Merge pull request #625 from stan-dev/use-rstantools

Use rstantools - Fix Build/Export Errors

Author: bgoodri

.github/workflows/R-CMD-check.yaml

@@ -12,63 +12,34 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
+    runs-on: ${{ matrix.os }}
 
-    name: ${{ matrix.config.rstan }} RStan - ${{ matrix.config.os }} (${{ matrix.config.r }})
+    name: R CMD CHECK - ${{ matrix.os }} (${{ matrix.r }})
 
     strategy:
       fail-fast: false
       matrix:
-        config:
-          - {os: macOS-latest, r: 'devel', rstan: 'CRAN'}
-          - {os: macOS-latest, r: 'release', rstan: 'CRAN'}
-          - {os: windows-latest, r: 'devel', rstan: 'CRAN'}
-          - {os: windows-latest, r: 'release', rstan: 'CRAN'}
-          - {os: ubuntu-latest, r: 'devel', rstan: 'CRAN'}
-          - {os: ubuntu-latest, r: 'release', rstan: 'CRAN'}
-          - {os: ubuntu-latest, r: 'oldrel', rstan: 'CRAN'}
-
-          - {os: macOS-latest, r: 'release', rstan: 'Preview'}
-          - {os: windows-latest, r: 'release', rstan: 'Preview'}
+        os: [macOS-latest, windows-latest, ubuntu-latest, ubuntu-24.04-arm]
+        r: ['devel', 'release', 'oldrel']
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      TESTTHAT_CPUS: 4
 
     steps:
-      - uses: n1hility/cancel-previous-runs@v2
+      - uses: n1hility/cancel-previous-runs@master
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          workflow: R-CMD-check.yaml
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@main
 
-      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r@v2-branch
         with:
-          r-version: ${{ matrix.config.r }}
+          r-version: ${{ matrix.r }}
 
-      - uses: r-lib/actions/setup-pandoc@v2
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-pandoc@v2-branch
+      - uses: r-lib/actions/setup-r-dependencies@v2-branch
         with:
-          cache-version: 2
           extra-packages: any::rcmdcheck any::betareg any::HSAUR3 any::biglm any::gamm4 any::V8
-
-      - name: Install RStan Preview if Needed
-        run: |
-          if ("${{ matrix.config.rstan }}" == "Preview") {
-            install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
-          }
-        shell: Rscript {0}
-
-      - uses: r-lib/actions/check-r-package@v2
-        with:
-          args: 'c("--no-manual", "--as-cran", "--ignore-vignettes")'
-          build_args: '"--no-build-vignettes"'
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+      - uses: r-lib/actions/check-r-package@v2-branch

.gitignore

@@ -8,11 +8,15 @@ src/stan_files/*.hpp
 src/rstanarm.so
 src/rstanarm.dll
 src/init.o
-man/*.Rd
 !man/rstanarm-internal.Rd
 vignettes/*.R
 !vignettes/*.Rmd
 vignettes/*.html
 vignettes/*_files
 .DS_Store
 revdep/*
+*.o
+*.cc
+*.h
+src/Makevars
+R/stanmodels.R

R/misc.R

@@ -596,6 +596,10 @@ get_x.default <- function(object, ...) {
   object[["x"]] %ORifNULL% model.matrix(object)
 }
 #' @export
+get_x.betareg <- function(object, ...) {
+  model.matrix(object$terms[["mean"]], model.frame(object), contrasts = object$contrasts[["contrasts"]])
+}
+#' @export
 get_x.gamm4 <- function(object, ...) {
   as.matrix(object[["x"]])
 }

R/stanmodels.R

@@ -1,25 +1,20 @@
 # Part of the rstanarm package for estimating model parameters
 # Copyright (C) 2015, 2016, 2017 Trustees of Columbia University
-# 
+#
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
-# 
+#
 # This program is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
-# 
+#
 # You should have received a copy of the GNU General Public License
 # along with this program; if not, write to the Free Software
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
-.onLoad <- function(libname, pkgname) {
-  modules <- paste0("stan_fit4", names(stanmodels), "_mod")
-  for (m in modules) loadModule(m, what = TRUE)
-}
-
 .onAttach <- function(...) {
   ver <- utils::packageVersion("rstanarm")
   packageStartupMessage("This is rstanarm version ", ver)

R/zzz.R

@@ -0,0 +1,2 @@
+#! /bin/sh
+"${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()"

cleanup

@@ -0,0 +1,2 @@
+#! /bin/sh
+"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "rstantools::rstan_config()"