Merge pull request #6 from stan-dev/init_cpp

add init_cpp function and also call it from rstan_package_skeleton

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: rstantools
 Type: Package
 Title: Tools for Developing R Packages Interfacing with 'Stan'
-Version: 1.2.0
-Date: 2017-03-17
+Version: 1.2.1
+Date: 2017-03-29
 Authors@R: c(person("Jonah", "Gabry", email = "jsg2201@columbia.edu",
                     role = c("aut", "cre")),
              person("Ben", "Goodrich", email = "benjamin.goodrich@columbia.edu",
@@ -27,7 +27,7 @@ Suggests:
     rstan (>= 2.14.1),
     rstanarm (>= 2.14.1),
     shinystan (>= 2.2.1),
-    loo (>= 1.0.0),
+    loo (>= 1.1.0),
     testthat,
     covr,
     knitr,

NAMESPACE

@@ -5,6 +5,7 @@ S3method(posterior_interval,default)
 S3method(predictive_error,default)
 S3method(predictive_interval,default)
 S3method(prior_summary,default)
+export(init_cpp)
 export(log_lik)
 export(loo_linpred)
 export(loo_pit)

NEWS.md

@@ -1,3 +1,9 @@
+# rstantools 1.2.1
+(Github issue/PR numbers in parentheses)
+
+* Add `init_cpp` function for generating `src/init.cpp` in order to pass R CMD
+check in R 3.4.x. `rstan_package_skeleton` calls `init_cpp` internally. (#6)
+
 # rstantools 1.2.0
 
 (Github issue/PR numbers in parentheses)

R/init_cpp.R

@@ -0,0 +1,53 @@
+#' Register functions implemented in C++
+#'
+#' If you set up your package using \code{\link{rstan_package_skeleton}} before
+#' version \code{1.2.1} of \pkg{rstantools} it may be necessary for you to call
+#' this function yourself in order to pass \code{R CMD check} in \R \code{>=
+#' 3.4}. If you used \code{rstan_package_skeleton} in \pkg{rstantools} version
+#' \code{1.2.1} or later then this has already been done automatically.
+#'
+#' @export
+#' @param name The name of your package as a string.
+#' @param path The path to the root directory for your package as a string. If
+#'   not specified it is assumed that this is already the current working
+#'   directory.
+#' @return This function is only called for its side effect of writing the
+#'   necessary \code{init.cpp} file to the package's \code{src/} directory.
+#'
+init_cpp <- function(name, path) {
+  file <- file.path("src", "init.cpp")
+  if (!missing(path))
+    file <- file.path(path, file)
+
+  cat(
+    "// Generated by the rstantools package\n\n",
+    "#include <R.h>",
+    "#include <Rinternals.h>",
+    "#include <R_ext/Rdynload.h>",
+    "#include <R_ext/Visibility.h>",
+    "#include <Rversion.h>",
+    sep = "\n",
+    file = file,
+    append = FALSE
+  )
+
+  cat(
+    "\n\nstatic const R_CallMethodDef CallEntries[] = {",
+    "  {NULL, NULL, 0}",
+    "};",
+    sep = "\n",
+    file = file,
+    append = TRUE
+  )
+
+  cat(
+    paste0("\n\nvoid attribute_visible R_init_", name, "(DllInfo *dll) {"),
+    "  // next line is necessary to avoid a NOTE from R CMD check",
+    "  R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);",
+    "  R_useDynamicSymbols(dll, TRUE); // necessary for .onLoad() to work",
+    "}",
+    sep = "\n",
+    file = file,
+    append = TRUE
+  )
+}

R/rstan_package_skeleton.R

@@ -1,5 +1,5 @@
 # This file is part of rstantools
-# Copyright (C) 2015, 2016 Trustees of Columbia University
+# Copyright (C) 2015, 2016, 2017 Trustees of Columbia University
 #
 # rstantools is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
@@ -163,6 +163,8 @@ rstan_package_skeleton <-
       destfile = file.path(SRC, "Makevars.win"),
       quiet = TRUE
     )
+    # register cpp (src/init.cpp)
+    init_cpp(name, path = DIR)
 
     message("Updating R directory ...", domain = NA)
     R <- file.path(DIR, "R")

tests/testthat/test-rstan_package_skeleton.R

@@ -36,6 +36,11 @@ test_that(".stan file included", {
 test_that("R/stanmodels.R file included", {
   expect_true("R/stanmodels.R" %in% pkg_files)
 })
+test_that("src/init.cpp file included", {
+  expect_true("src/init.cpp" %in% pkg_files)
+  init <- readLines(file.path(pkg_path, "src/init.cpp"))
+  expect_true(any(grepl("R_init_testPackage", init)))
+})
 
 test_that("messages are generated", {
   expect_message(