Grooming up to regular Bioc package

.Rbuildignore

@@ -1 +1,4 @@
 TODO.org
+^.*\.Rproj$
+^\.Rproj\.user$
+README.md

DESCRIPTION

@@ -1,14 +1,16 @@
 Package: codetoolsBioC
 Title: Bioconductor Extensions for R Code Analysis Tools
 Description: Bioconductor extensions for R code analysis tools.
-Version: 0.1-0
+Version: 0.99.0
 Authors@R: c(
   person("Patrick", "Aboyoun", role="aut"),
   person("Martin", "Maechler", role="aut"),
   person("Henrik", "Bengtsson", role="ctb"),
   person("Bioconductor Package Maintainer", role="cre", email="[email protected]"))
 Depends: R (>= 2.1)
-Imports: codetools, methods, utils
+Imports: codetools, methods, utils, stats
 Suggests: stats4, Matrix, aroma.core
 License: Artistic-2.0
+Encoding: UTF-8
 biocViews: Infrastructure
+RoxygenNote: 7.1.0

NAMESPACE

@@ -1,9 +1,18 @@
-import(codetools)
-
-importFrom("methods", findClass, findFunction, getClassDef, getClasses,
-           getFunction, isClass, listFromMlist, slot)
+# Generated by roxygen2: do not edit by hand
 
-importFrom("utils", find, packageDescription)
-
-export(findExternalDeps, writeNamespaceImports, getRdFileNames,
-       writeRUnitRunner)
+export(findExternalDeps)
+export(getRdFileNames)
+export(writeNamespaceImports)
+export(writeRUnitRunner)
+import(codetools)
+importFrom(methods,findClass)
+importFrom(methods,findFunction)
+importFrom(methods,getClassDef)
+importFrom(methods,getClasses)
+importFrom(methods,getFunction)
+importFrom(methods,isClass)
+importFrom(methods,listFromMlist)
+importFrom(methods,slot)
+importFrom(stats,setNames)
+importFrom(utils,find)
+importFrom(utils,packageDescription)

NEWS.md

@@ -0,0 +1,4 @@
+# codetoolsBioC 0.99.0
+
+* Added a `NEWS.md` file to track changes to the package.
+* Started the process to make this a fully fledged Bioc package

R/codetoolsBioc-pkg.R

@@ -0,0 +1,13 @@
+#' codetoolsBioc
+#'
+#' `codetoolsBioc` is a Bioconductor package that provides ...
+#' 
+#' @import codetools
+#' @importFrom methods findClass findFunction getClassDef getClasses
+#' getFunction isClass listFromMlist slot
+#' @importFrom utils find packageDescription
+#' @importFrom stats setNames
+#'
+#' @name codetoolsBioc-pkg
+#' @docType package
+NULL

R/findExternalDeps.R

@@ -18,6 +18,29 @@ loadRequiredPackages <- function(package)
     }
 }
 
+
+
+#' Find External Dependencies of a Package
+#' 
+#' Finds external dependencies of a package.
+#' 
+#' The result is an approximation based upon the findings of \code{findGlobals}
+#' and an exploration of the package namespace.
+#' 
+#' @param package the quoted name of the package to analyze.
+#' @return A list with four components: \code{S4Classes}, \code{S4Methods},
+#' \code{functions}, and \code{variables}. Each of these components in turn
+#' holds a named list of character vectors of object names from external
+#' packages.
+#' @author Patrick Aboyoun
+#' @export
+#' @seealso \code{\link[codetools]{findGlobals}},
+#' %\code{\link[codetools]{checkUsagePackage}}, Rd file not found.
+#' @keywords programming
+#' @examples
+#' 
+#' library(stats4)
+#' findExternalDeps("stats4")
 findExternalDeps <- function(package) {
     loadRequiredPackages(package)
     pkgEnv <- getPackageEnvironment(package)

R/getNamespaceFileImports.R

@@ -21,7 +21,7 @@ getNamespaceFileImports <- function(package, lib.loc = .libPaths()) {
     } else {
         fgen <- fileContents[["general"]]
         nms.fgen <- names(fgen)
-	X <- setNames(seq_along(fgen), nms.fgen)
+        X <- setNames(seq_along(fgen), nms.fgen)
         funsAndVars <- lapply(X, function(i) {
             x.i <- fgen[[i]]
             isFunction <- vapply(x.i, function(y)

R/getRdFileNames.R

@@ -1,3 +1,27 @@
+#' Track Rd file names at which 'topic' is documented
+#' 
+#' Tracks the Rd file names at which a given 'topic' (alias) is documented.
+#' 
+#' @param topic A length-one character vector specifying the topic (alias).
+#' @param package A character vector given the packages to search for Rd file
+#' names that document the \code{topic} , or 'NULL'. By default, all the
+#' packages in the search path are used.
+#' @author Chao-Jen Wong \email{cwon2@@fhcrc.org}
+#' @export
+#' @keywords programming
+#' @examples
+#' 
+#' getRdFileNames("rbind")
+#' 
+#' isInstalled <- function(pkg)
+#'   inherits(suppressWarnings(packageDescription(pkg)), "packageDescription")
+#' 
+#' if (isInstalled("IRanges"))
+#'   getRdFileNames("rbind", package=c("base", "IRanges"))
+#' 
+#' if (isInstalled("Biobase"))
+#'   getRdFileNames("ExpressionSet", "Biobase")
+#' 
 getRdFileNames <- function(topic, package=NULL)
 {
    ## Imports
@@ -26,5 +50,4 @@ getRdFileNames <- function(topic, package=NULL)
    paths <- unlist(paths)
 
    data.frame(packages=basename(names(paths)), Rd.file=basename(paths))
- }
-
+}

R/utility-functions.R

@@ -11,11 +11,9 @@ getPackageEnvironment <- function(package) {
 ## common idioms
 ulapply <- function(...) unlist(lapply(...))
 
-suniquec <-
-    function(X, Y, what)
+suniquec <- function(X, Y, what) {
     ## optionally subset Y by elements named 'what', then make unique
     ## set with X
-{
     if (!missing(what))
         Y <- ulapply(Y, "[[", what)
     sort(unique(c(X, Y)))

R/writeNamespaceImports.R

@@ -1,12 +1,45 @@
-writeNamespaceImports <-
-    function(package, file = "", append = TRUE, quote = FALSE,
-             width = 0.9 * getOption("width"))
-{
+#' Write NAMESPACE file imports statements
+#' 
+#' Writes imports statements that can be included in a package's NAMESPACE
+#' file.
+#' 
+#' The result is an approximation based upon the findings of
+#' \code{\link{findExternalDeps}}. S4 class dependencies are embedded into
+#' importClassesFrom statements, S4 methods dependencies are embedded into
+#' importMethodsFrom statements, and all other dependencies are embedded into
+#' importFrom statements.
+#' 
+#' See the document "Writing R Extensions" that is hosted on CRAN for more
+#' details on the proper construction of a NAMESPACE file.
+#' 
+#' @param package the quoted name of the package to analyze.
+#' @param file either a character string naming a file or an open writing
+#' connection. \code{""} indicates writing to the console.
+#' @param append logical. If \code{TRUE}, the output is appended to the file.
+#' If \code{FALSE}, any existing file with the specified name is destroyed and
+#' a new one is created. This argument is only used if \code{file} is a
+#' character string.
+#' @param quote logical. If \code{TRUE}, all import fields will be
+#' double-quoted.  If \code{FALSE}, only non-standard names like
+#' \code{[<-.fractions} will be double-quoted.
+#' @param width a positive integer giving the target column for wrapping lines
+#' in the output.
+#' @author Patrick Aboyoun
+#' @export
+#' @seealso \code{\link{findExternalDeps}}
+#' @keywords programming
+#' @examples
+#' 
+#' library(stats4)
+#' writeNamespaceImports("stats4")
+#' 
+writeNamespaceImports <- function(package, file = "", append = TRUE, quote = FALSE,
+                                  width = 0.9 * getOption("width")) {
     writeImports <- function(x, prefix, file, width) {
         Rkeywords <-
-          c("NULL", "NA", "TRUE", "FALSE", "Inf", "NaN", "NA_integer_",
-            "NA_real_", "NA_character_", "NA_complex_", "function", "while",
-            "repeat", "for", "if", "in", "else", "next", "break", "...")
+            c("NULL", "NA", "TRUE", "FALSE", "Inf", "NaN", "NA_integer_",
+              "NA_real_", "NA_character_", "NA_complex_", "function", "while",
+              "repeat", "for", "if", "in", "else", "next", "break", "...")
         for (i in which(!(names(x) %in% ignoredPackages))) {
             if (quote) {
                 qstring1 <- "\""
@@ -37,7 +70,7 @@ writeNamespaceImports <-
     }
     if (!inherits(file, "connection"))
         stop("'file' must be a character string or connection")
-
+    
     allDeps <- findExternalDeps(package)
     allDepNames <- sort(unique(ulapply(allDeps, names)))
     allDepNames <- allDepNames[!(allDepNames %in% ignoredPackages)]

R/writeRUnitRunner.R

@@ -1,3 +1,33 @@
+#' Write an R code file containing a .test function to run RUnit tests
+#' 
+#' This function generates an R code file containing a single function
+#' \code{.test} that can be used to run the RUnit unit tests of a package. The
+#' generated \code{.test} function is customized for the specified package and
+#' takes care of setting up RUnit options, configuring the location of unit
+#' test files, and generating helpful summary data when tests fail.
+#' 
+#' 
+#' Copy the generated file, or its contents, into your package source.  You can
+#' add an additional R script in pkg/tests that loads your package and then
+#' calls \code{pkg:::.test()}.  This will ensure that unit tests are run during
+#' R CMD check and that a unit test failure will result in an ERROR report from
+#' R CMD check.
+#' 
+#' @param pkg Package name: a \code{.test} function will be generated
+#' customized for the specified package name.
+#' @param file Determines the file where code for the \code{.test} function
+#' will be written.
+#' @return Called for the side-effect of creating a file containing the
+#' \code{.test} function definition customized for \code{pkg}.
+#' @author Seth Falcon
+#' @export
+#' @examples
+#' 
+#'   tf <- tempfile()
+#'   writeRUnitRunner("foo", tf)
+#'   lines <- readLines(tf)
+#'   file.remove(tf)
+#' 
 writeRUnitRunner <- function(pkg, file = "runit_runner.R")
 {
     line <- paste0("BiocGenerics:::testPackage(\"", pkg, "\")")

README.md

@@ -0,0 +1,10 @@
+# codetoolsBioC
+
+The goal of `codetoolsBioc` is...
+
+## Installation
+
+```
+remotes::install_github("Bioconductor/codetoolsBioc")
+remotes::install_github("federicomarini/codetoolsBioc") # for the current fork...
+```