diff --git a/packrat/init.R b/packrat/init.R deleted file mode 100644 index ea4db78..0000000 --- a/packrat/init.R +++ /dev/null @@ -1,226 +0,0 @@ -local({ - - ## Helper function to get the path to the library directory for a - ## given packrat project. - getPackratLibDir <- function(projDir = NULL) { - path <- file.path("packrat", "lib", R.version$platform, getRversion()) - - if (!is.null(projDir)) { - - ## Strip trailing slashes if necessary - projDir <- sub("/+$", "", projDir) - - ## Only prepend path if different from current working dir - if (!identical(normalizePath(projDir), normalizePath(getwd()))) - path <- file.path(projDir, path) - } - - path - } - - ## Ensure that we set the packrat library directory relative to the - ## project directory. Normally, this should be the working directory, - ## but we also use '.rs.getProjectDirectory()' if necessary (e.g. we're - ## rebuilding a project while within a separate directory) - libDir <- if (exists(".rs.getProjectDirectory")) - getPackratLibDir(.rs.getProjectDirectory()) - else - getPackratLibDir() - - ## Unload packrat in case it's loaded -- this ensures packrat _must_ be - ## loaded from the private library. Note that `requireNamespace` will - ## succeed if the package is already loaded, regardless of lib.loc! - if ("packrat" %in% loadedNamespaces()) - try(unloadNamespace("packrat"), silent = TRUE) - - if (suppressWarnings(requireNamespace("packrat", quietly = TRUE, lib.loc = libDir))) { - - # Check 'print.banner.on.startup' -- when NA and RStudio, don't print - print.banner <- packrat::get_opts("print.banner.on.startup") - if (print.banner == "auto" && is.na(Sys.getenv("RSTUDIO", unset = NA))) { - print.banner <- TRUE - } else { - print.banner <- FALSE - } - return(packrat::on(print.banner = print.banner)) - } - - ## Escape hatch to allow RStudio to handle bootstrapping. This - ## enables RStudio to provide print output when automagically - ## restoring a project from a bundle on load. - if (!is.na(Sys.getenv("RSTUDIO", unset = NA)) && - is.na(Sys.getenv("RSTUDIO_PACKRAT_BOOTSTRAP", unset = NA))) { - Sys.setenv("RSTUDIO_PACKRAT_BOOTSTRAP" = "1") - setHook("rstudio.sessionInit", function(...) { - # Ensure that, on sourcing 'packrat/init.R', we are - # within the project root directory - if (exists(".rs.getProjectDirectory")) { - owd <- getwd() - setwd(.rs.getProjectDirectory()) - on.exit(setwd(owd), add = TRUE) - } - source("packrat/init.R") - }) - return(invisible(NULL)) - } - - ## Bootstrapping -- only performed in interactive contexts, - ## or when explicitly asked for on the command line - if (interactive() || "--bootstrap-packrat" %in% commandArgs(TRUE)) { - - needsRestore <- "--bootstrap-packrat" %in% commandArgs(TRUE) - - message("Packrat is not installed in the local library -- ", - "attempting to bootstrap an installation...") - - ## We need utils for the following to succeed -- there are calls to functions - ## in 'restore' that are contained within utils. utils gets loaded at the - ## end of start-up anyhow, so this should be fine - library("utils", character.only = TRUE) - - ## Install packrat into local project library - packratSrcPath <- list.files(full.names = TRUE, - file.path("packrat", "src", "packrat") - ) - - ## No packrat tarballs available locally -- try some other means of installation - if (!length(packratSrcPath)) { - - message("> No source tarball of packrat available locally") - - ## There are no packrat sources available -- try using a version of - ## packrat installed in the user library to bootstrap - if (requireNamespace("packrat", quietly = TRUE) && packageVersion("packrat") >= "0.2.0.99") { - message("> Using user-library packrat (", - packageVersion("packrat"), - ") to bootstrap this project") - } - - ## Couldn't find a user-local packrat -- try finding and using devtools - ## to install - else if (requireNamespace("devtools", quietly = TRUE)) { - message("> Attempting to use devtools::install_github to install ", - "a temporary version of packrat") - library(stats) ## for setNames - devtools::install_github("rstudio/packrat") - } - - ## Try downloading packrat from CRAN if available - else if ("packrat" %in% rownames(available.packages())) { - message("> Installing packrat from CRAN") - install.packages("packrat") - } - - ## Fail -- couldn't find an appropriate means of installing packrat - else { - stop("Could not automatically bootstrap packrat -- try running ", - "\"'install.packages('devtools'); devtools::install_github('rstudio/packrat')\"", - "and restarting R to bootstrap packrat.") - } - - # Restore the project, unload the temporary packrat, and load the private packrat - if (needsRestore) - packrat::restore(prompt = FALSE, restart = TRUE) - - ## This code path only reached if we didn't restart earlier - unloadNamespace("packrat") - requireNamespace("packrat", lib.loc = libDir, quietly = TRUE) - return(packrat::on()) - - } - - ## Multiple packrat tarballs available locally -- try to choose one - ## TODO: read lock file and infer most appropriate from there; low priority because - ## after bootstrapping packrat a restore should do the right thing - if (length(packratSrcPath) > 1) { - warning("Multiple versions of packrat available in the source directory;", - "using packrat source:\n- ", shQuote(packratSrcPath)) - packratSrcPath <- packratSrcPath[[1]] - } - - - lib <- file.path("packrat", "lib", R.version$platform, getRversion()) - if (!file.exists(lib)) { - dir.create(lib, recursive = TRUE) - } - - message("> Installing packrat into project private library:") - message("- ", shQuote(lib)) - - surround <- function(x, with) { - if (!length(x)) return(character()) - paste0(with, x, with) - } - - - ## Invoke install.packages() in clean R session - peq <- function(x, y) paste(x, y, sep = " = ") - installArgs <- c( - peq("pkgs", surround(packratSrcPath, with = "'")), - peq("lib", surround(lib, with = "'")), - peq("repos", "NULL"), - peq("type", surround("source", with = "'")) - ) - - fmt <- "utils::install.packages(%s)" - installCmd <- sprintf(fmt, paste(installArgs, collapse = ", ")) - - ## Write script to file (avoid issues with command line quoting - ## on R 3.4.3) - installFile <- tempfile("packrat-bootstrap", fileext = ".R") - writeLines(installCmd, con = installFile) - on.exit(unlink(installFile), add = TRUE) - - fullCmd <- paste( - surround(file.path(R.home("bin"), "R"), with = "\""), - "--vanilla", - "--slave", - "-f", - surround(installFile, with = "\"") - ) - system(fullCmd) - - ## Tag the installed packrat so we know it's managed by packrat - ## TODO: should this be taking information from the lockfile? this is a bit awkward - ## because we're taking an un-annotated packrat source tarball and simply assuming it's now - ## an 'installed from source' version - - ## -- InstallAgent -- ## - installAgent <- "InstallAgent: packrat 0.4.9-3" - - ## -- InstallSource -- ## - installSource <- "InstallSource: source" - - packratDescPath <- file.path(lib, "packrat", "DESCRIPTION") - DESCRIPTION <- readLines(packratDescPath) - DESCRIPTION <- c(DESCRIPTION, installAgent, installSource) - cat(DESCRIPTION, file = packratDescPath, sep = "\n") - - # Otherwise, continue on as normal - message("> Attaching packrat") - library("packrat", character.only = TRUE, lib.loc = lib) - - message("> Restoring library") - if (needsRestore) - packrat::restore(prompt = FALSE, restart = FALSE) - - # If the environment allows us to restart, do so with a call to restore - restart <- getOption("restart") - if (!is.null(restart)) { - message("> Packrat bootstrap successfully completed. 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Entering packrat mode...") - packrat::on() - } - - Sys.unsetenv("RSTUDIO_PACKRAT_BOOTSTRAP") - - } - -}) diff --git a/packrat/packrat.lock b/packrat/packrat.lock deleted file mode 100644 index 9d2f944..0000000 --- a/packrat/packrat.lock +++ /dev/null @@ -1,857 +0,0 @@ -PackratFormat: 1.4 -PackratVersion: 0.4.9.3 -RVersion: 3.5.1 -Repos: CRAN=https://cran.rstudio.com/ - -Package: BH -Source: CRAN -Version: 1.66.0-1 -Hash: 4cc8883584b955ed01f38f68bc03af6d - -Package: DBI -Source: CRAN -Version: 1.0.0 -Hash: 6abedd7919c4457604c0aa44529a6683 - -Package: DiagrammeR -Source: CRAN -Version: 1.0.0 -Hash: 09fbb1773ad6bf64dd4e8b2ea4f2bea4 -Requires: RColorBrewer, downloader, dplyr, glue, htmltools, - htmlwidgets, igraph, influenceR, magrittr, purrr, readr, rgexf, - rlang, rstudioapi, scales, stringr, tibble, tidyr, viridis, - visNetwork - -Package: FactoClass -Source: CRAN -Version: 1.2.7 -Hash: b82761277250232837e3791a983fcc41 -Requires: ade4, ggplot2, ggrepel, scatterplot3d, xtable - -Package: 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