init commit

.Rbuildignore

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+^packrat/
+^\.Rprofile$
+^.*\.Rproj$
+^\.Rproj\.user$

.Rprofile

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+#### -- Packrat Autoloader (version 0.4.8-1) -- ####
+source("packrat/init.R")
+#### -- End Packrat Autoloader -- ####

.gitignore

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+packrat/lib*/
+.Rproj.user

DESCRIPTION

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+Package: ghibli
+Type: Package
+Title: What the Package Does (Title Case)
+Version: 0.1.0
+Author: Who wrote it
+Maintainer: The package maintainer <yourself@somewhere.net>
+Description: More about what it does (maybe more than one line)
+    Use four spaces when indenting paragraphs within the Description.
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true

NAMESPACE

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+exportPattern("^[[:alpha:]]+")

R/colours.R

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+#' Complete list of palettes
+#'
+#' Use \code{\link{wes_palette}} to construct palettes of desired length.
+#'
+#' @export
+ghibli_palettes <- list(
+  MarnieLight1 = c("#A42820", "#5F5647", "#9B110E", "#3F5151", "#4E2A1E", "#550307", "#0C1707"),
+  MarnieMedium1 = c("#FAD510", "#CB2314", "#273046", "#354823", "#1E1E1E"),
+  MarnieDark1 = c("#E1BD6D", "#EABE94", "#0B775E", "#35274A" ,"#F2300F"),
+  MarnieLight2 = c("#A42820", "#5F5647", "#9B110E", "#3F5151", "#4E2A1E", "#550307", "#0C1707"),
+  MarnieMedium2 = c("#FAD510", "#CB2314", "#273046", "#354823", "#1E1E1E"),
+  MarnieDark2 = c("#E1BD6D", "#EABE94", "#0B775E", "#35274A" ,"#F2300F"),
+  PonyoLight = c("#899DA4", "#C93312", "#FAEFD1", "#DC863B"),
+  PonyoMedium = c("#9A8822", "#F5CDB4", "#F8AFA8", "#FDDDA0", "#74A089"),
+  PonyoDark = c("#3B9AB2", "#78B7C5", "#EBCC2A", "#E1AF00", "#F21A00"),
+  LaputaLight = c("#FF0000", "#00A08A", "#F2AD00", "#F98400", "#5BBCD6"),
+  LaputaMedium = c("#ECCBAE", "#046C9A", "#D69C4E", "#ABDDDE", "#000000"),
+  LaputaDark = c("#446455", "#FDD262", "#D3DDDC", "#C7B19C"),
+  MononokeLight = c("#DD8D29", "#E2D200", "#46ACC8", "#E58601", "#B40F20"),
+  MononokeMedium = c("#F3DF6C", "#CEAB07", "#D5D5D3", "#24281A"),
+  MononokeDark = c("#798E87", "#C27D38", "#CCC591", "#29211F"),
+  SpiritedLight = c("#85D4E3", "#F4B5BD", "#9C964A", "#CDC08C", "#FAD77B"),
+  SpiritedMedium = c("#D8B70A", "#02401B", "#A2A475", "#81A88D", "#972D15"),
+  SpiritedDark = c("#F1BB7B", "#FD6467", "#5B1A18", "#D67236"),
+  YesterdayLight = c("#E6A0C4", "#C6CDF7", "#D8A499", "#7294D4"),
+  YesterdayMedium = c("#E6A0C4", "#C6CDF7", "#D8A499", "#7294D4"),
+  YesterdayDark = c("#E6A0C4", "#C6CDF7", "#D8A499", "#7294D4")
+
+)
+
+#' A Wes Anderson palette generator
+#'
+#' These are a handful of color palettes from Wes Anderson movies.
+#'
+#' @param n Number of colors desired. Unfortunately most palettes now only
+#'   have 4 or 5 colors. But hopefully we'll add more palettes soon. All color
+#'   schemes are derived from the most excellent Tumblr blog:
+#'   \href{http://wesandersonpalettes.tumblr.com/}{Wes Anderson Palettes}.
+#'   If omitted, uses all colours.
+#' @param name Name of desired palette. Choices are:
+#'   \code{BottleRocket1}, \code{BottleRocket2},  \code{Rushmore1},
+#'   \code{Royal1}, \code{Royal2},  \code{Zissou1}, \code{Darjeeling1},
+#'   \code{Darjeeling2},  \code{Chevalier1} , \code{FantasticFox1} ,
+#'   \code{Moonrise1}, \code{Moonrise2}, \code{Moonrise3}, \code{Cavalcanti1},
+#'   \code{GrandBudapest1}, \code{GrandBudapest2}
+#' @param type Either "continuous" or "discrete". Use continuous if you want
+#'   to automatically interpolate between colours.
+#'   @importFrom graphics rgb rect par image text
+#' @return A vector of colours.
+#' @export
+#' @keywords colors
+#' @examples
+#' wes_palette("Royal1")
+#' wes_palette("GrandBudapest1")
+#' wes_palette("Cavalcanti1")
+#' wes_palette("Cavalcanti1", 3)
+#'
+#' # If you need more colours than normally found in a palette, you
+#' # can use a continuous palette to interpolate between existing
+#' # colours
+#' pal <- wes_palette(21, name = "Zissou1", type = "continuous")
+#' image(volcano, col = pal)
+wes_palette <- function(name, n, type = c("discrete", "continuous")) {
+  type <- match.arg(type)
+
+  pal <- wes_palettes[[name]]
+  if (is.null(pal))
+    stop("Palette not found.")
+
+  if (missing(n)) {
+    n <- length(pal)
+  }
+
+  if (type == "discrete" && n > length(pal)) {
+    stop("Number of requested colors greater than what palette can offer")
+  }
+
+  out <- switch(type,
+                continuous = grDevices::colorRampPalette(pal)(n),
+                discrete = pal[1:n]
+  )
+  structure(out, class = "palette", name = name)
+}
+
+#' @export
+#' @importFrom graphics rect par image text
+#' @importFrom grDevices rgb
+print.palette <- function(x, ...) {
+  n <- length(x)
+  old <- par(mar = c(0.5, 0.5, 0.5, 0.5))
+  on.exit(par(old))
+
+  image(1:n, 1, as.matrix(1:n), col = x,
+        ylab = "", xaxt = "n", yaxt = "n", bty = "n")
+
+  rect(0, 0.9, n + 1, 1.1, col = rgb(1, 1, 1, 0.8), border = NA)
+  text((n + 1) / 2, 1, labels = attr(x, "name"), cex = 1, family = "serif")
+}

ghibli.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

man/hello.Rd

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+\name{hello}
+\alias{hello}
+\title{Hello, World!}
+\usage{
+hello()
+}
+\description{
+Prints 'Hello, world!'.
+}
+\examples{
+hello()
+}

packrat/init.R

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+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)) {
+
+    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
+      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)
+    }
+    lib <- normalizePath(lib, winslash = "/")
+
+    message("> Installing packrat into project private library:")
+    message("- ", shQuote(lib))
+
+    surround <- function(x, with) {
+      if (!length(x)) return(character())
+      paste0(with, x, with)
+    }
+
+    ## The following is performed because a regular install.packages call can fail
+    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 = "'"))
+    )
+    installCmd <- paste(sep = "",
+                        "utils::install.packages(",
+                        paste(installArgs, collapse = ", "),
+                        ")")
+
+    fullCmd <- paste(
+      surround(file.path(R.home("bin"), "R"), with = "\""),
+      "--vanilla",
+      "--slave",
+      "-e",
+      surround(installCmd, 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 0.4.8-1'
+
+    ## -- 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")
+    restore(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. ",
+              "Restarting R and entering packrat mode...")
+      return(restart())
+    }
+
+    # Callers (source-erers) can define this hidden variable to make sure we don't enter packrat mode
+    # Primarily useful for testing
+    if (!exists(".__DONT_ENTER_PACKRAT_MODE__.") && interactive()) {
+      message("> Packrat bootstrap successfully completed. Entering packrat mode...")
+      packrat::on()
+    }
+
+    Sys.unsetenv("RSTUDIO_PACKRAT_BOOTSTRAP")
+
+  }
+
+})

packrat/packrat.lock

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+PackratFormat: 1.4
+PackratVersion: 0.4.8.1
+RVersion: 3.4.0
+Repos: BioCsoft=https://bioconductor.org/packages/3.5/bioc,
+    BioCann=https://bioconductor.org/packages/3.5/data/annotation,
+    BioCexp=https://bioconductor.org/packages/3.5/data/experiment,
+    BioCextra=https://bioconductor.org/packages/3.5/extra,
+    CRAN=https://cran.rstudio.com/
+
+Package: packrat
+Source: CRAN
+Version: 0.4.8-1
+Hash: 6ad605ba7b4b476d84be6632393f5765