Merge pull request #157 from rsetienne/develop

v4.3.4

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 4.3.3
-Date: 2023-03-10
-Depends: R (>= 4.1.0)
+Version: 4.3.4
+Date: 2023-03-16
+Depends: R (>= 4.2.0)
 biocViews:
 Imports: 
     deSolve,
@@ -111,6 +111,7 @@ Description: Simulates and computes the (maximum) likelihood of a dynamical
     extinction. See e.g. Valente et al. 2015. Ecology Letters 18: 844-852,
     <DOI:10.1111/ele.12461>.
 NeedsCompilation: yes
+SystemRequirements: C++17
 Encoding: UTF-8
 VignetteBuilder: knitr
 URL: https://github.com/rsetienne/DAISIE

NEWS.md

@@ -1,3 +1,13 @@
+# DAISIE 4.3.4
+
+* Require C++17 via `CXX_STD` flag on Makevars[.win].
+* Add SystemRequirements: C++17 to DESCRIPTION as for that standard 
+"Writing R Extensions" requires it be explicitly stated.
+* Depends on R (>= 4.2.0) due to C++17 requirement on Windows due to Rtools 4.0,
+which is used for R 4.0-4.1. Toolchain for Rtools 4.0 is gcc 8.3 but "GCC 9.1 
+was the first release with non-experimental C++17 support". as per 
+https://gcc.gnu.org/.
+
 # DAISIE 4.3.3
 
 * Address problem detected by valgrind: unitialized member variable 

src/DAISIE_CS.cpp

@@ -1,7 +1,6 @@
 // [[Rcpp::plugins(cpp14)]]
 // [[Rcpp::depends(BH)]]
 
-
 //' @export daisie_odeint_cs
 
 #include "config.h"
@@ -16,7 +15,7 @@ namespace {
   // maximal number of steps the solver is executing.
   // prevents odeint from getting stuckle
   // at-hoc - 'solution'.
-  static constexpr int default_max_cs_steps = 1'000'000;
+  static constexpr int default_max_cs_steps = 1000000;
   static int max_cs_steps = default_max_cs_steps;
 
   // step-size factor for adams_bashforth_moulton integration

src/DAISIE_IW.cpp

@@ -1,6 +1,9 @@
 //' @export daisie_odeint_iw
+
 // [[Rcpp::plugins(cpp14)]]
 // [[Rcpp::plugins(openmp)]]
+// [[Rcpp::depends(BH)]]
+// [[Rcpp::depends(RcppEigen)]]
 
 #include "config.h"
 #include "DAISIE_odeint.h"

src/DAISIE_odeint.h

@@ -12,7 +12,6 @@
 #include <stdexcept>
 #include <memory>
 
-
 using namespace Rcpp;
 using namespace boost::numeric::odeint;
 
@@ -45,7 +44,6 @@ class padded_vector_view
 
 namespace daisie_odeint {
 
-
   extern double abm_factor;
 
 
@@ -89,6 +87,7 @@ namespace daisie_odeint {
       {
         if (!J_) {
           // once-only, generic evaluation
+
           J_ = std::make_unique<matrix_t<double>>(J.size1(), J.size2());
           auto single = vector_t<double>(x.size(), 0);
           auto dxdt = vector_t<double>(x.size());
@@ -106,7 +105,7 @@ namespace daisie_odeint {
 
       RHS& rhs_;
       std::unique_ptr<matrix_t<double>> J_;
-    };
+  };
 
   }
 

src/Makevars

@@ -1,2 +1,2 @@
-CXX_STD = CXX14
+CXX_STD = CXX17
 PKG_CPPFLAGS = -D_HAS_AUTO_PTR_ETC=0

src/Makevars.win

@@ -1,2 +1,2 @@
-CXX_STD = CXX14
+CXX_STD = CXX17
 PKG_CPPFLAGS = -D_HAS_AUTO_PTR_ETC=0