From 31c6994ce3044e5d29d9b7852a71851af35a722c Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Wed, 20 Dec 2023 09:01:40 +0100 Subject: [PATCH] new version 2023.12.1 with two bug fixes and a new wrapper function --- .Rbuildignore | 2 + .Renviron | 1 + .Rprofile | 10 + DESCRIPTION | 14 +- NAMESPACE | 7 + NEWS.md | 10 + R/easy_redcap.R | 59 ++ R/read_redcap_tables.R | 2 +- R/utils.r | 2 + cran-comments.md | 43 +- man/easy_redcap.Rd | 22 + man/get_api_key.Rd | 17 + renv.lock | 634 ++++++++++++++++++++ renv/.gitignore | 7 + renv/activate.R | 1180 ++++++++++++++++++++++++++++++++++++++ renv/settings.json | 19 + tests/spelling.Rout.save | 25 + 17 files changed, 2042 insertions(+), 12 deletions(-) create mode 100644 .Rprofile create mode 100644 R/easy_redcap.R create mode 100644 man/easy_redcap.Rd create mode 100644 man/get_api_key.Rd create mode 100644 renv.lock create mode 100644 renv/.gitignore create mode 100644 renv/activate.R create mode 100644 renv/settings.json create mode 100644 tests/spelling.Rout.save diff --git a/.Rbuildignore b/.Rbuildignore index b6bdf3c..4c09a35 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,5 @@ +^renv$ +^renv\.lock$ ^.*\.Rproj$ ^\.Rproj\.user$ ^data-raw$ diff --git a/.Renviron b/.Renviron index a78fb09..991df51 100644 --- a/.Renviron +++ b/.Renviron @@ -1 +1,2 @@ _R_CHECK_FORCE_SUGGESTS_=FALSE + diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 0000000..22a9f55 --- /dev/null +++ b/.Rprofile @@ -0,0 +1,10 @@ +options( + renv.settings.snapshot.type = "explicit", + renv.config.auto.snapshot = TRUE, + renv.config.pak.enabled = TRUE +) +source("renv/activate.R") + +if (interactive()) { + suppressMessages(require(usethis)) +} diff --git a/DESCRIPTION b/DESCRIPTION index 91e9f9d..b2424bd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: REDCapCAST Title: REDCap Castellated Data Handling -Version: 23.6.2 +Version: 23.12.1 Authors@R: c( person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7559-1154")), @@ -32,7 +32,12 @@ Suggests: knitr, rmarkdown, gt, - keyring + usethis, + pak, + ggplot2, + roxygen2, + rhub, + devtools License: GPL (>= 3) Encoding: UTF-8 LazyData: true @@ -43,12 +48,15 @@ Imports: dplyr, REDCapR, tidyr, - tidyselect + tidyselect, + keyring, + purrr Collate: 'utils.r' 'process_user_input.r' 'REDCap_split.r' 'ds2dd.R' + 'easy_redcap.R' 'read_redcap_tables.R' 'redcap_wider.R' 'redcapcast_data.R' diff --git a/NAMESPACE b/NAMESPACE index 4aa7269..7cf22db 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,7 +4,9 @@ export(REDCap_split) export(clean_redcap_name) export(d2w) export(ds2dd) +export(easy_redcap) export(focused_metadata) +export(get_api_key) export(match_fields_to_form) export(read_redcap_tables) export(redcap_wider) @@ -14,5 +16,10 @@ export(strsplitx) importFrom(REDCapR,redcap_event_instruments) importFrom(REDCapR,redcap_metadata_read) importFrom(REDCapR,redcap_read) +importFrom(dplyr,left_join) +importFrom(keyring,key_get) +importFrom(keyring,key_list) +importFrom(keyring,key_set) +importFrom(purrr,reduce) importFrom(tidyr,pivot_wider) importFrom(tidyselect,all_of) diff --git a/NEWS.md b/NEWS.md index 655d8dd..708c7db 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,13 @@ +# REDCapCAST 23.12.1 + +One new function to ease secure dataset retrieval and a few bug fixes. + +### Functions + +* New: `easy_redcap()` function to ease the retrieval of a dataset with `read_redcap_tables()` with `keyring`-package based key storage, which handles secure API set, storage and retrieval. Relies on a small helper function, `get_api_key()`, which wraps relevant `keyring`-functions. Includes option to cast the data in a wide format with flag `widen.data`. +* Fix: `REDCap_split()`: when using this function on its own, supplying a data set with check boxes would fail if metadata is supplied as a tibble. Metadata is now converted to data.frame. Fixed. +* Fix: `read_redcap_tables()`: fixed bug when supplying events. + # REDCapCAST 23.6.2 This version marks the introduction of a few helper functions to handle database creation. diff --git a/R/easy_redcap.R b/R/easy_redcap.R new file mode 100644 index 0000000..f77a169 --- /dev/null +++ b/R/easy_redcap.R @@ -0,0 +1,59 @@ + +#' Retrieve project API key if stored, if not, set and retrieve +#' +#' @param key.name character vector of key name +#' +#' @return character vector +#' @importFrom keyring key_list key_get key_set +#' @export +get_api_key <- function(key.name) { + if (key.name %in% keyring::key_list()$service) { + keyring::key_get(service = key.name) + } else { + keyring::key_set(service = key.name, prompt = "Write REDCap API key:") + keyring::key_get(service = key.name) + } +} + + +#' Secure API key storage and data acquisition in one +#' +#' @param project.name The name of the current project (for key storage with +#' `keyring::key_set()`) +#' @param widen.data argument to widen the exported data +#' @param ... arguments passed on to `REDCapCAST::read_redcap_tables()` +#' +#' @return data.frame or list depending on widen.data +#' @importFrom purrr reduce +#' @importFrom dplyr left_join +#' @export +easy_redcap <- function(project.name, widen.data = TRUE, ...) { + project.name <- "ENIGMA" + + key <- get_api_key(key.name = paste0(project.name, "_REDCAP_API")) + + out <- read_redcap_tables( + token = key, + ... + ) + + all_names <- out |> + lapply(names) |> + Reduce(c, x = _) |> + unique() + + if (widen.data) { + if (!any(c("redcap_event_name", "redcap_repeat_instrument") %in% + all_names)) { + if (length(out) == 1) { + out <- out[[1]] + } else { + out <- out |> purrr::reduce(dplyr::left_join) + } + } else { + out <- out |> redcap_wider() + } + } + + out +} diff --git a/R/read_redcap_tables.R b/R/read_redcap_tables.R index 9664d91..8ef0cb1 100644 --- a/R/read_redcap_tables.R +++ b/R/read_redcap_tables.R @@ -55,7 +55,7 @@ read_redcap_tables <- function(uri, if (!is.null(events)){ event_test <- events %in% unique(arm_event_inst$data$unique_event_name) - if (any(!forms_test)){ + if (any(!event_test)){ stop("Not all supplied event names are valid") } } diff --git a/R/utils.r b/R/utils.r index d26ba16..86e4e02 100644 --- a/R/utils.r +++ b/R/utils.r @@ -144,6 +144,8 @@ sanitize_split <- function(l, #' match_fields_to_form <- function(metadata, vars_in_data) { + metadata <- data.frame(metadata) + field_form_name <- grepl(".*([Ff]ield|[Ff]orm)[._][Nn]ame$",names(metadata)) field_type <- grepl(".*[Ff]ield[._][Tt]ype$",names(metadata)) diff --git a/cran-comments.md b/cran-comments.md index 7c80a56..6d26696 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,13 +1,18 @@ -results$cran_summary() -For a CRAN submission we recommend that you fix all NOTEs, WARNINGs and ERRORs. -## Test environments -- R-hub windows-x86_64-devel (r-devel) -- R-hub ubuntu-gcc-release (r-release) -- R-hub fedora-clang-devel (r-devel) - ## R CMD check results +❯ On windows-x86_64-devel (r-devel) + checking CRAN incoming feasibility ... [15s] NOTE + Maintainer: 'Andreas Gammelgaard Damsbo ' + + Found the following (possibly) invalid URLs: + URL: https://github.com/SpectrumHealthResearch/REDCapRITS (moved to https://github.com/pegeler/REDCapRITS) + From: DESCRIPTION + README.md + Status: 200 + Message: OK + ❯ On windows-x86_64-devel (r-devel) checking for non-standard things in the check directory ... NOTE + Found the following files/directories: ''NULL'' ❯ On windows-x86_64-devel (r-devel) @@ -15,8 +20,30 @@ For a CRAN submission we recommend that you fix all NOTEs, WARNINGs and ERRORs. Found the following files/directories: 'lastMiKTeXException' +❯ On ubuntu-gcc-release (r-release) + checking CRAN incoming feasibility ... [8s/51s] NOTE + Maintainer: ‘Andreas Gammelgaard Damsbo ’ + + Found the following (possibly) invalid URLs: + URL: https://github.com/SpectrumHealthResearch/REDCapRITS (moved to https://github.com/pegeler/REDCapRITS) + From: DESCRIPTION + README.md + Status: 200 + Message: OK + ❯ On ubuntu-gcc-release (r-release), fedora-clang-devel (r-devel) checking HTML version of manual ... NOTE Skipping checking HTML validation: no command 'tidy' found -0 errors ✔ | 0 warnings ✔ | 3 notes ✖ +❯ On fedora-clang-devel (r-devel) + checking CRAN incoming feasibility ... [9s/57s] NOTE + Maintainer: ‘Andreas Gammelgaard Damsbo ’ + + Found the following (possibly) invalid URLs: + URL: https://github.com/SpectrumHealthResearch/REDCapRITS (moved to https://github.com/pegeler/REDCapRITS) + From: DESCRIPTION + README.md + Status: 200 + Message: OK + +0 errors ✔ | 0 warnings ✔ | 6 notes ✖ diff --git a/man/easy_redcap.Rd b/man/easy_redcap.Rd new file mode 100644 index 0000000..feb169b --- /dev/null +++ b/man/easy_redcap.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/easy_redcap.R +\name{easy_redcap} +\alias{easy_redcap} +\title{Secure API key storage and data acquisition in one} +\usage{ +easy_redcap(project.name, widen.data = TRUE, ...) +} +\arguments{ +\item{project.name}{The name of the current project (for key storage with +`keyring::key_set()`)} + +\item{widen.data}{argument to widen the exported data} + +\item{...}{arguments passed on to `REDCapCAST::read_redcap_tables()`} +} +\value{ +data.frame or list depending on widen.data +} +\description{ +Secure API key storage and data acquisition in one +} diff --git a/man/get_api_key.Rd b/man/get_api_key.Rd new file mode 100644 index 0000000..c154012 --- /dev/null +++ b/man/get_api_key.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/easy_redcap.R +\name{get_api_key} +\alias{get_api_key} +\title{Retrieve project API key if stored, if not, set and retrieve} +\usage{ +get_api_key(key.name) +} +\arguments{ +\item{key.name}{character vector of key name} +} +\value{ +character vector +} +\description{ +Retrieve project API key if stored, if not, set and retrieve +} diff --git a/renv.lock b/renv.lock new file mode 100644 index 0000000..1417a55 --- /dev/null +++ b/renv.lock @@ -0,0 +1,634 @@ +{ + "R": { + "Version": "4.3.1", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "R6": { + "Package": "R6", + "Version": "2.5.1", + 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"Hash": "c03fa420630029418f7e6da3667aac4a" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "bit64", + "cli", + "cpp11", + "crayon", + "glue", + "hms", + "lifecycle", + "methods", + "progress", + "rlang", + "stats", + "tibble", + "tidyselect", + "tzdb", + "vctrs", + "withr" + ], + "Hash": "390f9315bc0025be03012054103d227c" + }, + "withr": { + "Package": "withr", + "Version": "2.5.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats" + ], + "Hash": "4b25e70111b7d644322e9513f403a272" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.8", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "29240487a071f535f5e5d5a323b7afbd" + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 0000000..0ec0cbb --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..45b9da1 --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1180 @@ + +local({ + + # the requested version of renv + version <- "1.0.3" + attr(version, "sha") <- "1.0.3" + + # the project directory + 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) + + # 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 (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 + `%||%` <- 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) + + } + + 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))) + args$headers <- renv_bootstrap_download_custom_headers(url) + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$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()) { + + # retrieve package database + db <- tryCatch( + as.data.frame( + utils::available.packages(type = type, repos = repos), + 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_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + pat <- Sys.getenv("GITHUB_PAT") + if (nzchar(Sys.which("curl")) && nzchar(pat)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + 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(pat)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + 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$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$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 + 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.", + sep = "\n" + ) + 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 <- 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 + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% read(file), 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 %||% read(file), 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_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) + + # 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 0000000..74c1d4b --- /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": "explicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/tests/spelling.Rout.save b/tests/spelling.Rout.save new file mode 100644 index 0000000..17bf7b4 --- /dev/null +++ b/tests/spelling.Rout.save @@ -0,0 +1,25 @@ + +R version 3.4.1 (2017-06-30) -- "Single Candle" +Copyright (C) 2017 The R Foundation for Statistical Computing +Platform: x86_64-apple-darwin15.6.0 (64-bit) + +R is free software and comes with ABSOLUTELY NO WARRANTY. +You are welcome to redistribute it under certain conditions. +Type 'license()' or 'licence()' for distribution details. + +R is a collaborative project with many contributors. +Type 'contributors()' for more information and +'citation()' on how to cite R or R packages in publications. + +Type 'demo()' for some demos, 'help()' for on-line help, or +'help.start()' for an HTML browser interface to help. +Type 'q()' to quit R. + +> if(requireNamespace('spelling', quietly = TRUE)) ++ spelling::spell_check_test(vignettes = TRUE, error = FALSE, ++ skip_on_cran = TRUE) +All Done! +> +> proc.time() + user system elapsed + 0.372 0.039 0.408