Merge pull request #212 from metrumresearchgroup/dev

Release to CRAN
metrumresearchgroup · Mar 11, 2017 · 314d2a1 · 314d2a1
2 parents 8b1b49c + 0e5afaf
commit 314d2a1
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,5 @@
+cran-comments.md
+Rchecks
 .github
 inst/doc
 Doxyfile

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mrgsolve
 Type: Package
-Version: 0.7.10.9007
+Version: 0.8.2
 Title: Simulate from ODE-Based Population PK/PD and Systems Pharmacology
     Models
 Authors@R: c(
@@ -23,9 +23,7 @@ Description: Facilitates simulation from hierarchical, ordinary
     passed in and simulated data are returned as R objects.  A dosing event engine
     allows interventions (bolus and infusion) to be managed separately from the 
     model code. Differential equations are solved with the 'DLSODA' routine 
-    in 'ODEPACK' [A. C. Hindmarsh, 'ODEPACK, A Systematized Collection of ODE 
-    Solvers' in Scientific Computing, R. S. Stepleman et al. (eds.), 
-    North-Holland, Amsterdam, 1983, pp.55-64.]. 
+    in 'ODEPACK' (<https://computation.llnl.gov/casc/odepack/>). 
 License: GPL (>=2)
 Depends:
     R (>= 3.1.2),

diff --git a/R/package.R b/R/package.R
@@ -229,16 +229,12 @@ models <- function() {
   file.path(path.package("mrgsolve"), "models")
 }
 
-
 .onLoad <- function(libname, pkgname) {
   GLOBALS[["version"]] <- utils::packageVersion("mrgsolve")
 }
 
-
-.onAttach <- function(libname,pkgname) {
-  base::packageStartupMessage("mrgsolve: Community Edition")
-  base::packageStartupMessage("www.github.com/metrumresearchgroup/mrgsolve")
-
-}
+# .onAttach <- function(libname,pkgname) {
+#   base::packageStartupMessage("mrgsolve: Community Edition")
+# }
 
 
diff --git a/inst/include/odeproblem.h b/inst/include/odeproblem.h
@@ -88,10 +88,10 @@ typedef void main_deriv_func(int* neq, double* t,
 #define MRGSOLVE_GET_PRED_K21 (pred[3]/pred[4]) ///< rate constants for <code>$PKMODEL</code>
 
 
-deriv_func*  as_deriv_func( SEXP derivs);
-init_func*   as_init_func(  SEXP inits);
-table_func*  as_table_func( SEXP table);
-config_func* as_config_func(SEXP config);
+// deriv_func*  as_deriv_func( SEXP derivs);
+// init_func*   as_init_func(  SEXP inits);
+// table_func*  as_table_func( SEXP table);
+// config_func* as_config_func(SEXP config);
 
 extern "C"{DL_FUNC tofunptr(SEXP a);}
 

diff --git a/inst/include/tofunptr.h b/inst/include/tofunptr.h
diff --git a/inst/project/housemodel.RDS b/inst/project/housemodel.RDS
diff --git a/src/odeproblem.cpp b/src/odeproblem.cpp
@@ -85,12 +85,12 @@ odeproblem::odeproblem(Rcpp::NumericVector param,
 
   for(int i=0; i < npar_; ++i) Param[i] =       double(param[i]);
   for(int i=0; i < neq_;  ++i) Init_value[i] =  double(init[i]);
-  
-  Inits = as_init_func(funs["main"]);
-  Table = as_table_func(funs["table"]);
-  Derivs = as_deriv_func(funs["ode"]);
-  Config = as_config_func(funs["config"]);
-  
+
+  *reinterpret_cast<void**>(&Inits) = R_ExternalPtrAddr(funs["main"]); 
+  *reinterpret_cast<void**>(&Table) = R_ExternalPtrAddr(funs["table"]);
+  *reinterpret_cast<void**>(&Derivs) = R_ExternalPtrAddr(funs["ode"]);
+  *reinterpret_cast<void**>(&Config) = R_ExternalPtrAddr(funs["config"]);
+
   Capture.assign(n_capture_,0.0);
 
   simeta = resim(&dosimeta,reinterpret_cast<void*>(this));
@@ -635,39 +635,39 @@ double PolyExp(const double& x,
  * @param inits address for <code>$MAIN</code> function
  * 
  */
-init_func* as_init_func(SEXP inits) {
-  return(reinterpret_cast<init_func *>(tofunptr(inits))); 
-}
+// init_func* as_init_func(SEXP inits) {
+//   //return(reinterpret_cast<init_func *>(tofunptr(inits)));
+// }
 
 /**
  * Get pointer for <code>$ODE</code> function. 
  * 
  * @param derivs address for <code>$ODE</code> function
  * 
  */
-deriv_func* as_deriv_func(SEXP derivs) {
-  return(reinterpret_cast<deriv_func *>(tofunptr(derivs))); 
-}
+// deriv_func* as_deriv_func(SEXP derivs) {
+//   //return(reinterpret_cast<deriv_func *>(tofunptr(derivs)));
+// }
 
 /**
  * Get pointer for <code>$TABLE</code> function. 
  * 
  * @param table address for <code>$TABLE</code> function
  * 
  */
-table_func* as_table_func(SEXP table) {
-  return(reinterpret_cast<table_func*>(tofunptr(table)));
-}
+// table_func* as_table_func(SEXP table) {
+//   //return(reinterpret_cast<table_func*>(tofunptr(table)));
+// }
 
 /**
  * Get pointer for <code>$PREAMBLE</code> function. 
  * 
  * @param config address for <code>$PREAMBLE</code> function
  * 
  */
-config_func* as_config_func(SEXP config) {
-  return(reinterpret_cast<config_func*>(tofunptr(config)));
-}
+// config_func* as_config_func(SEXP config) {
+//   //return(reinterpret_cast<config_func*>(tofunptr(config)));
+// }
 
 void odeproblem::copy_parin(const Rcpp::List& parin) {
   this->tol(Rcpp::as<double>(parin["atol"]),Rcpp::as<double>(parin["rtol"]));
@@ -679,11 +679,10 @@ void odeproblem::copy_parin(const Rcpp::List& parin) {
 }
 
 void odeproblem::copy_funs(const Rcpp::List& funs) {
-  Inits = as_init_func(funs["main"]);
-  Table = as_table_func(funs["table"]);
-  Derivs = as_deriv_func(funs["ode"]);
-  Config = as_config_func(funs["config"]);
-
+  *reinterpret_cast<void**>(&Inits) = R_ExternalPtrAddr(funs["main"]); 
+  *reinterpret_cast<void**>(&Table) = R_ExternalPtrAddr(funs["table"]);
+  *reinterpret_cast<void**>(&Derivs) = R_ExternalPtrAddr(funs["ode"]);
+  *reinterpret_cast<void**>(&Config) = R_ExternalPtrAddr(funs["config"]);
 }
 
 void odeproblem::advan(int x) {

diff --git a/src/tofunptr.c b/src/tofunptr.c