From fba0e7a8e58a735233263a489f31fd47f76c095e Mon Sep 17 00:00:00 2001 From: dereckmezquita Date: Sat, 6 Jul 2024 15:23:39 -0500 Subject: [PATCH] Precommit not working. --- .Rbuildignore | 3 - .Rprofile | 1 - .pre-commit-config.yaml | 85 --- DESCRIPTION | 2 +- NAMESPACE | 1 + R/ddplot.R | 8 - R/dmplot.R | 3 + R/stat_movingaverages.R | 38 +- R/stat_shade_ranges.R | 70 ++- R/theme_dereck.R | 15 +- check-install.sh | 31 - demo/macd.R | 8 +- inst/WORDLIST | 26 + renv.lock | 850 --------------------------- renv/.gitignore | 7 - renv/activate.R | 1220 --------------------------------------- renv/settings.json | 19 - 17 files changed, 102 insertions(+), 2285 deletions(-) delete mode 100644 .Rprofile delete mode 100644 .pre-commit-config.yaml delete mode 100644 R/ddplot.R create mode 100644 R/dmplot.R delete mode 100755 check-install.sh delete mode 100644 renv.lock delete mode 100644 renv/.gitignore delete mode 100644 renv/activate.R delete mode 100644 renv/settings.json diff --git a/.Rbuildignore b/.Rbuildignore index 55b18ce..6728b26 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,8 +1,5 @@ .graphics ^.*\.Rproj$ ^\.Rproj\.user$ -^\.pre-commit-config\.yaml$ -^renv$ -^renv\.lock$ demo/ dev/ diff --git a/.Rprofile b/.Rprofile deleted file mode 100644 index 81b960f..0000000 --- a/.Rprofile +++ /dev/null @@ -1 +0,0 @@ -source("renv/activate.R") diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml deleted file mode 100644 index a7c8e46..0000000 --- a/.pre-commit-config.yaml +++ /dev/null @@ -1,85 +0,0 @@ -# All available hooks: https://pre-commit.com/hooks.html -# R specific hooks: https://github.com/lorenzwalthert/precommit -repos: -- repo: https://github.com/lorenzwalthert/precommit - rev: v0.4.2 - hooks: - - id: readme-rmd-rendered - - id: style-files - args: [--style_pkg=styler, --style_fun=tidyverse_style, --indent_by=4] - exclude: dev/.*| - - id: roxygenize - # codemeta must be above use-tidy-description when both are used - # - id: codemeta-description-updated - - id: use-tidy-description - - id: spell-check - exclude: > - (?x)^( - .*\.[rR]| - .*\.feather| - .*\.jpeg| - .*\.pdf| - .*\.png| - .*\.py| - .*\.RData| - .*\.rds| - .*\.Rds| - .*\.Rproj| - .*\.sh| - (.*/|)\.gitignore| - (.*/|)\.gitlab-ci\.yml| - (.*/|)\.lintr| - (.*/|)\.pre-commit-.*| - (.*/|)\.Rbuildignore| - (.*/|)\.Renviron| - (.*/|)\.Rprofile| - (.*/|)\.travis\.yml| - (.*/|)appveyor\.yml| - (.*/|)NAMESPACE| - (.*/|)renv/settings\.dcf| - (.*/|)renv\.lock| - (.*/|)WORDLIST| - \.github/workflows/.*| - data/.*| - )$ - - id: lintr - args: [--warn_only] - exclude: dev/.*| - - id: parsable-R - exclude: dev/.*| - - id: no-browser-statement - exclude: dev/.*| - - id: no-print-statement - exclude: dev/.*| - - id: no-debug-statement - exclude: dev/.*| - - id: deps-in-desc - exclude: dev/.*| - args: [--allow_private_imports] - - id: pkgdown -- repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 - hooks: - - id: check-added-large-files - args: ['--maxkb=200'] - - id: file-contents-sorter - files: '^\.Rbuildignore$' - - id: end-of-file-fixer - exclude: '\.Rd' -- repo: https://github.com/pre-commit-ci/pre-commit-ci-config - rev: v1.6.1 - hooks: - # Only required when https://pre-commit.ci is used for config validation - - id: check-pre-commit-ci-config -- repo: local - hooks: - - id: forbid-to-commit - name: Don't commit common R artifacts - entry: Cannot commit .Rhistory, .RData, .Rds or .rds. - language: fail - files: '\.(Rhistory|RData|Rds|rds)$' - # `exclude: ` to allow committing specific files - -ci: - autoupdate_schedule: monthly - skip: [pkgdown] diff --git a/DESCRIPTION b/DESCRIPTION index 74147db..ac2e5e3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,7 +17,7 @@ License: All rights reserved. Encoding: UTF-8 LazyData: true VignetteBuilder: knitr -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Suggests: knitr, rmarkdown, diff --git a/NAMESPACE b/NAMESPACE index d13b5cf..ef0cfa8 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,4 +8,5 @@ export(stat_shade_ranges) export(theme_dereck_dark) export(theme_dereck_light) import(data.table) +import(ggplot2) importFrom(ggplot2,'%+replace%') diff --git a/R/ddplot.R b/R/ddplot.R deleted file mode 100644 index 8e06fcd..0000000 --- a/R/ddplot.R +++ /dev/null @@ -1,8 +0,0 @@ -# package description ----------------------------------------------------- - -#' @title `dmplot`: Dereck's library for plotting financial and other time series datasets. -#' -#' @docType package -#' -#' @import data.table -NULL diff --git a/R/dmplot.R b/R/dmplot.R new file mode 100644 index 0000000..4b5d557 --- /dev/null +++ b/R/dmplot.R @@ -0,0 +1,3 @@ +#' @import ggplot2 +#' @import data.table +NULL diff --git a/R/stat_movingaverages.R b/R/stat_movingaverages.R index aaf49d1..2aa83ab 100644 --- a/R/stat_movingaverages.R +++ b/R/stat_movingaverages.R @@ -1,4 +1,3 @@ - # df <- data.table::fread("data/kucoin_prices.csv") StatMovingAverage <- ggplot2::ggproto( @@ -32,14 +31,14 @@ StatMovingAverage <- ggplot2::ggproto( #' @title Moving averages `ggplot2` layer #' @author Dereck Mezquita -#' -#' @description +#' +#' @description #' `stat_movingaverages` is a `ggplot2` layer that allows you to plot moving averages on a `ggplot2` plot either by providing the column names `ggplot2::aes` of the previously calculated metrics. -#' +#' #' You are free to use whatever algorithm you desire; the result will be two line plots one for a short moving average and one for a long moving average. -#' +#' #' To use this layer provide `ggplot2::aes` values for `x` (datetime x-axis) and `short` and `long` (y-axis). -#' +#' #' See examples for more details. #' #' @param mapping A `ggplot2::aes` object (required - default `NULL`). @@ -47,7 +46,7 @@ StatMovingAverage <- ggplot2::ggproto( #' @param linewidth A `numeric` vector of length one; the width of the line (optional - default `1.75`). #' @param alpha A `numeric` vector of length one; the alpha of the line (optional - default `0.75`). #' @param colour A named or unnamed `list` with three elements "short" and "long". These are the colours for the short and long moving averages (optional - default `list(short = "red", long = "blue")`). -#' +#' #' @section Aesthetics: #' \code{stat_movingaverages} understands the following aesthetics (required aesthetics are in bold): #' \itemize{ @@ -55,39 +54,39 @@ StatMovingAverage <- ggplot2::ggproto( #' \item \strong{short} -- the values for the short moving average (y-axis). #' \item \strong{long} -- the values for the long moving average (y-axis) #' } -#' +#' #' @details -#' +#' #' This is a `ggplot2` extension; it is used with the `+` operator for adding a layer to a `ggplot2` object. #' #' @return A `ggplot2::layer` object. #' #' @examples -#' +#' #' # get some financial data #' # kucoin is private package - you can use any data source #' ticker <- "BTC/USDT" -#' +#' #' dt <- kucoin::get_market_data( #' symbols = ticker, #' from = "2022-11-28 15:29:43 EST", # lubridate::now() - lubridate::days(7), -#' to = "2022-12-05 15:29:31 EST",# lubridate::now(), +#' to = "2022-12-05 15:29:31 EST", # lubridate::now(), #' frequency = "1 hour" #' ) -#' +#' #' dt -#' +#' #' # we need a function that calculates the indicator for us #' # typically I like to write my own functions in C++; in this case we will use TTR's #' # the stat expects a named list to be returned - we redefine ttr #' ema <- function(close, n = 2, wilder = TRUE) { #' return(as.list(as.data.frame(TTR::EMA(close, n = n, wilder = wilder)))) #' } -#' +#' #' # calculate the short and long moving averages #' dt[, ema_short := ema(close, n = 10, wilder = TRUE)] #' dt[, ema_long := ema(close, n = 50, wilder = TRUE)] -#' +#' #' dt |> #' ggplot2::ggplot(ggplot2::aes( #' x = datetime, @@ -117,7 +116,7 @@ StatMovingAverage <- ggplot2::ggproto( #' axis.text.x = ggplot2::element_text(angle = 75, vjust = 0.925, hjust = 0.975), #' panel.grid.minor = ggplot2::element_blank() #' ) -#' +#' #' @export stat_movingaverages <- function( @@ -134,8 +133,7 @@ stat_movingaverages <- function( short = "yellow", long = "purple" ), - ... -) { + ...) { list( ggplot2::layer( stat = StatMovingAverage, @@ -187,5 +185,3 @@ stat_movingaverages <- function( # # allows user to choose which values to use for calculations # # accepts wilder as an additional argument # stat_movingaverages(ggplot2::aes(y = close), FUN = TTR::SMA) - - diff --git a/R/stat_shade_ranges.R b/R/stat_shade_ranges.R index e5c423f..abcd088 100644 --- a/R/stat_shade_ranges.R +++ b/R/stat_shade_ranges.R @@ -1,4 +1,9 @@ - +#' StatShadedDateRange +#' +#' @rdname ggplot2-ggproto +#' @format NULL +#' @usage NULL +#' @export StatShadedDateRange <- ggplot2::ggproto( "StatShadedDateRange", ggplot2::Stat, @@ -66,32 +71,50 @@ StatShadedDateRange <- ggplot2::ggproto( ) -#' @title Shaded Date Ranges `ggplot2` layer -#' @author Dereck Mezquita +#' Shaded Date Ranges ggplot2 layer #' -#' @param mapping A `ggplot2::aes` object (required - default `NULL`). -#' @param data A `data.table` object (required - default `NULL`). -#' @param ... Additional arguments passed to `ggplot2::layer`. +#' This function creates a ggplot2 layer that shades date ranges based on grouped data. +#' It's particularly useful for highlighting specific periods in time series data. #' -#' @details +#' @param mapping Set of aesthetic mappings created by \code{\link[ggplot2]{aes}}. +#' Must include `x` for dates and `group` for categorizing ranges. +#' @param data The data to be displayed in this layer. If NULL, the default, +#' the data is inherited from the plot data as specified in the call to \code{\link[ggplot2]{ggplot}}. +#' @param geom The geometric object to use display the data. Default is "linerange". +#' @param position Position adjustment, either as a string, or the result of a call to a position adjustment function. Default is "identity". +#' @param na.rm If FALSE, the default, missing values are removed with a warning. +#' If TRUE, missing values are silently removed. +#' @param show.legend logical. Should this layer be included in the legends? +#' NA, the default, includes if any aesthetics are mapped. +#' @param inherit.aes If FALSE, overrides the default aesthetics, +#' rather than combining with them. +#' @param ... Other arguments passed on to \code{\link[ggplot2]{layer}}. +#' These are often aesthetics, used to set an aesthetic to a fixed value. #' -#' This is a `ggplot2` extension; it is used with the `+` operator for adding a layer to a `ggplot2` object. -#' -#' You can set the colour by fill aesthetic with a column. +#' @return A ggplot2 layer object. #' -#' @return A `ggplot2::layer` object. -#' #' @examples #' \dontrun{ -#' dt |> -#' ggplot2::ggplot(ggplot2::aes(x = datetime)) + -#' ggplot2::geom_line(ggplot2::aes(y = close), linewidth = 1.5, colour = "white") + -#' plots$stat_shade_ranges(ggplot2::aes(group = call, fill = call), alpha = 0.25) + -#' ggplot2::scale_color_manual( -#' name = "call", -#' values = c("buy" = "green", "sell" = "red", "none" = "gray"), -#' aesthetics = "fill" -#' ) +#' library(ggplot2) +#' library(data.table) +#' +#' # Create sample data +#' dt <- data.table( +#' datetime = seq(as.POSIXct("2023-01-01"), as.POSIXct("2023-12-31"), by = "day"), +#' close = runif(365, 100, 200), +#' call = sample(c("buy", "sell", "none"), 365, replace = TRUE, prob = c(0.3, 0.3, 0.4)) +#' ) +#' +#' # Create plot with shaded ranges +#' ggplot(dt, aes(x = datetime)) + +#' geom_line(aes(y = close), linewidth = 1.5, colour = "white") + +#' stat_shade_ranges(aes(group = call, fill = call), alpha = 0.25) + +#' scale_fill_manual( +#' name = "Call", +#' values = c("buy" = "green", "sell" = "red", "none" = "gray") +#' ) + +#' theme_minimal() + +#' labs(title = "Stock Price with Buy/Sell Signals", x = "Date", y = "Price") #' } #' #' @export @@ -103,8 +126,7 @@ stat_shade_ranges <- function( na.rm = TRUE, show.legend = NA, inherit.aes = TRUE, - ... -) { + ...) { list( ggplot2::layer( stat = StatShadedDateRange, @@ -120,4 +142,4 @@ stat_shade_ranges <- function( ) ) ) -} \ No newline at end of file +} diff --git a/R/theme_dereck.R b/R/theme_dereck.R index 0974741..a3b3ee9 100644 --- a/R/theme_dereck.R +++ b/R/theme_dereck.R @@ -10,7 +10,7 @@ #' ggplot2::ggplot(ggplot2::aes(x = Sepal.Length, y = Sepal.Width)) + #' ggplot2::geom_point(ggplot2::aes(color = Species, shape = Species)) + #' ggplot2::labs(title = "Iris data", subtitle = "Classic data", x = "Sepal Length", y = "Sepal Width") + -#' ggplot2::facet_grid(~ Species) + +#' ggplot2::facet_grid(~Species) + #' dmplot::theme_dereck_light() #' #' data.frame(year = time(nhtemp), tmps = as.matrix(nhtemp)) |> @@ -24,20 +24,16 @@ theme_dereck_light <- function(base_size = 11, base_family = "") { ggplot2::theme_bw(base_size = base_size, base_family = base_family) %+replace% ggplot2::theme( plot.title = ggplot2::element_text(face = "bold", hjust = 1, margin = ggplot2::margin(0, 0, 5, 0, unit = "pt")), # 0.5 centres when position is set to "plot" plot.subtitle = ggplot2::element_text(hjust = 1, vjust = 0.015, margin = ggplot2::margin(0, 0, 5, 0, unit = "pt")), - panel.background = ggplot2::element_blank(), # panel.border = ggplot2::element_rect(color = "#afafaf", fill = NA), axis.line = ggplot2::element_blank(), panel.border = ggplot2::element_blank(), - panel.grid.minor = ggplot2::element_line(color = "#454545", size = 0.135, linetype = "dotted"), panel.grid.major = ggplot2::element_line(color = "#aaaaaa", size = 0.175, linetype = "longdash"), # axis.line = ggplot2::element_line(color = "#afafaf"), axis.ticks = ggplot2::element_line(color = "#aaaaaa"), - strip.background = ggplot2::element_rect(fill = "white", colour = "#676767"), - legend.position = "bottom", legend.title = ggplot2::element_text(vjust = 0.85) # adjust title position higher to key when bottom ) @@ -55,7 +51,7 @@ theme_dereck_light <- function(base_size = 11, base_family = "") { #' ggplot2::ggplot(ggplot2::aes(x = Sepal.Length, y = Sepal.Width)) + #' ggplot2::geom_point(ggplot2::aes(color = Species, shape = Species)) + #' ggplot2::labs(title = "Iris data", subtitle = "Classic data", x = "Sepal Length", y = "Sepal Width") + -#' ggplot2::facet_grid(~ Species) + +#' ggplot2::facet_grid(~Species) + #' dmplot::theme_dereck_dark() #' #' data.frame(year = time(nhtemp), tmps = as.matrix(nhtemp)) |> @@ -74,23 +70,20 @@ theme_dereck_dark <- function(base_size = 12, base_family = "") { # panel.border = ggplot2::element_rect(color = "#afafaf", fill = NA), axis.line = ggplot2::element_blank(), panel.border = ggplot2::element_blank(), - panel.grid.minor = ggplot2::element_line(color = "white", size = 0.135, linetype = "dotted"), panel.grid.major = ggplot2::element_line(color = "#aaaaaa", size = 0.175, linetype = "longdash"), # axis.line = ggplot2::element_line(color = "#afafaf"), axis.ticks = ggplot2::element_line(color = "#aaaaaa"), - strip.background = ggplot2::element_rect(fill = "white", colour = "#676767"), - legend.position = "bottom", legend.title = ggplot2::element_text(vjust = 0.85), # adjust title position higher to key when bottom # dark theme configs plot.background = ggplot2::element_rect(fill = "#333333"), panel.background = ggplot2::element_rect(fill = "#1E1E1E"), - legend.background = ggplot2::element_rect(fill = "#252526"), # + legend.background = ggplot2::element_rect(fill = "#252526"), # text = ggplot2::element_text(colour = "#CFCFCF"), axis.text = ggplot2::element_text(colour = "#CFCFCF") ) -} \ No newline at end of file +} diff --git a/check-install.sh b/check-install.sh deleted file mode 100755 index cf07667..0000000 --- a/check-install.sh +++ /dev/null @@ -1,31 +0,0 @@ -#!/usr/bin/env bash - -# if $1 does not match either check or install -if [[ $1 != "check" ]] && [[ $1 != "install" ]] && [[ $1 != "check-install" ]]; then - echo "Usage: package-management.sh [check|install|check-install]" -fi - -if [[ $1 == "check" ]]; then - Rscript -e "devtools::check()" -fi - -if [[ $1 == "install" ]]; then - # get name of current directory - PROJECT_DIR=$(pwd) - PKGNAME=$(basename $(pwd)) - cd .. - R CMD build $PKGNAME - R CMD INSTALL --no-multiarch --with-keep.source $PKGNAME - cd $PROJECT_DIR -fi - -if [[ $1 == "check-install" ]]; then - Rscript -e "devtools::check()" - # get name of current directory - PROJECT_DIR=$(pwd) - PKGNAME=$(basename $(pwd)) - cd .. - R CMD build $PKGNAME - R CMD INSTALL --no-multiarch --with-keep.source $PKGNAME - cd $PROJECT_DIR -fi diff --git a/demo/macd.R b/demo/macd.R index e4cf24f..ac9e3a3 100644 --- a/demo/macd.R +++ b/demo/macd.R @@ -1,4 +1,3 @@ - # get some financial data # kucoin is private package - you can use any data source ticker <- "BTC/USDT" @@ -6,7 +5,7 @@ ticker <- "BTC/USDT" dt <- kucoin::get_market_data( symbols = ticker, from = "2022-11-28 15:29:43 EST", # lubridate::now() - lubridate::days(7), - to = "2022-12-05 15:29:31 EST",# lubridate::now(), + to = "2022-12-05 15:29:31 EST", # lubridate::now(), frequency = "1 hour" ) @@ -15,7 +14,9 @@ dt # we need a function that calculates the indicator for us # typically I like to write my own functions in C++; in this case we will use TTR's # the stat expects a named list to be returned - we redefine ttr -macd <- function(x, s = 12, l = 26, k = 9) {as.list(as.data.frame(TTR::MACD(x, s, l, k)))} +macd <- function(x, s = 12, l = 26, k = 9) { + as.list(as.data.frame(TTR::MACD(x, s, l, k))) +} # macd(dt$close) dt[, c("macd", "macd_signal") := macd(close, s = 12, l = 26, k = 9)] @@ -41,4 +42,3 @@ na.omit(dt) |> axis.text.x = ggplot2::element_text(angle = 75, vjust = 0.925, hjust = 0.975), panel.grid.minor = ggplot2::element_blank() ) - diff --git a/inst/WORDLIST b/inst/WORDLIST index 00741f5..f82f287 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,23 +1,49 @@ +aes +api aut +bb bioconductor +Bollinger +bollingerbands +BTC +colour +colours cre +csv +datetime dereck Dereck +Dereck's dereckmezquita +derecksnotes +Dereck’s dmplot ggplot io jira +jpeg +jpg knitr kucoin LazyData +lfs +Lifecycle +linewidth LinkingTo +macd +MACD +mavg mezquita Mezquita +movingaverages ORCID +png rcmdcheck rmarkdown RoxygenNote todo +USDT vcs VignetteBuilder +ymax +ymin diff --git a/renv.lock b/renv.lock deleted file mode 100644 index 0ebbbb1..0000000 --- a/renv.lock +++ /dev/null @@ -1,850 +0,0 @@ -{ - 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} - } -} diff --git a/renv/.gitignore b/renv/.gitignore deleted file mode 100644 index 0ec0cbb..0000000 --- a/renv/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -library/ -local/ -cellar/ -lock/ -python/ -sandbox/ -staging/ diff --git a/renv/activate.R b/renv/activate.R deleted file mode 100644 index d13f993..0000000 --- a/renv/activate.R +++ /dev/null @@ -1,1220 +0,0 @@ - -local({ - - # the requested version of renv - version <- "1.0.7" - attr(version, "sha") <- NULL - - # the project directory - project <- Sys.getenv("RENV_PROJECT") - if (!nzchar(project)) - project <- getwd() - - # use start-up diagnostics if enabled - diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") - if (diagnostics) { - start <- Sys.time() - profile <- tempfile("renv-startup-", fileext = ".Rprof") - utils::Rprof(profile) - on.exit({ - utils::Rprof(NULL) - elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) - writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) - writeLines(sprintf("- Profile: %s", profile)) - print(utils::summaryRprof(profile)) - }, add = TRUE) - } - - # figure out whether the autoloader is enabled - enabled <- local({ - - # first, check config option - override <- getOption("renv.config.autoloader.enabled") - if (!is.null(override)) - return(override) - - # if we're being run in a context where R_LIBS is already set, - # don't load -- presumably we're being run as a sub-process and - # the parent process has already set up library paths for us - rcmd <- Sys.getenv("R_CMD", unset = NA) - rlibs <- Sys.getenv("R_LIBS", unset = NA) - if (!is.na(rlibs) && !is.na(rcmd)) - return(FALSE) - - # next, check environment variables - # TODO: prefer using the configuration one in the future - envvars <- c( - "RENV_CONFIG_AUTOLOADER_ENABLED", - "RENV_AUTOLOADER_ENABLED", - "RENV_ACTIVATE_PROJECT" - ) - - for (envvar in envvars) { - envval <- Sys.getenv(envvar, unset = NA) - if (!is.na(envval)) - return(tolower(envval) %in% c("true", "t", "1")) - } - - # enable by default - TRUE - - }) - - # bail if we're not enabled - if (!enabled) { - - # if we're not enabled, we might still need to manually load - # the user profile here - profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") - if (file.exists(profile)) { - cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") - if (tolower(cfg) %in% c("true", "t", "1")) - sys.source(profile, envir = globalenv()) - } - - return(FALSE) - - } - - # avoid recursion - if (identical(getOption("renv.autoloader.running"), TRUE)) { - warning("ignoring recursive attempt to run renv autoloader") - return(invisible(TRUE)) - } - - # signal that we're loading renv during R startup - options(renv.autoloader.running = TRUE) - on.exit(options(renv.autoloader.running = NULL), add = TRUE) - - # signal that we've consented to use renv - options(renv.consent = TRUE) - - # load the 'utils' package eagerly -- this ensures that renv shims, which - # mask 'utils' packages, will come first on the search path - library(utils, lib.loc = .Library) - - # unload renv if it's already been loaded - if ("renv" %in% loadedNamespaces()) - unloadNamespace("renv") - - # load bootstrap tools - `%||%` <- 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 deleted file mode 100644 index ffdbb32..0000000 --- a/renv/settings.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "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 -}