Merge develop branch

.github/workflows/main.yml

@@ -9,10 +9,12 @@ name: R-CMD-check
     branches:
       - develop
       - experimental
+      - StanHeaders_*
   pull_request:
     branches:
       - develop
       - experimental
+      - StanHeaders_*
 
 jobs:
   R-CMD-check:
@@ -80,7 +82,6 @@ jobs:
           remotes::install_cran("rcmdcheck")
           remotes::install_cran("rstantools", type = "source")
           remotes::install_cran("sessioninfo")
-          remotes::install_github("hsbadr/RcppEigen@develop")
           if (utils::packageVersion("sessioninfo") >= "1.2.1") {
             sessioninfo::session_info(pkgs = "installed", include_base = TRUE)
           } else {

StanHeaders/.Rbuildignore

@@ -25,6 +25,7 @@ cleanup.win
 revdep
 install-github.R
 inst/doc/.install_extras
+vignettes/.install_extras
 .*\.o$
 .*\.a$
 \.gitignore$

StanHeaders/DESCRIPTION

@@ -34,7 +34,7 @@ Authors@R: c(person("Ben",family="Goodrich", email="benjamin.goodrich@columbia.e
 URL: https://mc-stan.org/
 Description: The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
 Imports: RcppParallel (>= 5.1.4)
-Suggests: Rcpp, BH (>= 1.75.0-0), knitr (>= 1.36), rmarkdown, Matrix, methods, rstan
+Suggests: Rcpp, BH (>= 1.75.0-0), knitr (>= 1.36), rmarkdown, Matrix, methods, rstan, withr
 LinkingTo: RcppEigen (>= 0.3.3.9.3), RcppParallel (>= 5.1.4)
 VignetteBuilder: knitr
 SystemRequirements: GNU make, pandoc

StanHeaders/R/stanFunction.R

@@ -1,5 +1,5 @@
 stanFunction <- function(function_name, ..., env = parent.frame(), rebuild = FALSE,
-                         cacheDir = getOption("rcpp.cache.dir", tempdir()), 
+                         cacheDir = getOption("rcpp.cache.dir", tempdir()),
                          showOutput = verbose, verbose = getOption("verbose")) {
   make_type <- function(x, recursive = FALSE) {
     is_array <- is.list(x)
@@ -44,16 +44,16 @@ stanFunction <- function(function_name, ..., env = parent.frame(), rebuild = FAL
   int_lists <- types == "const std::vector<int >&"
   if (any(int_lists)) types[int_lists] <- "const List&"
   code <- paste0("auto ", function_name, "(",
-                 paste(types, names(types), collapse = ", "), 
-                 ") { return stan::math::", function_name, "(", 
+                 paste(types, names(types), collapse = ", "),
+                 ") { return stan::math::", function_name, "(",
                  paste(ifelse(double_lists,
                               paste0("std::vector<double>(", names(types), ".begin(), ",
                                                              names(types), ".end())"),
                               ifelse(int_lists,
                                      paste0("std::vector<int>(", names(types), ".begin(), ",
                                                                  names(types), ".end())"),
                                      names(types))), collapse = ", "), "); }")
-  incl <- dir(system.file("include", "stan", "math", "prim", 
+  incl <- dir(system.file("include", "stan", "math", "prim",
                           package = "StanHeaders", mustWork = TRUE),
               pattern = "hpp$")
   incl <- setdiff(incl, "core.hpp")
@@ -66,18 +66,21 @@ stanFunction <- function(function_name, ..., env = parent.frame(), rebuild = FAL
     on.exit(options(useFancyQuotes = op))
     incl <- c(incl, paste0('#include ', dQuote(create_rng)))
     code <- sub(") {", ", const int random_seed = 0) {", code, fixed = TRUE)
-    code <- sub(" return ", 
+    code <- sub(" return ",
                 "boost::ecuyer1988 base_rng__ = stan::services::util::create_rng(random_seed, 0); return ",
                 code)
       code <- sub("); }", ", base_rng__); }", code, fixed = TRUE)
   }
-  old_USE_CXX14 <- Sys.getenv("USE_CXX14")
-  on.exit(Sys.setenv(USE_CXX14 = old_USE_CXX14))
-  Sys.setenv(USE_CXX14 = "1")
-  Rcpp::cppFunction(code, depends = c("StanHeaders", "RcppEigen", "BH"),
-                    includes = incl, env = env, rebuild = rebuild, 
-                    cacheDir = cacheDir,
-                    showOutput = showOutput, verbose = verbose)
+  withr::with_makevars(
+    c(
+      PKG_CXXFLAGS = CxxFlags(as_character = TRUE),
+      PKG_LIBS = LdFlags(as_character = TRUE)
+    ),
+    Rcpp::cppFunction(code, depends = c("StanHeaders", "RcppEigen", "BH"),
+                      includes = incl, env = env, rebuild = rebuild,
+                      cacheDir = cacheDir,
+                      showOutput = showOutput, verbose = verbose)
+  )
   if (grepl("_rng$", function_name)) {
     fun <- get(function_name, envir = env, mode = "function")
     formals(fun, envir = env)$random_seed <- quote(sample.int(.Machine$integer.max, size = 1L))

StanHeaders/cleanup

@@ -5,30 +5,11 @@ rm -Rf inst/include/src \
        inst/include/stan \
        inst/include/libsundials || true
 
-mkdir -p inst/include/src || true
-cp -Rf inst/include/upstream/src/stan inst/include/src/stan || true
+cp -Rf inst/include/upstream/src inst/include/src || true
+cp -Rf inst/include/upstream/lib/stan_math inst/include/mathlib || true
 cp -Rf inst/include/upstream/lib/stan_math/stan inst/include/stan || true
+cp -Rf inst/include/upstream/lib/stan_math/lib/sundials_* inst/include/libsundials || true
 cp -Rf inst/include/upstream/lib/stan_math/lib/sundials_*/include/* inst/include/ || true
 cp -Rf inst/include/upstream/lib/stan_math/lib/sundials_*/src/* src/ || true
 
-# Prepare TBB objects and headers
-if [ ! -z "STANHEADERS_TBB_STATIC" ] && [ -z "$TBB_LIB" ] && [ ! -d src/tbb ]; then
-    cp -Rv inst/include/upstream/lib/stan_math/lib/tbb_*/src/tbb* src/ || true
-    cp -Rv inst/include/upstream/lib/stan_math/lib/tbb_*/src/rml src/ || true
-    cp -Rv inst/include/upstream/lib/stan_math/lib/tbb_*/include/serial inst/include/ || true
-    cp -Rv inst/include/upstream/lib/stan_math/lib/tbb_*/include/*tbb* inst/include/ || true
-    cp -v inst/include/upstream/lib/stan_math/lib/tbb_*/include/*tbb*/*.h inst/include/tbb/ || true
-    cp -v inst/include/upstream/lib/stan_math/lib/tbb_*/src/tbb/*.h inst/include/tbb/ || true
-    echo '#define __TBB_VERSION_STRINGS(N) "Empty"' > src/tbb/version_string.ver || true
-fi
-
-if [ ! -z "$TBB_LIB" ]; then
-    rm -Rf src/tbb* || true
-    rm -Rf src/rml || true
-    rm -Rf inst/include/serial || true
-    rm -Rf inst/include/*tbb* || true
-fi
-
-rm -Rf inst/include/upstream || true
-
 exit $?

StanHeaders/cleanup.win

@@ -5,30 +5,11 @@ rm -Rf inst/include/src \
        inst/include/stan \
        inst/include/libsundials || true
 
-mkdir -p inst/include/src || true
-cp -Rf inst/include/upstream/src/stan inst/include/src/stan || true
+cp -Rf inst/include/upstream/src inst/include/src || true
+cp -Rf inst/include/upstream/lib/stan_math inst/include/mathlib || true
 cp -Rf inst/include/upstream/lib/stan_math/stan inst/include/stan || true
+cp -Rf inst/include/upstream/lib/stan_math/lib/sundials_* inst/include/libsundials || true
 cp -Rf inst/include/upstream/lib/stan_math/lib/sundials_*/include/* inst/include/ || true
 cp -Rf inst/include/upstream/lib/stan_math/lib/sundials_*/src/* src/ || true
 
-# Prepare TBB objects and headers
-if [ ! -z "STANHEADERS_TBB_STATIC" ] && [ -z "$TBB_LIB" ] && [ ! -d src/tbb ]; then
-    cp -Rv inst/include/upstream/lib/stan_math/lib/tbb_*/src/tbb* src/ || true
-    cp -Rv inst/include/upstream/lib/stan_math/lib/tbb_*/src/rml src/ || true
-    cp -Rv inst/include/upstream/lib/stan_math/lib/tbb_*/include/serial inst/include/ || true
-    cp -Rv inst/include/upstream/lib/stan_math/lib/tbb_*/include/*tbb* inst/include/ || true
-    cp -v inst/include/upstream/lib/stan_math/lib/tbb_*/include/*tbb*/*.h inst/include/tbb/ || true
-    cp -v inst/include/upstream/lib/stan_math/lib/tbb_*/src/tbb/*.h inst/include/tbb/ || true
-    echo '#define __TBB_VERSION_STRINGS(N) "Empty"' > src/tbb/version_string.ver || true
-fi
-
-if [ ! -z "$TBB_LIB" ]; then
-    rm -Rf src/tbb* || true
-    rm -Rf src/rml || true
-    rm -Rf inst/include/serial || true
-    rm -Rf inst/include/*tbb* || true
-fi
-
-rm -Rf inst/include/upstream || true
-
 exit $?

StanHeaders/inst/CITATION

@@ -1,6 +1,6 @@
 citHeader("To cite StanHeaders in publications use:")
 
-citEntry(entry = "Misc", 
+bibentry(bibtype = "Misc",
          title = "{StanHeaders}: Headers for the {R} interface to {Stan}",
          author = person(given = "Stan Development Team"),
          note = "R package version 2.21.0-6",
@@ -9,5 +9,5 @@ citEntry(entry = "Misc",
          textVersion =
            paste("Stan Development Team (2018).",
                  title = "StanHeaders: Headers for the {R} interface to {Stan}.",
-                 "https://mc-stan.org/.") 
+                 "https://mc-stan.org/.")
 )

StanHeaders/inst/include/libsundials

@@ -1 +1 @@
-upstream/lib/stan_math/lib/sundials_6.1.1/
+upstream/lib/stan_math/lib/sundials_5.6.1/