Issue 7: Resolve initial CRAN issues.

.Rbuildignore

@@ -14,4 +14,7 @@
 ^\.pre-commit-config\.yaml$
 ^doc$
 ^Meta$
-^README\.html$
+^README\.html$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
+^.vscode$

.gitignore

@@ -6,3 +6,5 @@
 inst/doc
 /doc/
 /Meta/
+.vscode/
+CRAN-SUBMISSION

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: staninside
-Title: Facilitating the Use of Stan Within Packages
+Title: "Facilitating the Use of 'Stan' Within Packages"
 Version: 0.0.4
 Authors@R: 
     person(given = "Michael",
@@ -8,13 +8,12 @@ Authors@R:
            email = "me.dewitt.jr@gmail.com",
            comment = c(ORCID = "0000-0001-8940-1967"))
 Description: Infrastructure and functions that can be used for 
-    integrating Stan code into stand alone R packages which in turn use the 
-    CmdStan engine (often accessed through CmdStanR). Using CmdStanR and 
-    pre-written Stan code can make package installation easy and less prone to 
-    fail because it removes the need for Rcpp and RStan packages(and their dependencies). 
-    Using CmdStanR will also afford users the opportunity to use the latest developments
-    within CmdStan. However, building these packages requires some work and this
-    package provides tools to assist with that process.
+    integrating 'Stan' (Carpenter et al., 2017 <doi:10.18637/jss.v076.i01>) code into 
+    stand alone R packages which in turn use the  'CmdStan' engine (often accessed through 
+    'CmdStanR' (Stan Development Team, 2025 <https://mc-stan.org/users/interfaces/cmdstanr/>)). 
+    Using 'CmdStanR' and pre-written 'Stan' code can make package installation easy. Using 'staninside'
+    offers a way to cache user-compiled 'Stan' models in user-specified directories reducing the need
+    to recompile the same model multiple times.
 License: MIT + file LICENSE
 URL: https://github.com/medewitt/staninside, https://medewitt.github.io/staninside/
 BugReports: https://github.com/medewitt/staninside/issues

R/copy_models.R

@@ -5,7 +5,8 @@
 #'
 #' @param pkgname a string, the name of the package
 #' @param local_location a file path representing the desired location
-#'   of the local copy.
+#'   of the local copy. If "default" is provided, the function will use
+#'   the user cache directory for the package.
 #' @returns file path of newly created files
 #' @importFrom fs dir_create dir_exists file_copy
 #' @export
@@ -15,8 +16,16 @@
 #' copy_models(pkgname = "staninside", local_location = local_location)
 copy_models <- function(pkgname = "staninside", local_location = NULL) {
   if (is.null(local_location)) {
+    stop("A location must be provided")
+  }
+
+  if (local_location == "default") {
     local_location <- rappdirs::user_cache_dir(appname = pkgname)
     cli::cli_alert("`{local_location}` will be used")
+  } else {
+    if (!dir.exists(local_location)) {
+      stop("The directory you have indicated does not exist")
+    }
   }
 
   stan_code_to_copy <- find_stan_code(pkgname)

R/find_stan_code.R

@@ -12,9 +12,7 @@
 #' @examples
 #' find_stan_code(pkgname = "staninside")
 find_stan_code <- function(pkgname = "staninside") {
-  if (!pkgname %in% rownames(installed.packages())) {
-    stop(sprintf("`%s` is not an installed package.\n", pkgname))
-  }
+  requireNamespace(pkgname)
 
   stan_pkg_location <- fs::dir_ls(system.file(package = pkgname),
     glob = "*.stan", recurse = TRUE

R/setup_stan_package.R

@@ -3,8 +3,7 @@
 #' Create directory and helper files for a Stan package using
 #' CmdStanR
 #'
-#' @param loc a file.path indicating package root with a default of the
-#'     current working directory
+#' @param loc a file.path indicating package root.
 #' @param use_all a logical indicating if each section of Stan code
 #'     should have it's own directory with a default of \code{TRUE}
 #' @returns invisible null
@@ -22,12 +21,12 @@
 #' @export
 
 setup_stan_package <- function(loc = NULL, use_all = TRUE) {
-  if (!is.null(loc)) {
-    if (!dir.exists(loc)) {
-      stop("The directory you have indicated does not exist,")
-    }
-  } else {
-    loc <- getwd()
+  if (is.null(loc)) {
+    stop("A location must be provided")
+  }
+
+  if (!dir.exists(loc)) {
+    stop("The directory you have indicated does not exist,")
   }
 
   target_path <- file.path(loc, "inst", "stan")

cran-comments.md

@@ -0,0 +1,14 @@
+## R CMD check results
+
+0 errors  | 0 warnings | 0 notes
+
+* This is a new package and a resubmission
+* This package has been tested on local MAC and rub using the Rhub Github Actions tools to test Linux, Mac, Windows. 
+
+### Issue resolved from submission
+- Properly cited methods in the DESCRIPTION
+- Update packages, software, and APIs with single quotations
+- Removed all `getwd` statements as defaults and require user to explicity enter file path
+- Vignettes do not utilize any local, package, or user directories
+- Title has double quotes
+- Removed use of `installed.packages()` to use `requireNamespace`

inst/WORDLIST

@@ -1,41 +1,45 @@
-aut
-BugReports
-cli
 CMD
 CmdStan
 CmdStanR
 Codecov
+Github
+ORCID
+RStan
+Rcpp
+TMPDIR
+al
+cmdstanr
+doi
+et
+filespace
+jss
+pre
+testthat
+tinytest
+BugReports
+CRAN
 Config
+DeWitt
+LazyData
+Roxygen
+RoxygenNote
+VignetteBuilder
+aut
+cli
 covr
 cran
-CRAN
 cre
 dewitt
-DeWitt
 dplyr
-filespace
 fs
 github
-Github
 gmail
 https
 knitr
-LazyData
 medewitt
 michaeldewittjr
-ORCID
-pre
 rappdirs
-Rcpp
 rmarkdown
-Roxygen
-RoxygenNote
 rstan
-RStan
 staninside
-testthat
-tidyverse
-tinytest
-TMPDIR
-VignetteBuilder
-cmdstanr
+tidyverse

tests/testthat/test-clear_stan_cache.R

@@ -1,21 +1,15 @@
+test_clearing_cache <- function() {
+  # Copy over models
+  app_loc <- tempdir()
+  loc <- copy_models(pkgname = "staninside", local_location = app_loc)
 
+  copied_over_files <- all(c("test.stan", "func.stan") %in% basename(loc))
 
+  clear_stan_cache(pkgname = "staninside")
 
-test_clearing_cache <- function(){
-
-	# Copy over models
-	app_loc <- rappdirs::user_cache_dir("staninside")
-	loc <- copy_models(pkgname = "staninside", local_location  = app_loc)
-
-	copied_over_files <- all(c("test.stan", "func.stan") %in% basename(loc))
-
-	clear_stan_cache(pkgname = "staninside")
-
-	all_removed <- !isTRUE(lapply(loc, file.exists))
-
-	all(copied_over_files,all_removed)
-
+  all_removed <- !isTRUE(lapply(loc, file.exists))
 
+  all(copied_over_files, all_removed)
 }
 
 test_that("stan files can be copied over and cleared", {

tests/testthat/test-copy_models.R

@@ -1,7 +1,7 @@
 # Make model available
 
 local_location <- tempdir()
-copy_models(pkgname = "staninside", local_location  = local_location)
+copy_models(pkgname = "staninside", local_location = local_location)
 
 test_stan <- list.files(local_location, full.names = TRUE, pattern = "test.stan")
 
@@ -10,7 +10,9 @@ test_that("models from test package have been copied", {
 })
 
 test_that("test that all stan directories are available", {
-	expect_true(dir.exists(file.path(local_location, "functions")))
+  expect_true(dir.exists(file.path(local_location, "functions")))
 })
 
-
+test_that("test that when no location is provided, an error is thrown", {
+  expect_error(copy_models(pkgname = "staninside"))
+})

tests/testthat/test-setup_stan_package.R

@@ -6,9 +6,13 @@ test_that("full process functional", {
   expect_true(dir.exists(file.path(test_dir, "inst", "stan")))
 })
 test_that("sub directories created functional", {
-	expect_true(dir.exists(file.path(test_dir, "inst", "stan", "data")))
+  expect_true(dir.exists(file.path(test_dir, "inst", "stan", "data")))
 })
 
 test_that("fails on invalid path", {
-	expect_error(setup_stan_package("blerg"))
+  expect_error(setup_stan_package("blerg"))
+})
+
+test_that("fails on no location", {
+  expect_error(setup_stan_package())
 })

vignettes/.gitignore

@@ -1,2 +1,4 @@
 *.html
 *.R
+CRAN-SUBMISSION
+CRAN*

vignettes/using-staninside.Rmd

@@ -37,7 +37,8 @@ If a package developer were to build a package with `staninside`, they first cou
 Next, to build the appropriate structure the author could call
 
 ```r
-setup_stan_package()
+temp_dir <- tempdir()
+setup_stan_package(loc = temp_dir)
 ```
 
 This function will create the following directory tree:
@@ -77,7 +78,7 @@ fit_my_data <- function(my_data){
         "Use `staninside::clear_stan_cache('mypackage')` if you need to refresh")
     } else {
         cli::cli_alert_info("Copying Stan models to cache")
-        staninside::copy_models(this_pkg())
+        staninside::copy_models(pkgname = "mypackage", local_location = local_location)
         cli::cli_alert_success("Models copied!")
     }