try to work without std::make_unique [skip vbump] (#354)

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: mmrm
 Title: Mixed Models for Repeated Measures
-Version: 0.3.3.9000
+Version: 0.3.4
 Authors@R: c(
     person("Daniel", "Sabanes Bove", , "[email protected]", role = c("aut", "cre")),
     person("Julia", "Dedic", , "[email protected]", role = "aut"),
@@ -72,7 +72,7 @@ Suggests:
     microbenchmark,
     mockery,
     parallelly (>= 1.32.0),
-    parsnip (>= 1.0.4),
+    parsnip (>= 1.1.0),
     purrr,
     rmarkdown,
     sasr,
@@ -97,7 +97,6 @@ LazyData: true
 NeedsCompilation: yes
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-SystemRequirements: C++14
 Collate:
     'between-within.R'
     'catch-routine-registration.R'

NEWS.md

@@ -1,4 +1,4 @@
-# mmrm 0.3.3.9000
+# mmrm 0.3.4
 
 ### New Features
 

R/zzz.R

@@ -11,7 +11,7 @@
   )
 
   register_on_load(
-    "parsnip", c("1.0.4", NA),
+    "parsnip", c("1.1.0", NA),
     callback = parsnip_add_mmrm,
     message = emit_tidymodels_register_msg
   )
@@ -74,24 +74,24 @@ register_on_load <- function(pkg,
 check_package_version <- function(pkg, ver = c(NA_character_, NA_character_)) {
   assert_character(ver, len = 2L)
   pkg_ver <- utils::packageVersion(pkg)
-  ver <- lapply(ver, numeric_version, strict = FALSE)
+  ver <- numeric_version(ver, strict = FALSE)
 
   warn_version <- function(pkg, pkg_ver, ver) {
-    ver_na <- is.na(vapply(ver, is.na, logical(1L)))
+    ver_na <- is.na(ver)
     warning(sprintf(
       "Cannot register mmrm for use with %s (v%s). Version %s required.",
       pkg, pkg_ver,
       if (!any(ver_na)) {
-        sprintf("%s to %s", ver[[1]], ver[[2]])
-      } else if (!is.na(ver[[1]])) {
-        paste0(">= ", ver[[1]])
-      } else if (!is.na(ver[[2]])) {
-        paste0("<= ", ver[[1]])
+        sprintf("%s to %s", ver[1], ver[2])
+      } else if (ver_na[2]) {
+        paste0(">= ", ver[1])
+      } else if (ver_na[1]) {
+        paste0("<= ", ver[2])
       }
     ))
   }
 
-  if (identical(pkg_ver < ver[[1]], TRUE) || identical(pkg_ver > ver[[2]], TRUE)) {
+  if (identical(pkg_ver < ver[1], TRUE) || identical(pkg_ver > ver[2], TRUE)) {
     warn_version(pkg, pkg_ver, ver)
     return(invisible(FALSE))
   }

src/Makevars

@@ -1,2 +1 @@
-CXX_STD = CXX14
 PKG_CXXFLAGS = -D TMBAD_FRAMEWORK -D EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS

src/chol_cache.h

@@ -3,6 +3,7 @@
 
 #include "covariance.h"
 #include "utils.h"
+
 // Base class of spatial and non-spatial Cholesky.
 template <class Type>
 struct lower_chol_base {
@@ -98,7 +99,7 @@ struct lower_chol_spatial: virtual lower_chol_base<Type> {
 
 template <class T, class Base, class D1, class D2>
 struct cache_obj {
-  std::map<int, std::unique_ptr<Base>> cache;
+  std::map<int, std::shared_ptr<Base>> cache;
   int n_groups;
   bool is_spatial;
   int n_visits;
@@ -108,9 +109,9 @@ struct cache_obj {
     for (int r = 0; r < n_groups; r++) {
       // Use unique pointers here to better manage resource.
       if (is_spatial) {
-        this->cache[r] = std::make_unique<D1>(theta.segment(r * theta_one_group_size, theta_one_group_size), cov_type);
+        this->cache[r] = std::make_shared<D1>(theta.segment(r * theta_one_group_size, theta_one_group_size), cov_type);
       } else {
-        this->cache[r] = std::make_unique<D2>(theta.segment(r * theta_one_group_size, theta_one_group_size), n_visits, cov_type);
+        this->cache[r] = std::make_shared<D2>(theta.segment(r * theta_one_group_size, theta_one_group_size), n_visits, cov_type);
       }
     }
   }

vignettes/package_structure.Rmd

@@ -128,8 +128,7 @@ This file implements the `P`, `Q` and `R` matrix calculations which are needed f
 ### `Makevars`
 
 This file specifies additional flags used in the source code compilation. 
-We specify here the use of `C++14` such that `std::make_unique()` is available.
-Also we ask `TMB` to use the `TMB` automatic differentiation framework (instead of the default `CppAD` framework) to be more efficient, and disable useless warnings from the `Eigen` library compilation.
+We ask `TMB` to use the `TMB` automatic differentiation framework (instead of the default `CppAD` framework) to be more efficient, and disable useless warnings from the `Eigen` library compilation.
 
 Note that additional flags such as `-Wno-ignored-attributes` cannot be included here because they are compiler specific. These can instead be specified in local `~/.R/Makevars` files.