From 11d7d5c342161a081b3d161995499a8afd8fbe4f Mon Sep 17 00:00:00 2001
From: karissawhiting <whitingk@mskcc.org>
Date: Thu, 25 Apr 2024 16:39:36 -0400
Subject: [PATCH] add packages

---
 .Rbuildignore     |  2 ++
 .gitignore        |  1 +
 DESCRIPTION       | 23 +++++++++++++
 NAMESPACE         |  2 ++
 R/attach.R        | 83 +++++++++++++++++++++++++++++++++++++++++++++++
 R/utils.R         | 55 +++++++++++++++++++++++++++++++
 R/zzz.R           | 12 +++++++
 genomeverse.Rproj | 22 +++++++++++++
 8 files changed, 200 insertions(+)
 create mode 100644 .Rbuildignore
 create mode 100644 .gitignore
 create mode 100644 DESCRIPTION
 create mode 100644 NAMESPACE
 create mode 100644 R/attach.R
 create mode 100644 R/utils.R
 create mode 100644 R/zzz.R
 create mode 100644 genomeverse.Rproj

diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..a4ef341
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,2 @@
+^genomeverse\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..cd67eac
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+.Rproj.user
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000..07272b3
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,23 @@
+Package: genomeverse
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R: 
+    person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
+    license
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Imports: 
+    cbioportalR,
+    cli,
+    crayon,
+    gnomeR (>= 1.2.0.9004),
+    oncokbR (>= 0.0.0.9001),
+    rstudioapi,
+    utils
+Remotes:  
+    MSKCC-Epi-Bio/gnomeR,
+    karissawhiting/oncokbR
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..6ae9268
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,2 @@
+# Generated by roxygen2: do not edit by hand
+
diff --git a/R/attach.R b/R/attach.R
new file mode 100644
index 0000000..1c30df2
--- /dev/null
+++ b/R/attach.R
@@ -0,0 +1,83 @@
+
+pkgs <- c("cbioportalR", "gnomeR", "oncokbR")
+
+genomeverse_attach <- function() {
+  # Create `to_load` which is a character vector of all genomeverse
+  # packages not loaded in the current R session.
+  to_load <- check_loaded()
+
+  # If to_load has length 0, all main packages are loaded.
+  # Nothing will be attached.
+  if (length(to_load) == 0) {
+    return(invisible())
+  }
+
+  # Create a line rule with two text labels:
+  # "Attaching packages" on the left-hand side and
+  # genomeverse with the package version on the right-hand side
+  load_header <- cli::rule(
+    left = crayon::bold("Attaching packages"),
+    right = paste0("genomeverse ", package_version("genomeverse"))
+  )
+
+  # Return a character string containing the package version for each of genomeverse's constituents
+  versions <- vapply(to_load, package_version, character(1))
+
+  packages <- paste0(
+    crayon::green(cli::symbol$tick), " ", crayon::blue(format(to_load)), " ",
+    crayon::col_align(versions, max(crayon::col_nchar(versions)))
+  )
+
+  # Format for two columns
+  # if there is an odd number of packages, add ""
+  if (length(packages) %% 2 == 1) {
+    packages <- append(packages, "")
+  }
+  # Divide the packages into column 1 and 2
+  col1 <- seq_len(length(packages) / 2)
+  # paste the packages in column one with a space and those not in column 1
+  info <- paste0(packages[col1], "     ", packages[-col1])
+
+  # display the message!
+  msg(load_header)
+  msg(paste(info, collapse = "\n"))
+
+  # Load the constituent packages!
+  # character.only = TRUE must be used in order to
+  # supply character strings to `library()`
+  suppressPackageStartupMessages(
+    lapply(to_load, library, character.only = TRUE)
+  )
+
+  # Thanks for playing
+  invisible()
+
+}
+
+# Detach all loaded packages for seeing the pretty startup message (:
+genomeverse_detach <- function() {
+  pak <- paste0("package:", c(pkgs, "genomeverse"))
+  lapply(pak[pak %in% search()], detach, character.only = TRUE)
+  invisible()
+}
+
+#' List all packages imported by genomeverse
+#'
+#' @export
+#'
+#' @examples
+#' genomeverse_packages()
+genomeverse_packages <- function() {
+  # get all imports from genomeverse's package description file
+  raw <- utils::packageDescription("genomeverse")$Imports
+  # return a character vector of all the imports
+  imports <- strsplit(raw, ",")[[1]]
+  # "^\\s+" matches white space at the beginning of a character string
+  # "\\s+$ matches white space at the end of a character string
+  parsed <- gsub("^\\s+|\\s+$", "", imports)
+  # for each import, take only the first complete word (i.e. the package name)
+  names <- vapply(strsplit(parsed, "\\s+"), "[[", 1, FUN.VALUE = character(1))
+
+  return(names)
+
+}
diff --git a/R/utils.R b/R/utils.R
new file mode 100644
index 0000000..375498f
--- /dev/null
+++ b/R/utils.R
@@ -0,0 +1,55 @@
+
+text_col <- function(x) {
+
+  # If RStudio API is not available and/or does not have the getThemeInfo
+  # button, exit function leaving default color of black
+  if (!rstudioapi::isAvailable() || !rstudioapi::hasFun("getThemeInfo")) {
+    return(x)
+  }
+
+  # Get theme information for RStudio
+  theme <- rstudioapi::getThemeInfo()
+
+  # If it's a dark theme, make the text color white; otherwise black.
+  if (isTRUE(theme$dark)) crayon::white(x) else crayon::black(x)
+
+}
+
+# Format the package version to indicate development versions when printed on
+# the command line
+package_version <- function(x) {
+  # packageVersion returns an object with class 'package_version' and 'numeric_version'
+  # unclass removes those and it becomes a numeric
+  version <- unclass(utils::packageVersion(x))[[1]]
+
+  # if the length of the numeric version vector is > 3,
+  # as happens with development packages, coerce those
+  # dev version numbers to red
+  if (length(version) > 3) {
+    version[4:length(version)] <- crayon::red(as.character(version[4:length(version)]))
+  }
+
+  # concatenate the result
+  paste0(version, collapse = ".")
+
+}
+
+# Create a message function for start-up that dynamically changes text color
+msg <- function(...) {
+  packageStartupMessage(text_col(...))
+}
+
+
+# Check which of the main genomeverse packages
+# are currently loaded
+# The search() function  returns a character vector containing packages
+# attached to the current R session.
+check_loaded <- function() {
+  paks <- paste0("package:", pkgs)
+  pkgs[!paks %in% search()]
+}
+
+# Is a package attached?
+is_attached <- function(x) {
+  paste0("package:", x) %in% search()
+}
diff --git a/R/zzz.R b/R/zzz.R
new file mode 100644
index 0000000..475dfe7
--- /dev/null
+++ b/R/zzz.R
@@ -0,0 +1,12 @@
+.onAttach <- function(...) {
+  # See if any packages are needed
+  needed <- pkgs[!is_attached(pkgs)]
+  # If no packages are needed, return
+  if (length(needed) == 0) {
+    return()
+    # Otherwise, attach any needed packages
+  } else {
+    genomeverse_attach()
+  }
+
+}
diff --git a/genomeverse.Rproj b/genomeverse.Rproj
new file mode 100644
index 0000000..69fafd4
--- /dev/null
+++ b/genomeverse.Rproj
@@ -0,0 +1,22 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace