[wip] adding stan

.github/workflows/r-cmd-check.yaml

@@ -22,11 +22,11 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,  r: 'release'}
-          - {os: ubuntu-latest,  r: 'oldrel-1'}
-          - {os: macOS-latest,   r: 'release'} 
+          - {os: windows-latest, r: 'release', rtools: '43'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release', rtools: ''}
+          - {os: ubuntu-latest,  r: 'release', rtools: ''}
+          - {os: ubuntu-latest,  r: 'oldrel-1', rtools: ''}
+          - {os: macOS-latest,   r: 'release', rtools: ''} 
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -50,9 +50,15 @@ jobs:
           C:\JAGS-latest.exe /S
         shell: cmd
 
+      - name: executable Permissions
+        run: |
+          chmod +x configure
+          chmod +x configure.win
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          rtools-version: ${{ matrix.config.rtools }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 

DESCRIPTION

@@ -31,28 +31,41 @@ Depends:
   tscount
 License: MIT + file LICENSE
 Imports:
-  arrow,
-  bslib,
-  coda,
-  english,
-  htmltools,
-  httr,
-  jsonlite,
-  knitr,
-  markdown,
-  portalr  (>= 0.4.0),
-  rmarkdown,
-  runjags,
-  scoringRules,
-  shiny,
-  stats,
-  viridis,
-  yaml
+    arrow,
+    bslib,
+    coda,
+    english,
+    htmltools,
+    httr,
+    jsonlite,
+    knitr,
+    markdown,
+    methods,
+    portalr (>= 0.4.0),
+    Rcpp (>= 0.12.0),
+    RcppParallel (>= 5.0.1),
+    rmarkdown,
+    rstan (>= 2.18.1),
+    rstantools (>= 2.3.1),
+    runjags,
+    scoringRules,
+    shiny,
+    stats,
+    viridis,
+    yaml
 Suggests:
   pkgdown,
   testthat
-SystemRequirements: JAGS 4.x.y; libcurl; gsl
+SystemRequirements: GNU make
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
+Biarch: true
+LinkingTo: 
+    BH (>= 1.66.0),
+    Rcpp (>= 0.12.0),
+    RcppEigen (>= 0.3.3.3.0),
+    RcppParallel (>= 5.0.1),
+    rstan (>= 2.18.1),
+    StanHeaders (>= 2.18.0)

R/stanmodels.R

@@ -0,0 +1 @@
+# Generated by rstantools.  Do not edit by hand.

configure

@@ -0,0 +1,5 @@
+#! /bin/sh
+
+# Generated by rstantools.  Do not edit by hand.
+
+"${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()"

configure.win

@@ -0,0 +1,5 @@
+#! /bin/sh
+
+# Generated by rstantools.  Do not edit by hand.
+
+"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "rstantools::rstan_config()"

inst/include/stan_meta_header.hpp

@@ -0,0 +1 @@
+// Insert all #include<foo.hpp> statements here

inst/stan/include/license.stan

@@ -0,0 +1,14 @@
+/*
+    portalcasting 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.
+
+    portalcasting 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 portalcasting.  If not, see <http://www.gnu.org/licenses/>.
+*/