical(info$isdir, TRUE)) { + 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() + + } + + fmt <- "* Bootstrapping with tarball at path '%s'." + msg <- sprintf(fmt, tarball) + message(msg) + + tarball + + } + renv_bootstrap_download_github <- function(version) { enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") @@ -292,7 +387,13 @@ local({ bin <- R.home("bin") exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" r <- file.path(bin, exe) - args <- c("--vanilla", "CMD", "INSTALL", "-l", shQuote(library), shQuote(tarball)) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + output <- system2(r, args, stdout = TRUE, stderr = TRUE) message("Done!") @@ -485,18 +586,33 @@ local({ renv_bootstrap_library_root <- function(project) { + prefix <- renv_bootstrap_profile_prefix() + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) if (!is.na(path)) - return(path) + return(paste(c(path, prefix), collapse = "/")) - path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) - if (!is.na(path)) { + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { name <- renv_bootstrap_library_root_name(project) - return(file.path(path, name)) + return(paste(c(path, prefix, name), collapse = "/")) } - prefix <- renv_bootstrap_profile_prefix() - paste(c(project, prefix, "renv/library"), 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")) + } } @@ -562,7 +678,7 @@ local({ return(profile) # check for a profile file (nothing to do if it doesn't exist) - path <- file.path(project, "renv/local/profile") + path <- renv_bootstrap_paths_renv("profile", profile = FALSE) if (!file.exists(path)) return(NULL) @@ -573,7 +689,7 @@ local({ # set RENV_PROFILE profile <- contents[[1L]] - if (nzchar(profile)) + if (!profile %in% c("", "default")) Sys.setenv(RENV_PROFILE = profile) profile @@ -583,7 +699,7 @@ local({ renv_bootstrap_profile_prefix <- function() { profile <- renv_bootstrap_profile_get() if (!is.null(profile)) - return(file.path("renv/profiles", profile)) + return(file.path("profiles", profile, "renv")) } renv_bootstrap_profile_get <- function() { @@ -607,6 +723,178 @@ local({ 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_json_read <- function(file = NULL, text = NULL) { + + text <- paste(text %||% read(file), collapse = "\n") + + # find strings in the JSON + 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("[[{]", "list(", transformed) + transformed <- gsub("[]}]", ")", transformed) + 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_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_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_remap(json[[i]], map)) + } + } + + json + + } # load the renv profile, if any renv_bootstrap_profile_load(project) diff --git a/renv/settings.dcf b/renv/settings.dcf index fc4e479..169d82f 100644 --- a/renv/settings.dcf +++ b/renv/settings.dcf @@ -1,8 +1,10 @@ +bioconductor.version: external.libraries: ignored.packages: 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