Merge pull request #118 from stan-dev/prepare-v2.4.0

rstantools v2.4.0

.github/workflows/check-standalone.yaml

@@ -42,8 +42,7 @@ jobs:
 
       - name: Checkout lgpr package
         run: |
-          git clone https://github.com/andrjohns/lgpr
-          cd lgpr && git checkout array-syntax
+          git clone https://github.com/jtimonen/lgpr
 
       - name: Check against CRAN StanHeaders and CRAN RStan
         run: |

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: rstantools
 Type: Package
 Title: Tools for Developing R Packages Interfacing with 'Stan'
-Version: 	2.3.1.1
-Date: 2023-07-18
+Version: 2.4.0
+Date: 2024-01-22
 Authors@R:
     c(person(given = "Jonah",
              family = "Gabry",
@@ -53,6 +53,6 @@ Suggests:
     roxygen2 (>= 6.0.1),
     rmarkdown,
     rstudioapi
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -24,6 +24,7 @@ export(predictive_interval)
 export(prior_summary)
 export(rstan_config)
 export(rstan_create_package)
+export(rstantools_load_code)
 export(use_rstan)
 importFrom(RcppParallel,RcppParallelLibs)
 importFrom(stats,quantile)

NEWS.md

@@ -1,3 +1,10 @@
+# rstantools 2.4.0
+
+* Update to match CRAN's patched version by @jgabry in #114
+* Include additional template imports to suppress NOTEs by @andrjohns in #115
+* Fix packages with stanfunctions under rstan 2.33+ by @andrjohns in #117
+
+
 # rstantools 2.3.1
 
 * Deprecated `init_cpp`. (#105)

R/rstan_create_package.R

@@ -46,7 +46,7 @@
 #' @param stan_files A character vector with paths to `.stan` files to include
 #'   in the package.
 #' @param roxygen Should \pkg{roxygen2} be used for documentation?  Defaults to
-#'   `TRUE`. If so, a file `R/{pkgname}-package.R`` is added to the package with
+#'   `TRUE`. If so, a file `R/{pkgname}-package.R` is added to the package with
 #'   roxygen tags for the required import lines. See the **Note** section below
 #'   for advice specific to the latest versions of \pkg{roxygen2}.
 #' @param travis Should a `.travis.yml` file be added to the package directory?

R/rstan_package_utils.R

@@ -103,3 +103,24 @@
   }
   invisible(acc)
 }
+
+#' Helper function for loading code in roxygenise
+#'
+#' Adapted from the \code{sourceDir} function defined
+#' by \code{example(source)}.
+#'
+#' @param path Path to directory containing code to load
+#' @param trace Whether to print file names as they are loaded
+#' @param ... Additional arguments passed to \code{\link{source}}
+#'
+#' @return \code{NULL}
+#' @export
+rstantools_load_code <- function(path, trace = TRUE, ...) {
+  op <- options(); on.exit(options(op)) # to reset after each 
+  for (nm in list.files(path, pattern = "[.][RrSsQq]$")) {
+    if (trace) cat(nm, ":")
+    source(file.path(path, nm), ...)
+    if (trace) cat("\n")
+    options(op)
+  }
+}

tests/testthat/test-rstan_create_package.R

@@ -94,8 +94,7 @@ for(ii in 1:ntest) {
       skip_on_cran()
       skip_on_travis()
     }
-    example(source) # defines the sourceDir() function
-    try(roxygen2::roxygenize(pkg_dest_path, load_code = sourceDir), silent = TRUE)
+    try(roxygen2::roxygenize(pkg_dest_path, load_code = rstantools_load_code), silent = TRUE)
     pkgbuild::compile_dll(pkg_dest_path)
     tmp <- capture.output(load_out <- pkgload::load_all(pkg_dest_path,
                                                  export_all = TRUE,

vignettes/minimal-rstan-package.Rmd

@@ -238,15 +238,12 @@ for `lm_stan` and update the `NAMESPACE` so the function is exported, i.e.,
 available to users when the package is installed.  This can be done with the
 function `roxygen2::roxygenize()`, which needs to be called twice initially.
 
-```{r, results = "hide"}
-example(source) # defines the sourceDir() function
-```
 ```{r, eval = FALSE}
-try(roxygen2::roxygenize(load_code = sourceDir), silent = TRUE)
+try(roxygen2::roxygenize(load_code = rstantools_load_code), silent = TRUE)
 roxygen2::roxygenize()
 ```
 ```{r, echo=FALSE, results="hide"}
-try(roxygen2::roxygenize(PATH, load_code = sourceDir), silent = TRUE)
+try(roxygen2::roxygenize(PATH, load_code = rstantools_load_code), silent = TRUE)
 roxygen2::roxygenize(PATH)
 ```