Merge pull request #154 from rsetienne/develop

DAISIE 4.3.2

.github/workflows/R-CMD-check.yaml

@@ -12,7 +12,7 @@ jobs:
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
-    if: "contains(github.event.head_commit.message, '[run ci]') || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop')"
+    if: "contains(github.event.head_commit.message, '[run ci]') || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') || github.event.pull_request"
 
     strategy:
       fail-fast: false

.github/workflows/test-coverage.yaml

@@ -9,7 +9,7 @@ name: test-coverage
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
-    if: "contains(github.event.head_commit.message, '[run ci]') || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop')"
+    if: "contains(github.event.head_commit.message, '[run ci]') || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') || github.event.pull_request"
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -1,11 +1,10 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 4.3.1
-Date: 2023-02-10
+Version: 4.3.2
+Date: 2023-02-24
 Depends: R (>= 4.1.0)
 biocViews:
-SystemRequirements: C++17
 Imports: 
     deSolve,
     graphics,
@@ -112,6 +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++14
 Encoding: UTF-8
 VignetteBuilder: knitr
 URL: https://github.com/rsetienne/DAISIE

NAMESPACE

@@ -42,7 +42,6 @@ export(create_pars)
 export(create_trait_pars)
 export(create_trait_pars_2K)
 export(daisie_odeint_cs)
-export(daisie_odeint_iw)
 import(Rcpp)
 importFrom(doParallel,registerDoParallel)
 importFrom(foreach,"%dopar%")

NEWS.md

@@ -1,3 +1,10 @@
+# DAISIE 4.3.2
+
+* Apply CRAN suggested fixes to clang16 issues with deprecated C++ functions included the Boost library, which are used in some of the stepper functions.
+  * Add config.h in a macro, checking for, and setting, `_HAS_AUTO_PTR_ETC` and `BOOST_NO_AUTO_PTR`.
+  * Change SystemRequirements in DESCRIPTION from C++17 to C++14.
+This same fix was applied in package `'DDD'` version 5.2.1.
+
 # DAISIE 4.3.1
 
 * Fix issue that prevented 'covr' from running correctly.

R/RcppExports.R

@@ -9,9 +9,6 @@ NULL
 #' @name daisie_odeint_cs
 NULL
 
-#' @export daisie_odeint_iw
-NULL
-
 #' Driver for the boost::odeint solver
 #'
 #' @name daisie_odeint_iw

src/DAISIE_CS.cpp

@@ -1,10 +1,10 @@
-// [[Rcpp::plugins(cpp17)]]
+// [[Rcpp::plugins(cpp14)]]
 // [[Rcpp::depends(BH)]]
 
 
 //' @export daisie_odeint_cs
 
-
+#include "config.h"
 #include "DAISIE_odeint.h"
 
 using namespace daisie_odeint::jacobian_policy;

src/DAISIE_IW.cpp

@@ -1,9 +1,8 @@
 //' @export daisie_odeint_iw
-
-// [[Rcpp::plugins(cpp17)]]
+// [[Rcpp::plugins(cpp14)]]
 // [[Rcpp::plugins(openmp)]]
-// [[Rcpp::depends(RcppEigen)]]
 
+#include "config.h"
 #include "DAISIE_odeint.h"
 #define EIGEN_USE_THREADS
 #include <RcppEigen.h>

src/DAISIE_odeint.h

@@ -1,12 +1,15 @@
+// [[Rcpp::plugins(cpp14)]]
+
 #pragma once
 #ifndef DAISIE_ODEINT_H_INCLUDED
 #define DAISIE_ODEINT_H_INCLUDED
 
-
+#include "config.h"
 #include "ublas_types.h"
 #include <boost/numeric/odeint.hpp>
 #include <algorithm>
 #include <stdexcept>
+#include <memory>
 
 
 using namespace Rcpp;
@@ -44,7 +47,7 @@ namespace daisie_odeint {
 
   extern double abm_factor;
 
-  
+
   template <typename Stepper, typename Rhs>
   inline void do_integrate(double atol, double rtol, Rhs rhs, state_type& y, double t0, double t1)
   {
@@ -72,7 +75,7 @@ namespace daisie_odeint {
 
   namespace jacobian_policy {
 
-    // Evaluator of the Jacobian for linear, time independent systems 
+    // Evaluator of the Jacobian for linear, time independent systems
     // dxdt = Ax => Jacobian = t(A)
     template <typename RHS>
     struct const_from_linear_rhs

src/DAISIE_types.h

@@ -1,2 +1,3 @@
 #pragma once
+#include "config.h"
 #include "odeint_types.h"

src/R_init_DAISIE.c

@@ -1,3 +1,6 @@
+// [[Rcpp::plugins(cpp14)]]
+
+#include"config.h"
 #include <R.h>
 #include <Rinternals.h>
 #include <stdlib.h> // for NULL

src/config.h

@@ -0,0 +1,22 @@
+#ifndef ODEINT_CONFIG_H_INCLUDED
+#define ODEINT_CONFIG_H_INCLUDED
+
+// [[Rcpp::plugins(cpp14)]]
+
+// Special case to make use of some steppers that would include
+// boost/functional.hpp
+#if __cplusplus >= 201703L
+#ifdef _HAS_AUTO_PTR_ETC
+#undef _HAS_AUTO_PTR_ETC
+#endif
+#define _HAS_AUTO_PTR_ETC 0
+#endif
+
+// Special case to make use of some steppers that would include
+// boost/get_pointer.hpp
+#ifdef BOOST_NO_AUTO_PTR
+#undef BOOST_NO_AUTO_PTR
+#endif
+#define BOOST_NO_AUTO_PTR
+
+#endif

src/ublas_types.h

@@ -1,7 +1,10 @@
+// [[Rcpp::plugins(cpp14)]]
+
 #pragma once
 #ifndef UBLAS_TYPES_H_INCLUDED
 #define UBLAS_TYPES_H_INCLUDED
 
+#include "config.h"
 #include <RcppCommon.h>
 #include <boost/numeric/ublas/vector.hpp>
 #include <boost/numeric/ublas/matrix.hpp>