Fix linking error when exposing SUNDIALS/KINSOL functions or model me…

…thods (#977)

* Fix linking error with SUNDIALS

* Add test

* Add handling for Linux systems needing -fPIC

* Update test-model-expose-functions.R

.gitignore

@@ -7,3 +7,4 @@
 inst/doc
 dev-helpers.R
 release-prep.R
+*.DS_Store

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cmdstanr
 Title: R Interface to 'CmdStan'
-Version: 0.8.0
+Version: 0.8.0.9000
 Date: 2024-05-18
 Authors@R:
     c(person(given = "Jonah", family = "Gabry", role = "aut",

R/utils.R

@@ -727,18 +727,38 @@ get_cmdstan_flags <- function(flag_name) {
   paste(flags, collapse = " ")
 }
 
+check_sundials_fpic <- function(verbose) {
+  if (!os_is_linux()){
+    return(invisible(NULL))
+  }
+  sundials_flags <- get_cmdstan_flags("CPPFLAGS_SUNDIALS")
+  local_flags <- cmdstan_make_local()
+  if (any(grepl("-fPIC", c(sundials_flags, local_flags), fixed = TRUE))) {
+    return(invisible(NULL))
+  }
+  if (interactive()) {
+    message("SUNDIALS needs to be compiled with -fPIC when exposing functions or ",
+            "model methods on Linux.\n",
+            "Updating your make/local file to include -fPIC and rebuilding CmdStan now...")
+  }
+  cmdstan_make_local(cpp_options = list("CPPFLAGS_SUNDIALS += -fPIC"), append = TRUE)
+  rebuild_cmdstan(quiet = !verbose)
+  if (interactive()) {
+    message("CmdStan has been rebuilt, continuing with model compilation...")
+  }
+}
+
 rcpp_source_stan <- function(code, env, verbose = FALSE, ...) {
+  check_sundials_fpic(verbose)
   cxxflags <- get_cmdstan_flags("CXXFLAGS")
   cmdstanr_includes <- system.file("include", package = "cmdstanr", mustWork = TRUE)
   cmdstanr_includes <- paste0(" -I\"", cmdstanr_includes,"\"")
-  libs <- c("LDLIBS", "LIBSUNDIALS", "TBB_TARGETS", "LDFLAGS_TBB")
+  libs <- c("LDLIBS", "LIBSUNDIALS", "TBB_TARGETS", "LDFLAGS_TBB", "SUNDIALS_TARGETS")
   libs <- paste(sapply(libs, get_cmdstan_flags), collapse = " ")
   if (.Platform$OS.type == "windows") {
     libs <- paste(libs, "-fopenmp")
   }
-  lib_paths <- c("/stan/lib/stan_math/lib/tbb/",
-                 "/stan/lib/stan_math/lib/sundials_6.1.1/lib/")
-  withr::with_path(paste0(cmdstan_path(), lib_paths),
+  withr::with_path(repair_path(file.path(cmdstan_path(),"stan/lib/stan_math/lib/tbb")),
     withr::with_makevars(
       c(
         USE_CXX14 = 1,

tests/testthat/test-model-expose-functions.R

@@ -419,3 +419,17 @@ test_that("Exposing functions with precompiled model gives meaningful error", {
     fixed = TRUE
   )
 })
+
+test_that("Functions with SUNDIALS/KINSOL methods link correctly", {
+  modcode <- "
+    functions {
+      vector dummy_functor(vector guess, vector theta, data array[] real tails, data array[] int x_i) {
+        return [1, 1]';
+      }
+      vector call_solver(vector guess, vector theta, data array[] real tails, data array[] int x_i) {
+        return algebra_solver_newton(dummy_functor, guess, theta, tails, x_i);
+      }
+    }"
+  mod <- cmdstan_model(write_stan_file(modcode), force_recompile=TRUE)
+  expect_no_error(mod$expose_functions())
+})