Convert rstan to a suggests to avoid windows installation issues

.Rbuildignore

@@ -23,3 +23,4 @@
 
 ^CONTRIBUTING.md$
 ^local$
+^inst/stan/MMRM.rds$

.github/workflows/on_pr_main.yaml

@@ -12,7 +12,7 @@ name: On Pull Request
 jobs:
 
   rcmdcheck:
-
+    
     strategy:
       fail-fast: true
       matrix:
@@ -29,10 +29,7 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-
-      - name: Build src
-        uses: ./.github/actions/build-src
-
+
       - name: Check
         uses: ./.github/actions/rcmdcheck
         with:
@@ -54,9 +51,6 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
 
-      - name: Build src
-        uses: ./.github/actions/build-src
-
       - name: Build Vignettes
         run: |
           Rscript ./vignettes/build.R

.github/workflows/on_push.yaml

@@ -17,10 +17,7 @@ jobs:
 
       - name: Checkout
         uses: actions/checkout@v3
-
-      - name: Build src
-        uses: ./.github/actions/build-src
-
+
       - name: testthat
         run: |
           options(crayon.enabled = TRUE, cli.dynamic = FALSE)
@@ -36,11 +33,6 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
 
-      - name: Build src
-        uses: ./.github/actions/build-src
-        with:
-          refresh: false
-
       - name: Document Code
         run: |
           options(crayon.enabled = TRUE, cli.dynamic = FALSE)

.gitignore

@@ -61,3 +61,7 @@ docs
 
 
 local/
+
+inst/stan/*.rds
+inst/stan/*.RDS
+inst/stan/*.Rds

DESCRIPTION

@@ -33,28 +33,16 @@ Suggests:
     lubridate,
     purrr,
     ggplot2,
-    R.rsp
-Biarch: true
+    R.rsp,
+    rstan (>= 2.26.0)
 Config/testthat/edition: 3
 Imports:
     mmrm,
     pkgload,
     Matrix,
     methods,
-    Rcpp (>= 0.12.0),
-    RcppParallel (>= 5.0.1),
-    rstan (>= 2.26.0),
-    rstantools (>= 2.1.1),
     R6,
     assertthat
-LinkingTo: 
-    BH (>= 1.66.0),
-    Rcpp (>= 0.12.0),
-    RcppEigen (>= 0.3.3.3.0),
-    RcppParallel (>= 5.0.1),
-    rstan (>= 2.26.0),
-    StanHeaders (>= 2.26.0)
-SystemRequirements: GNU make
 Depends: 
     R (>= 3.4.0)
 License: Apache License (>= 2)

NAMESPACE

@@ -71,13 +71,9 @@ export(strategy_MAR)
 export(validate)
 export(validate_analyse_pars)
 import(R6)
-import(Rcpp)
 import(methods)
 importFrom(assertthat,assert_that)
 importFrom(mmrm,VarCorr)
-importFrom(rstan,extract)
-importFrom(rstan,sampling)
-importFrom(rstan,summary)
 importFrom(stats,as.formula)
 importFrom(stats,binomial)
 importFrom(stats,coef)
@@ -100,4 +96,3 @@ importFrom(stats,var)
 importFrom(stats,vcov)
 importFrom(utils,capture.output)
 importFrom(utils,relist)
-useDynLib(rbmi, .registration = TRUE)

NEWS.md

@@ -1,4 +1,8 @@
 
+# rbmi (development version)
+
+* Downgraded rstan to a `Suggests` dependency and opt to compile "just in time" rather than at installation time. This is intended to make installation easier for user who don't use `method_bayes()` (#405)
+
 # rbmi 1.2.6
 
 * Updated unit tests to fix false-positive error on CRAN's testing servers

R/mcmc.R

@@ -44,11 +44,7 @@
 #' - `samples`: a named list containing the draws for each parameter. It corresponds to the output of [extract_draws()].
 #' - `fit`: a `stanfit` object.
 #'
-#'
-#' @import Rcpp
 #' @import methods
-#' @importFrom rstan sampling
-#' @useDynLib rbmi, .registration = TRUE
 fit_mcmc <- function(
     designmat,
     outcome,
@@ -59,6 +55,8 @@ fit_mcmc <- function(
     quiet = FALSE
 ) {
 
+    ensure_stan_is_available()
+
     n_imputations <- method$n_samples
     burn_in <- method$burn_in
     seed <- method$seed
@@ -96,7 +94,7 @@ fit_mcmc <- function(
     )
 
     sampling_args <- list(
-        object = stanmodels$MMRM,
+        object = get_stan_model(),
         data = stan_data,
         pars = c("beta", "Sigma"),
         chains = 1,
@@ -123,7 +121,7 @@ fit_mcmc <- function(
     sampling_args$seed <- seed
 
     stan_fit <- record({
-        do.call(sampling, sampling_args)
+        do.call(rstan::sampling, sampling_args)
     })
 
     if (!is.null(stan_fit$errors)) {
@@ -240,10 +238,9 @@ split_dim <- function(a, n) {
 #'   of the list is a list with length equal to 1 if `same_cov = TRUE` or equal to the
 #'   number of groups if `same_cov = FALSE`.
 #'
-#' @importFrom rstan extract
 extract_draws <- function(stan_fit) {
 
-    pars <- extract(stan_fit, pars = c("beta", "Sigma"))
+    pars <- rstan::extract(stan_fit, pars = c("beta", "Sigma"))
     names(pars) <- c("beta", "sigma")
 
     ##################### from array to list
@@ -268,7 +265,6 @@ extract_draws <- function(stan_fit) {
 #' @return
 #' A named vector containing the ESS for each parameter of the model.
 #'
-#' @importFrom rstan summary
 get_ESS <- function(stan_fit) {
     return(rstan::summary(stan_fit, pars = c("beta", "Sigma"))$summary[, "n_eff"])
 }
@@ -646,3 +642,51 @@ validate.stan_data <- function(x, ...) {
         msg = "Invalid Stan Data Object"
     )
 }
+
+
+
+#' Ensure rstan is available
+#'
+#' This function checks if the rstan package is installed.
+#' If it is not installed, an error message is thrown.
+#'
+#' @keywords internal
+ensure_stan_is_available <- function() {
+    if (!requireNamespace("rstan", quietly = TRUE)) {
+        stop("`method_bayes()` requires that the `rstan` package is installed. Please install it and try again.")
+    }
+}
+
+
+# Environment variable to store the compiled stan model
+# This is needed to prevent rstan from recompiling the model each time
+# https://discourse.mc-stan.org/t/rstan-sometimes-recompiles-to-avoid-crashing-r-session/4911
+STAN_ENV <- new.env()
+
+
+#' Get the compiled Stan model
+#'
+#' @description
+#' Get the compiled Stan model.
+#' If the model has already been compiled, return it from memory.
+#' If not, compile the model and return it.
+#'
+#' @param model_env An environment where the compiled model is stored.
+#' @return
+#' A `stanfit` object.
+#' @keywords internal
+get_stan_model <- function(model_env = STAN_ENV) {
+    model_file <- if (file.exists("inst/stan/MMRM.stan")) {
+        "inst/stan/MMRM.stan"
+    } else if (file.exists("stan/MMRM.stan")) {
+        "stan/MMRM.stan"
+    } else {
+        system.file("stan/MMRM.stan", package = "rbmi")
+    }
+    model_env$model <- rstan::stan_model(
+        file = model_file,
+        auto_write = TRUE,
+        save_dso = TRUE
+    )
+    model_env$model
+}

R/utilities.R

@@ -512,21 +512,3 @@ as_dataframe <- function(x) {
     row.names(x2) <- NULL
     return(x2)
 }
-
-
-
-#' Do not run this function
-#' 
-#' This function only exists to suppress the false positive
-#' from R CMD Check about unused libraries
-#' 
-#' Both rstantools and RcppParallel are required but are only used at
-#' installation time. In the case of RcppParallel it is used in the
-#' `src/Makevars` file which is created on the fly during installation
-#' by rstantools. rstantools is used in the `configure` file.
-#' 
-do_not_run <- function() {
-    rstantools::use_rstan()
-    RcppParallel::CxxFlags()
-}
-