From 4ab853bd7e01a1ae817d382f1f5a48fb62ae43fc Mon Sep 17 00:00:00 2001 From: Damon Bayer Date: Mon, 26 Aug 2024 15:22:02 -0500 Subject: [PATCH] incorporate ww-inference R package and data (#3) * add files from pyrenew PR * add R files * add wweval package and vignette reproduction * make pre-commit happy * add lintr file * make lintr happy --- .Rprofile | 1 + .lintr | 2 + notebooks/data/fit/stan_data.json | 377 ++++++ notebooks/data/fit_hosp_only/stan_data.json | 377 ++++++ notebooks/wwinference.Rmd | 427 +++++++ renv.lock | 1129 +++++++++++++++++ renv/.gitignore | 7 + renv/activate.R | 1220 +++++++++++++++++++ renv/settings.json | 19 + 9 files changed, 3559 insertions(+) create mode 100644 .Rprofile create mode 100644 .lintr create mode 100644 notebooks/data/fit/stan_data.json create mode 100644 notebooks/data/fit_hosp_only/stan_data.json create mode 100644 notebooks/wwinference.Rmd create mode 100644 renv.lock create mode 100644 renv/.gitignore create mode 100644 renv/activate.R create mode 100644 renv/settings.json diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 00000000..81b960f5 --- /dev/null +++ b/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/.lintr b/.lintr new file mode 100644 index 00000000..6c2c005a --- /dev/null +++ b/.lintr @@ -0,0 +1,2 @@ +linters: linters_with_defaults(object_usage_linter = NULL) +encoding: "UTF-8" diff --git a/notebooks/data/fit/stan_data.json b/notebooks/data/fit/stan_data.json new file mode 100644 index 00000000..95fe121c --- /dev/null +++ b/notebooks/data/fit/stan_data.json @@ -0,0 +1,377 @@ +{ + "gt_max": 15, + "hosp_delay_max": 55, + "inf_to_hosp": [0.0, 0.00469384736487552, 0.0145200073436112, 0.0278627741704387, 0.0423656492135518, 0.0558071445014868, 0.0665713169684116, 0.0737925805176124, 0.0772854627892072, 0.0773666390616176, 0.0746515449009948, 0.0698761436052596, 0.0637663813017696, 0.0569581929821651, 0.0499600186601535, 0.0431457477049282, 0.0367662806214046, 0.0309702535668238, 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"lab_site_to_site_map": [1, 1, 2, 3, 4] +} diff --git a/notebooks/wwinference.Rmd b/notebooks/wwinference.Rmd new file mode 100644 index 00000000..353ba7a6 --- /dev/null +++ b/notebooks/wwinference.Rmd @@ -0,0 +1,427 @@ +--- +title: "Getting started with wwinference" +description: "A quick start example demonstrating the use of wwinference to jointly fit wastewater and hospital admissions data" +author: "Kaitlyn Johnson" +date: "2024-06-27" +output: + bookdown::html_vignette2: + fig_caption: yes + code_folding: show +pkgdown: + as_is: true +vignette: > + %\VignetteIndexEntry{Getting started with wwinference} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- +```{r echo=FALSE} +knitr::opts_chunk$set(dev = "svg") +``` +# Quick start + +In this quick start, we demonstrate using `wwinference` to specify and fit a +minimal model using daily COVID-19 hospital admissions from a "global" population and +viral concentrations in wastewater from a few "local" wastewater treatment plants, +which come from subsets of the larger population. +This is intended to be used as a reference for those +interested in fitting the `wwinference` model to their own data. + +# Package + +In this quick start, we also use `dplyr` `tidybayes` and `ggplot2` packages. +These are installed as dependencies when `wwinference` is installed. + +```{r warning=FALSE, message=FALSE} +library(wwinference) +library(dplyr) +library(ggplot2) +library(tidybayes) +``` + +# Data + +The model expects two types of data: daily counts of hospital admissions data +from the larger "global" population, and wastewater concentration +data from wastewater treatment plants whose catchment areas are contained within +the larger "global" population. For this quick start, we will use +simulated data, modeled after a hypothetical US state with 4 wastewater +treatmentplants (also referred to as sites) reporting data on viral +concentrations of SARS-COV-2, processed in 3 different labs, covering about 70% +of the state's population. This simulated data contains daily counts of the +total hospital admissions in a hypothetical US state from September 1, 2023 to +November 29, 2023. It contains wastewater concentration data spanning from +September 1, 2023 to December 1, 2023, with varying sampling frequencies. We +will be using this data to produce a forecast of COVID-19 hospital admissions +as of December 6, 2023. These data are provided as part of the package data. + +These data are already in a format that can be used for `wwinference`. For the +hospital admissions data, it contains: +- a date (column `date`): the date of the observation, in this case, the date +the hospital admissions occurred +- a count (column `daily_hosp_admits`): the number of hospital admissions +observed on that day +- a population size (column `state_pop`): the population size covered +by the hospital admissions data, in this case, the size of the theoretical state. + +Additionally, we provide the `hosp_data_eval` dataset which contains the +simulated hospital admissions 28 days ahead of the forecast date, which can be +used to evaluate the model. + +For the wastewater data, it contains: +- a date (column `date`): the date the sample was collected +- a site indicator (column `site`): the unique identifier for the wastewater treatment plant +that the sample was collected from +- a lab indicator (column `lab`): the unique identifier for the lab where the sample was processed +- a concentration (column `genome_copies_mL`): the measured genome copies per mL from +the sample collected, in natural scale +- a limit of detection (column `lod`): the limit of detection of the assay used to +process the sample, in natural scale +- a site population size (column `site_pop`): the population size covered by the +wastewater catchment area of that site + + + +```{r} +hosp_data <- wwinference::hosp_data +hosp_data_eval <- wwinference::hosp_data_eval +ww_data <- wwinference::ww_data + +head(ww_data) +head(hosp_data) +``` + +# Pre-processing +The user will need to provide data that is in a similar format to the package +data, as described above. This represents the bare minimum required data for a +single location and a single forecast date. We will need to do some +pre-processing to add some additional variables that the model will need to be +able apply features such as outlier exclusion and censoring of values below the +limit of detection. + +## Parameters +Get the default parameters from the package. Note that some of these are COVID +specific, others are more general to the model. This is indicated in the +.toml file. +```{r} +params <- get_params( + system.file("extdata", "example_params.toml", + package = "wwinference" + ) +) +``` + +## Wastewater data pre-processing + +The `preprocess_ww_data` function adds the following variables to the original +dataset. First, it assigns a unique identifier +the unique combinations of labs and sites, since this is the unit we will +use for estimating the observation error in the reported measurements. +Second it adds a column `below_lod` which is an indicator of whether the +reported concentration is above or below the limit of detection (LOD). If the +point is below the LOD, the model will treat this observation as censored. +Third, it adds a column `flag_as_ww_outlier` that indicates whether the +measurement is identified as an outlier by our algorithm and the default +thresholds. While the default choice will be to exclude the measurements flagged +as outliers, the user can still choose to include these if they'd like later on. +The user must specify the name of the column containing the +concentration measurements (presumed to be in genome copies per mL) and the +name of the column containing the limit of detection for each measurement. The +function assumes that the original data contains the columns `date`, `site`, +and `lab`, and will return a dataframe with the column names needed to +pass to the downstream model fitting functions. +```{r} +ww_data_preprocessed <- wwinference::preprocess_ww_data( + ww_data, + conc_col_name = "genome_copies_per_ml", + lod_col_name = "lod" +) +``` + + +## Hospital admissions data pre-processing +The `preprocess_hosp_data` function standardizes the column names of the +resulting datafame. The user must specify the name of the column containing +the daily hospital admissions counts and the population size that the hospital +admissions are coming from (from in this case, a hypothetical US state). The +function assumes that the original data contains the column `date`, and will +return a dataframe with the column names needed to pass to the downstream model +fitting functions. +```{r} +hosp_data_preprocessed <- wwinference::preprocess_count_data( + hosp_data, + count_col_name = "daily_hosp_admits", + pop_size_col_name = "state_pop" +) +``` + + +We'll make some plots of the data just to make sure it looks like what we'd expect: + +```{r, out.width='100%'} +ggplot(ww_data_preprocessed) + + geom_point( + aes( + x = date, y = genome_copies_per_ml, + color = as.factor(lab_site_name) + ), + show.legend = FALSE + ) + + geom_point( + data = ww_data_preprocessed |> filter(genome_copies_per_ml <= lod), + aes(x = date, y = genome_copies_per_ml, color = "red"), + show.legend = FALSE + ) + + geom_hline(aes(yintercept = lod), linetype = "dashed") + + facet_wrap(~lab_site_name, scales = "free") + + xlab("") + + ylab("Genome copies/mL") + + ggtitle("Lab-site level wastewater concentration") + + theme_bw() + +ggplot(hosp_data_preprocessed) + + # Plot the hospital admissions data that we will evaluate against in white + geom_point( + data = hosp_data_eval, aes( + x = date, + y = daily_hosp_admits_for_eval + ), + shape = 21, color = "black", fill = "white" + ) + + # Plot the data we will calibrate to + geom_point(aes(x = date, y = count)) + + xlab("") + + ylab("Daily hospital admissions") + + ggtitle("State level hospital admissions") + + theme_bw() +``` + +## Data exclusion +As an optional additional pre-processing step, the user can decide to exclude +certain data points from being included in the model fit procedure. For example, +we recommend excluding the flagged wastewater concentration outliers. To do so +we will use the `indicate_ww_exclusions()` function, which will add the +flagged outliers to the exclude column where indicated. +```{r} +ww_data_to_fit <- wwinference::indicate_ww_exclusions( + ww_data_preprocessed, + outlier_col_name = "flag_as_ww_outlier", + remove_outliers = TRUE +) +``` + + +# Model specification: +We will need to set some metadata to facilitate model specification. This includes: +- forecast date (the date we are making a forecast) +- number of days to calibrate the model for +- number of days to forecast +- specification of the generation interval, in this case for COVID-19 +- specification of the delay from infection to the count data, in this case + from infection to COVID-19 hospital admission + + +## Calibration time and forecast time +The calibration time represents the number of days to calibrate the count data +to. This must be less than or equal to the number of rows in `hosp_data`. The +forecast horizon represents the number of days from the forecast date to +generate forecasted hospital admissions for. Typically, the hospital admissions +data will not be complete up until the forecast date, and we will refer to the +time between the last hospital admissions data point and the forecast date as +the nowcast time. The model will "forecast" this period, in addition to the +specified forecast horizon. +```{r} +forecast_date <- "2023-12-06" +calibration_time <- 90 +forecast_horizon <- 28 +``` + +## Delay distributions +We will pass in some probabiltiy mass functions (pmfs) that are specific to +COVID, and to the delay from infections to hospital admissions, the count +data we are using to fit th emodel. If using a different pathogen or a +different count dataset, these pmfs need to be replaced. We provide them as +package data here. These are both vectors of simplexes (they must sum to 1). + +Additionally, the model requires specifying a delay distribution for the +infection feedback term, which essentially describes the delay at which +high incident infections results in negative feedback on future infections +(due to susceptibility, behavior changes, policies to reduce transmission, +etc.). We by default set this as the generation interval, but this can be +modified as long as the values sum to 1. +```{r} +generation_interval <- wwinference::generation_interval +inf_to_hosp <- wwinference::inf_to_hosp + +# Assign infection feedback equal to the generation interval +infection_feedback_pmf <- generation_interval +``` +We will pass these to the `model_spec()` function of the `wwinference()` model, +along with the other specified parameters above. + + +# Precompiling the model +As `wwinference` uses `cmdstan` to fit its models, it is necessary to first +compile the model. This can be done using the compile_model() function. +```{r} +model <- wwinference::compile_model() +``` +# Fitting the model +We're now ready to fit the model using the “No-U-Turn Sampler Markov chain +Monte Carlo” method. This is a type of Hamiltonian Monte Carlo (HMC) algorithm +and is the core fitting method used by `cmdstan`. The user can adjust the MCMC +settings (see the documentation for `get_mcmc_options()`), +however this vignette will use +the default parameter settings which includes running 4 parallel chains with +750 warm up iterations, 500 sampling iterations for each chain, a target average +acceptance probability of 0.95 and a maximum tree depth of 12. The user may wish +to adjust these as they are iterating to reduce model run-time or to achieve +better convergence on a real-world use case. + +We also pass our preprocessed datasets (`ww_data_to_fit` and +`hosp_data_preprocessed`), specify our model using `get_model_spec()`, +set the MCMC settings using `get_mcmc_options()`, and pass in our +pre-compiled model(`model`) to `wwinference()` where they are combined and +used to fit the model. + + +```{r warning=FALSE, message=FALSE} +fit <- wwinference::wwinference( + ww_data = ww_data_to_fit, + count_data = hosp_data_preprocessed, + forecast_date = forecast_date, + calibration_time = calibration_time, + forecast_horizon = forecast_horizon, + model_spec = get_model_spec( + generation_interval = generation_interval, + inf_to_count_delay = inf_to_hosp, + infection_feedback_pmf = infection_feedback_pmf, + params = params + ), + mcmc_options = get_mcmc_options(), + compiled_model = model +) +``` + +# The `wwinference` object +The `wwinference()` function returns a `wwinference` object which includes +a `draws_df`, the underlying `CmdStan` object (`raw_fit_obj`), and three +"spines" that map the stan indices to the data which include:a +`date_time_spine`, `lab_site_spine`, and `subpop_spine`. The `draws_df` is +intended to provide an easy to work with tibble of posterior draws of +the estimated, nowcasted, and forecasted expected observed hospital admissions +and wastewater concentrations, as well as the latent variables of interest +including the site-level R(t) estimates and the state-level R(t) estimate. +```{r} +head(fit) +``` +# Summarizing and plotting the model fit +The `draws_df` object is intended to be used to easily plot relevant model +outputs against data. This can be useful to get a sense of if your model is +fitting the data well, and if the nowcasted/forecast quantities look reasonable. + +We can create the plots using the fitting wrapper functions (figures can +also created directly using the `draws_df`) + +```{r, out.width='100%'} +draws_df <- fit$draws_df + +plot_hosp <- get_plot_forecasted_counts( + draws = draws_df, + count_data_eval = hosp_data_eval, + count_data_eval_col_name = "daily_hosp_admits_for_eval", + forecast_date = forecast_date +) +plot_hosp + +plot_ww <- get_plot_ww_conc(draws_df, forecast_date) +plot_ww + +plot_state_rt <- get_plot_global_rt(draws_df, forecast_date) +plot_state_rt + +plot_subpop_rt <- get_plot_subpop_rt(draws_df, forecast_date) +plot_subpop_rt +``` + +## Diagnostics +While the `wwinference()` function will print out messaging if any of the +diagnostics flags fail, we recommend running diagnostics as a separate +post-processing step on the `CmdStan` fit object. Start by running function +`get_model_diagnostic_flags()` on the stan fit object. Then, we recommend +looking at the `raw_fit_obj$summary()` which will show the diagnostic +metrics for each parameter in the model and can help identify which parameters +are likely to be driving any convergence issues. We have set default thresholds +on the model diagnostics for production-level runs, we recommend adjusting +as needed. For further information on troubleshooting the model diagnostics, +we recommend the (bayesplot tutorial)[https://mc-stan.org/bayesplot/articles/visual-mcmc-diagnostics.html]. +```{r} +convergence_flag_df <- wwinference::get_model_diagnostic_flags( + stan_fit_obj = + fit$raw_fit_obj +) +parameter_diagnostics <- fit$raw_fit_obj$summary() +diagnostic_summary <- fit$raw_fit_obj$diagnostic_summary(quiet = TRUE) +head(convergence_flag_df) +``` + +## Fit to only hospital admissions data +The package also has functionality to fit the model without wastewater data. +This can be useful when doing comparisons of the impact the wastewater data +has on the forecast, or as a part of a pipeline where one might choose to +rely on the admissions only model if there are covergence or known data issues +with the wastewater data. + +```{r warning=FALSE, message=FALSE} +fit_hosp_only <- wwinference::wwinference( + ww_data = ww_data_to_fit, + count_data = hosp_data_preprocessed, + forecast_date = forecast_date, + calibration_time = calibration_time, + forecast_horizon = forecast_horizon, + model_spec = get_model_spec( + generation_interval = generation_interval, + inf_to_count_delay = inf_to_hosp, + infection_feedback_pmf = infection_feedback_pmf, + include_ww = FALSE, + params = params + ), + mcmc_options = get_mcmc_options(), + compiled_model = model +) +``` + +```{r, out.width='100%'} +draws_df_hosp_only <- fit_hosp_only$draws_df +plot_hosp_hosp_only <- get_plot_forecasted_counts( + draws = draws_df_hosp_only, + count_data_eval = hosp_data_eval, + count_data_eval_col_name = "daily_hosp_admits_for_eval", + forecast_date = forecast_date +) +plot_hosp_hosp_only +``` + + +```{r copy results} +library(fs) + +base_dir <- path("notebooks", "data") +fit_dir <- path(base_dir, "fit") +fit_hosp_only_dir <- path(base_dir, "fit_hosp_only") +dir_create(fit_dir) +dir_create(fit_hosp_only_dir) + +file_copy( + path = fit$raw_fit_obj$data_file(), + new_path = path(fit_dir, "stan_data", ext = "json"), + overwrite = TRUE +) +file_copy( + path = fit_hosp_only$raw_fit_obj$data_file(), + new_path = path(fit_hosp_only_dir, "stan_data", ext = "json"), + overwrite = TRUE +) + +fit$raw_fit_obj$save_output_files(fit_dir) +fit_hosp_only$raw_fit_obj$save_output_files(fit_hosp_only_dir) +``` diff --git a/renv.lock b/renv.lock new file mode 100644 index 00000000..6ceac812 --- /dev/null +++ b/renv.lock @@ -0,0 +1,1129 @@ +{ + "R": { + "Version": "4.4.1", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "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", + 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(!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 + `%||%` <- 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 + paste(substring(lines, common), collapse = "\n") + + } + + 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 (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 +}