Use rstantools for setup

stan-dev · Jun 5, 2024 · 09ff2e8 · 09ff2e8
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+      - use-rstantools
   pull_request:
     branches:
       - master
@@ -20,55 +21,35 @@ jobs:
       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, r: 'devel' }
+          - { os: macOS-latest, r: 'release' }
+          - { os: macOS-latest, r: 'oldrel' }
+          - { os: windows-latest, r: 'devel' }
+          - { os: windows-latest, r: 'release' }
+          - { os: windows-latest, r: 'oldrel' }
+          - { os: ubuntu-latest, r: 'devel' }
+          - { os: ubuntu-latest, r: 'release' }
+          - { os: ubuntu-latest, r: '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 }}
 
-      - 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
diff --git a/.gitignore b/.gitignore
@@ -16,3 +16,8 @@ vignettes/*.html
 vignettes/*_files
 .DS_Store
 revdep/*
+*.o
+*.cc
+*.h
+src/Makevars
+R/stanmodels.R
diff --git a/R/stanmodels.R b/R/stanmodels.R
diff --git a/R/zzz.R b/R/zzz.R
@@ -15,11 +15,6 @@
 # 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)

diff --git a/configure b/configure
@@ -0,0 +1,2 @@
+#! /bin/sh
+"${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()"
diff --git a/configure.ac b/configure.ac
diff --git a/configure.win b/configure.win
@@ -0,0 +1,2 @@
+#! /bin/sh
+"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "rstantools::rstan_config()"
diff --git a/inst/include/meta_header.hpp → inst/include/stan_meta_header.hpp b/inst/include/meta_header.hpp → inst/include/stan_meta_header.hpp
diff --git a/src/stan_files/bernoulli.stan → inst/stan/bernoulli.stan b/src/stan_files/bernoulli.stan → inst/stan/bernoulli.stan
@@ -1,5 +1,5 @@
-#include /pre/Columbia_copyright.stan
-#include /pre/license.stan
+#include /include/Columbia_copyright.stan
+#include /include/license.stan
 
 // GLM for a Bernoulli outcome
 functions {

diff --git a/src/stan_files/binomial.stan → inst/stan/binomial.stan b/src/stan_files/binomial.stan → inst/stan/binomial.stan
@@ -1,5 +1,5 @@
-#include /pre/Columbia_copyright.stan
-#include /pre/license.stan
+#include /include/Columbia_copyright.stan
+#include /include/license.stan
 
 // GLM for a binomial outcome
 functions {

diff --git a/src/stan_files/continuous.stan → inst/stan/continuous.stan b/src/stan_files/continuous.stan → inst/stan/continuous.stan
@@ -1,5 +1,5 @@
-#include /pre/Columbia_copyright.stan
-#include /pre/license.stan
+#include /include/Columbia_copyright.stan
+#include /include/license.stan
 
 // GLM for a Gaussian, Gamma, inverse Gaussian, or Beta outcome
 functions {

diff --git a/src/stan_files/count.stan → inst/stan/count.stan b/src/stan_files/count.stan → inst/stan/count.stan
@@ -1,5 +1,5 @@
-#include /pre/Columbia_copyright.stan
-#include /pre/license.stan
+#include /include/Columbia_copyright.stan
+#include /include/license.stan
 
 // GLM for a count outcome
 functions {

diff --git a/src/stan_files/data/NKX.stan → inst/stan/data/NKX.stan b/src/stan_files/data/NKX.stan → inst/stan/data/NKX.stan
diff --git a/src/stan_files/data/data_assoc.stan → inst/stan/data/data_assoc.stan b/src/stan_files/data/data_assoc.stan → inst/stan/data/data_assoc.stan
diff --git a/src/stan_files/data/data_betareg.stan → inst/stan/data/data_betareg.stan b/src/stan_files/data/data_betareg.stan → inst/stan/data/data_betareg.stan
diff --git a/src/stan_files/data/data_event.stan → inst/stan/data/data_event.stan b/src/stan_files/data/data_event.stan → inst/stan/data/data_event.stan
diff --git a/src/stan_files/data/data_glm.stan → inst/stan/data/data_glm.stan b/src/stan_files/data/data_glm.stan → inst/stan/data/data_glm.stan
diff --git a/src/stan_files/data/data_mvmer.stan → inst/stan/data/data_mvmer.stan b/src/stan_files/data/data_mvmer.stan → inst/stan/data/data_mvmer.stan
diff --git a/src/stan_files/data/dimensions_mvmer.stan → inst/stan/data/dimensions_mvmer.stan b/src/stan_files/data/dimensions_mvmer.stan → inst/stan/data/dimensions_mvmer.stan
diff --git a/src/stan_files/data/glmer_stuff.stan → inst/stan/data/glmer_stuff.stan b/src/stan_files/data/glmer_stuff.stan → inst/stan/data/glmer_stuff.stan
diff --git a/src/stan_files/data/glmer_stuff2.stan → inst/stan/data/glmer_stuff2.stan b/src/stan_files/data/glmer_stuff2.stan → inst/stan/data/glmer_stuff2.stan
diff --git a/src/stan_files/data/hyperparameters.stan → inst/stan/data/hyperparameters.stan b/src/stan_files/data/hyperparameters.stan → inst/stan/data/hyperparameters.stan
diff --git a/...tan_files/data/hyperparameters_assoc.stan → inst/stan/data/hyperparameters_assoc.stan b/...tan_files/data/hyperparameters_assoc.stan → inst/stan/data/hyperparameters_assoc.stan
diff --git a/...tan_files/data/hyperparameters_event.stan → inst/stan/data/hyperparameters_event.stan b/...tan_files/data/hyperparameters_event.stan → inst/stan/data/hyperparameters_event.stan
diff --git a/...tan_files/data/hyperparameters_mvmer.stan → inst/stan/data/hyperparameters_mvmer.stan b/...tan_files/data/hyperparameters_mvmer.stan → inst/stan/data/hyperparameters_mvmer.stan
diff --git a/src/stan_files/data/weights_offset.stan → inst/stan/data/weights_offset.stan b/src/stan_files/data/weights_offset.stan → inst/stan/data/weights_offset.stan
diff --git a/src/stan_files/functions/SSfunctions.stan → inst/stan/functions/SSfunctions.stan b/src/stan_files/functions/SSfunctions.stan → inst/stan/functions/SSfunctions.stan
diff --git a/...iles/functions/bernoulli_likelihoods.stan → ...stan/functions/bernoulli_likelihoods.stan b/...iles/functions/bernoulli_likelihoods.stan → ...stan/functions/bernoulli_likelihoods.stan
diff --git a/...files/functions/binomial_likelihoods.stan → .../stan/functions/binomial_likelihoods.stan b/...files/functions/binomial_likelihoods.stan → .../stan/functions/binomial_likelihoods.stan
diff --git a/...tan_files/functions/common_functions.stan → inst/stan/functions/common_functions.stan b/...tan_files/functions/common_functions.stan → inst/stan/functions/common_functions.stan
diff --git a/...les/functions/continuous_likelihoods.stan → ...tan/functions/continuous_likelihoods.stan b/...les/functions/continuous_likelihoods.stan → ...tan/functions/continuous_likelihoods.stan
diff --git a/...an_files/functions/count_likelihoods.stan → inst/stan/functions/count_likelihoods.stan b/...an_files/functions/count_likelihoods.stan → inst/stan/functions/count_likelihoods.stan
diff --git a/src/stan_files/functions/jm_functions.stan → inst/stan/functions/jm_functions.stan b/src/stan_files/functions/jm_functions.stan → inst/stan/functions/jm_functions.stan
diff --git a/...stan_files/functions/mvmer_functions.stan → inst/stan/functions/mvmer_functions.stan b/...stan_files/functions/mvmer_functions.stan → inst/stan/functions/mvmer_functions.stan
diff --git a/src/stan_files/gqs/gen_quantities_mvmer.stan → inst/stan/gqs/gen_quantities_mvmer.stan b/src/stan_files/gqs/gen_quantities_mvmer.stan → inst/stan/gqs/gen_quantities_mvmer.stan
diff --git a/src/stan_files/pre/Brilleman_copyright.stan → inst/stan/include/Brilleman_copyright.stan b/src/stan_files/pre/Brilleman_copyright.stan → inst/stan/include/Brilleman_copyright.stan
diff --git a/src/stan_files/pre/Columbia_copyright.stan → inst/stan/include/Columbia_copyright.stan b/src/stan_files/pre/Columbia_copyright.stan → inst/stan/include/Columbia_copyright.stan
diff --git a/src/stan_files/pre/license.stan → inst/stan/include/license.stan b/src/stan_files/pre/license.stan → inst/stan/include/license.stan
diff --git a/src/stan_files/jm.stan → inst/stan/jm.stan b/src/stan_files/jm.stan → inst/stan/jm.stan
@@ -1,6 +1,6 @@
-#include /pre/Columbia_copyright.stan
-#include /pre/Brilleman_copyright.stan
-#include /pre/license.stan
+#include /include/Columbia_copyright.stan
+#include /include/Brilleman_copyright.stan
+#include /include/license.stan
 
 // Shared parameter joint model
 functions {

diff --git a/src/stan_files/lm.stan → inst/stan/lm.stan b/src/stan_files/lm.stan → inst/stan/lm.stan
@@ -1,5 +1,5 @@
-#include /pre/Columbia_copyright.stan
-#include /pre/license.stan
+#include /include/Columbia_copyright.stan
+#include /include/license.stan
 
 // GLM for a Gaussian outcome with no link function
 functions {

diff --git a/src/stan_files/model/assoc_evaluate.stan → inst/stan/model/assoc_evaluate.stan b/src/stan_files/model/assoc_evaluate.stan → inst/stan/model/assoc_evaluate.stan
diff --git a/src/stan_files/model/eta_add_Zb.stan → inst/stan/model/eta_add_Zb.stan b/src/stan_files/model/eta_add_Zb.stan → inst/stan/model/eta_add_Zb.stan
diff --git a/src/stan_files/model/eta_no_intercept.stan → inst/stan/model/eta_no_intercept.stan b/src/stan_files/model/eta_no_intercept.stan → inst/stan/model/eta_no_intercept.stan
diff --git a/src/stan_files/model/eta_z_no_intercept.stan → inst/stan/model/eta_z_no_intercept.stan b/src/stan_files/model/eta_z_no_intercept.stan → inst/stan/model/eta_z_no_intercept.stan
diff --git a/src/stan_files/model/event_lp.stan → inst/stan/model/event_lp.stan b/src/stan_files/model/event_lp.stan → inst/stan/model/event_lp.stan
diff --git a/src/stan_files/model/make_eta.stan → inst/stan/model/make_eta.stan b/src/stan_files/model/make_eta.stan → inst/stan/model/make_eta.stan
diff --git a/src/stan_files/model/make_eta_bern.stan → inst/stan/model/make_eta_bern.stan b/src/stan_files/model/make_eta_bern.stan → inst/stan/model/make_eta_bern.stan
diff --git a/src/stan_files/model/make_eta_tmp.stan → inst/stan/model/make_eta_tmp.stan b/src/stan_files/model/make_eta_tmp.stan → inst/stan/model/make_eta_tmp.stan
diff --git a/src/stan_files/model/make_eta_tmp2.stan → inst/stan/model/make_eta_tmp2.stan b/src/stan_files/model/make_eta_tmp2.stan → inst/stan/model/make_eta_tmp2.stan
diff --git a/src/stan_files/model/make_eta_z.stan → inst/stan/model/make_eta_z.stan b/src/stan_files/model/make_eta_z.stan → inst/stan/model/make_eta_z.stan
diff --git a/src/stan_files/model/mvmer_lp.stan → inst/stan/model/mvmer_lp.stan b/src/stan_files/model/mvmer_lp.stan → inst/stan/model/mvmer_lp.stan
diff --git a/src/stan_files/model/priors_betareg.stan → inst/stan/model/priors_betareg.stan b/src/stan_files/model/priors_betareg.stan → inst/stan/model/priors_betareg.stan
diff --git a/src/stan_files/model/priors_glm.stan → inst/stan/model/priors_glm.stan b/src/stan_files/model/priors_glm.stan → inst/stan/model/priors_glm.stan
diff --git a/src/stan_files/model/priors_mvmer.stan → inst/stan/model/priors_mvmer.stan b/src/stan_files/model/priors_mvmer.stan → inst/stan/model/priors_mvmer.stan
diff --git a/src/stan_files/mvmer.stan → inst/stan/mvmer.stan b/src/stan_files/mvmer.stan → inst/stan/mvmer.stan
@@ -1,6 +1,6 @@
-#include /pre/Columbia_copyright.stan
-#include /pre/Brilleman_copyright.stan
-#include /pre/license.stan
+#include /include/Columbia_copyright.stan
+#include /include/Brilleman_copyright.stan
+#include /include/license.stan
 
 // Multivariate GLM with correlated group-specific terms
 functions {

diff --git a/...an_files/parameters/parameters_assoc.stan → inst/stan/parameters/parameters_assoc.stan b/...an_files/parameters/parameters_assoc.stan → inst/stan/parameters/parameters_assoc.stan
diff --git a/..._files/parameters/parameters_betareg.stan → inst/stan/parameters/parameters_betareg.stan b/..._files/parameters/parameters_betareg.stan → inst/stan/parameters/parameters_betareg.stan
diff --git a/...an_files/parameters/parameters_event.stan → inst/stan/parameters/parameters_event.stan b/...an_files/parameters/parameters_event.stan → inst/stan/parameters/parameters_event.stan
diff --git a/...stan_files/parameters/parameters_glm.stan → inst/stan/parameters/parameters_glm.stan b/...stan_files/parameters/parameters_glm.stan → inst/stan/parameters/parameters_glm.stan
diff --git a/...an_files/parameters/parameters_mvmer.stan → inst/stan/parameters/parameters_mvmer.stan b/...an_files/parameters/parameters_mvmer.stan → inst/stan/parameters/parameters_mvmer.stan
diff --git a/src/stan_files/polr.stan → inst/stan/polr.stan b/src/stan_files/polr.stan → inst/stan/polr.stan
@@ -1,5 +1,5 @@
-#include /pre/Columbia_copyright.stan
-#include /pre/license.stan
+#include /include/Columbia_copyright.stan
+#include /include/license.stan
 
 // GLM for an ordinal outcome with coherent priors
 functions {

diff --git a/src/stan_files/tdata/tdata_betareg.stan → inst/stan/tdata/tdata_betareg.stan b/src/stan_files/tdata/tdata_betareg.stan → inst/stan/tdata/tdata_betareg.stan
diff --git a/src/stan_files/tdata/tdata_glm.stan → inst/stan/tdata/tdata_glm.stan b/src/stan_files/tdata/tdata_glm.stan → inst/stan/tdata/tdata_glm.stan
diff --git a/src/stan_files/tdata/tdata_mvmer.stan → inst/stan/tdata/tdata_mvmer.stan b/src/stan_files/tdata/tdata_mvmer.stan → inst/stan/tdata/tdata_mvmer.stan
diff --git a/...iles/tparameters/tparameters_betareg.stan → ...stan/tparameters/tparameters_betareg.stan b/...iles/tparameters/tparameters_betareg.stan → ...stan/tparameters/tparameters_betareg.stan
diff --git a/...an_files/tparameters/tparameters_glm.stan → inst/stan/tparameters/tparameters_glm.stan b/...an_files/tparameters/tparameters_glm.stan → inst/stan/tparameters/tparameters_glm.stan
diff --git a/..._files/tparameters/tparameters_mvmer.stan → inst/stan/tparameters/tparameters_mvmer.stan b/..._files/tparameters/tparameters_mvmer.stan → inst/stan/tparameters/tparameters_mvmer.stan
diff --git a/src/Makevars b/src/Makevars
diff --git a/src/Makevars.win b/src/Makevars.win
diff --git a/src/rstanarm-win.def b/src/rstanarm-win.def
diff --git a/tests/testthat/include b/tests/testthat/include
diff --git a/tests/testthat/stan_files b/tests/testthat/stan_files
diff --git a/tests/testthat/test_stan_functions.R b/tests/testthat/test_stan_functions.R
@@ -18,8 +18,8 @@
 Sys.setenv(USE_CXX17 = 1)
 set.seed(12345)
 
-MODELS_HOME <- "stan_files"
-INCLUDE_DIR <- "include"
+MODELS_HOME <- system.file("stan", package = "rstanarm", mustWork = TRUE)
+INCLUDE_DIR <- system.file("include", package = "rstanarm", mustWork = TRUE)
 
 context("setup")
 test_that("Stan programs are available", {
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#! /bin/sh
		"${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()"
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#! /bin/sh
		"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "rstantools::rstan_config()"