First demo commit

.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

@@ -0,0 +1,13 @@
+Package: ekplektoR
+Type: Package
+Title: Network Analysis for Cell- and Systems Biology
+Version: 0.1.0
+Author: Boris Steipe et al.
+Maintainer: Boris Steipe <[email protected]>
+Description: ekplektor combines a workflow for affected-subnetwork discovery in
+    cancer genome data and analysis tools.
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+Suggests: testthat
+RoxygenNote: 6.0.1

NAMESPACE

@@ -0,0 +1 @@
+exportPattern("^[[:alpha:]]+")

R/hello.R

@@ -0,0 +1,12 @@
+# hello.R
+#
+# This is an example function which prints 'Hello, world!' and returns the first
+# seven Fibonacci numbers.
+#
+
+hello <- function() {
+  print("Hello, world!")
+  return(c(1, 1, 2, 3, 5, 8, 13))
+}
+
+# [END]

README

@@ -0,0 +1,22 @@
+ekplektoR
+
+----------------------------------------------
+This package follows the structure and process
+suggested by Hadley Wickham in:
+
+
+  R Packages
+  http://r-pkgs.had.co.nz/
+
+-----------------------------------------------
+Some useful keyboard shortcuts for package authoring:
+
+  Build and Reload Package:  'Cmd + Shift + B'
+  Check Package:             'Cmd + Shift + E'
+  Test Package:              'Cmd + Shift + T'
+-----------------------------------------------
+
+Run before every commit:
+   library(devtools)
+   devtools::check()  # or Cmd + Shift + E
+DO NOT SUBMIT CODE that does not pass without error, warnings and notes.

ekplektoR.Rproj

@@ -0,0 +1,19 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: XeLaTeX
+
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

man/hello.Rd

@@ -0,0 +1,12 @@
+\name{hello}
+\alias{hello}
+\title{Hello, World!}
+\usage{
+hello()
+}
+\description{
+Prints 'Hello, world!'.
+}
+\examples{
+hello()
+}

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(ekplektoR)
+
+test_check("ekplektoR")

tests/testthat/testHello.R

@@ -0,0 +1,10 @@
+# testHello.R
+#
+#
+context("Demo test")
+
+test_that("hello.R returns a vector with the first seven Fibonacci numbers", {
+    expect_equal(sum(hello()), 33)
+})
+
+# [END]