Merge pull request #635 from nlmixr2/634-move-rinternals

Move Rinternals inclusion order down
nlmixr2 · Dec 13, 2023 · a16e0cd · a16e0cd
2 parents 2878bf8 + 33f7e81
commit a16e0cd
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Showing 14 changed files with 51 additions and 77 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: rxode2
-Version: 2.1.0
+Version: 2.1.1
 Title: Facilities for Simulating from ODE-Based Models
 Authors@R: c(
    person("Matthew L.","Fidler",

diff --git a/inst/include/rxode2.h b/inst/include/rxode2.h
@@ -5,13 +5,13 @@
 #define __rxode2_H__
 #define rxLlikSaveSize 9
 
-
+#include <stdbool.h>
+#include <rxode2parse.h>
 #include <R.h>
 #include <Rinternals.h>
+#include <Rversion.h>
 #include <Rmath.h>
-#include <stdbool.h>
 #include <R_ext/Rdynload.h>
-#include <rxode2parse.h>
 
 #define rc_buf_read _rxode2_rc_buf_read
 #define sIniTo _rxode2_sIniTo
@@ -78,7 +78,7 @@ typedef void (*t_dydt_lsoda_dum)(int *neq, double *t, double *A, double *DADT);
 typedef void (*t_jdum_lsoda)(int *neq, double *t, double *A,int *ml, int *mu, double *JAC, int *nrowpd);
 typedef int (*t_dydt_liblsoda)(double t, double *y, double *ydot, void *data);
 typedef void (*t_ode_current)(void);
-  
+
 typedef void (*t_set_solve)(rx_solve *);
 typedef rx_solve *(*t_get_solve)(void);
 
@@ -128,7 +128,7 @@ static inline void _splitYj(int *yj, int *dist,  int *trans) {
   *trans = *yj - *dist*10;
   *dist  = *dist + 1;
 }
-// Inverse 
+// Inverse
 static inline double _powerDi(double x, double lambda, int yj0, double low, double high)  __attribute__((unused));
 static inline double _powerDi(double x, double lambda, int yj0, double low, double high){
   if (!R_finite(x)) return NA_REAL;
@@ -170,7 +170,7 @@ static inline double _powerDi(double x, double lambda, int yj0, double low, doub
     return (high-low)/(1+exp(-x))+low; // expit
   case 3:
     return exp(x);
-  case 2: 
+  case 2:
     return x;
   case 0:
     if (lambda == 1.0) return (x+1.0);
@@ -351,7 +351,7 @@ static inline double _powerDDD(double x, double lambda, int yj0, double low, dou
   case 3:
     if (x <= _eps) x0 = _eps;
     return -1/(x0*x0);
-  case 2: 
+  case 2:
     return 0;
   case 0:
     if (lambda == 1.0) return 0;
@@ -396,7 +396,7 @@ static inline double _powerL(double x, double lambda, int yj0, double low, doubl
     if (xl <= _eps) hl2 = _eps;
     return log(hl)-log(xl)-log(hl2);
     /* return 0; */
-  case 3: 
+  case 3:
     if (x <= _eps) x0 = _eps;
     return -log(x0);
   case 2:
@@ -415,12 +415,12 @@ static inline double _powerL(double x, double lambda, int yj0, double low, doubl
   // logLik approximation
   // y^(lambda)/lambda - 1/lambda
   // dh/dy = y^(lambda-1)
-  // log(dh/dy) = (lambda-1)*log(y) + log(lambda) 
+  // log(dh/dy) = (lambda-1)*log(y) + log(lambda)
   //
   // (x + 1.0)^(lambda)/lambda - 1/lambda
   // dh/dy = (x+1.0)^(lambda-1)
   // log(dh/dy) = (lambda-1)*log(x+1.0)
-  
+
   // For negative values yj becomes
   // (-x+1)^(2-lambda)/(2-lambda) - 1/(2-lambda)
   // dh/dy = (-x+1)^(1-lambda)
@@ -464,12 +464,12 @@ static inline double _powerDL(double x, double lambda, int yj0, double low, doub
   // logLik approximation
   // y^(lambda)/lambda - 1/lambda
   // dh/dy = y^(lambda-1)
-  // log(dh/dy) = (lambda-1)*log(y) + log(lambda) 
+  // log(dh/dy) = (lambda-1)*log(y) + log(lambda)
   //
   // (x + 1.0)^(lambda)/lambda - 1/lambda
   // dh/dy = (x+1.0)^(lambda-1)
   // log(dh/dy) = (lambda-1)*log(x+1.0)
-  
+
   // For negative values yj becomes
   // (-x+1)^(2-lambda)/(2-lambda) - 1/(2-lambda)
   // dh/dy = (-x+1)^(1-lambda)

diff --git a/src/approx.c b/src/approx.c
@@ -2,14 +2,11 @@
 #define STRICT_R_HEADERS
 #include <stdio.h>
 #include <stdarg.h>
-#include <R.h>
-#include <Rinternals.h>
-#include <Rmath.h>
-#include <R_ext/Rdynload.h>
 #include "../inst/include/rxode2.h"
 #include <rxode2parseHandleEvid.h>
 #include <rxode2parseGetTime.h>
 #include "seed.h"
+
 #define safe_zero(a) ((a) == 0 ? DBL_EPSILON : (a))
 #define _as_zero(a) (fabs(a) < sqrt(DBL_EPSILON) ? 0.0 : a)
 #define _as_dbleps(a) (fabs(a) < sqrt(DBL_EPSILON) ? ((a) < 0 ? -sqrt(DBL_EPSILON)  : sqrt(DBL_EPSILON)) : a)

diff --git a/src/call_dvode.c b/src/call_dvode.c
@@ -6,15 +6,9 @@
 #include "dop853.h"
 #define max(a, b) ((a) > (b) ? (a) : (b))
 #define STRICT_R_HEADERS
-#include <R.h>
-#include <Rinternals.h>
-#include <Rmath.h> //Rmath includes math.
-#include <R_ext/Rdynload.h>
 #include <PreciseSums.h>
 #include "../inst/include/rxode2.h"
 
-
-
 //--------------------------------------------------------------------------
 
 // These are now allocated via R structures in Rcpp.
@@ -39,7 +33,7 @@ extern void rxode2_assign_fn_pointers(SEXP mv){
   if (rxode2_current_fn_pointer_id_ != cur){
     rxAssignPtrC(mv);
     rxode2_current_fn_pointer_id_ = cur;
-  } 
+  }
 }
 
 SEXP rxModelVarsC(char *ptr);

diff --git a/src/cfode_static.c b/src/cfode_static.c
@@ -1,9 +1,9 @@
 #define STRICT_R_HEADERS
-#include <R.h>
-#include <Rinternals.h>
 #include "lsoda.h"
 #include "common.h"
 #include "cfode_static.h"
+#include <R.h>
+#include <Rinternals.h>
 
 void RSprintf(const char *format, ...);
 
@@ -35,5 +35,5 @@ void printcm12(void) {
 		if((i + 1) % 4 == 0) RSprintf("\n  ");
 	}
 	RSprintf("};\n");
-	
+
 }
diff --git a/src/dop853.c b/src/dop853.c
@@ -3,12 +3,12 @@
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h> /* dj: malloc.h */
-#include <R.h>
-#include <Rinternals.h>
-/* #include <malloc.h> */
 #include <limits.h>
 #include <memory.h>
+/* #include <malloc.h> */
 #include "dop853.h"
+#include <R.h>
+#include <Rinternals.h>
 
 #ifdef ENABLE_NLS
 #include <libintl.h>
@@ -390,13 +390,13 @@ static int dopcor (int *nptr, FcnEqDiff fcn, double x, double* y, double xend,
   nfcn += 2;
   reject = 0;
   xold = x;
-  
+
   if (iout)
     {
       irtrn = 1;
       hout = 1.0;
       xout = x;
-      solout (naccpt+1, xold, x, y, nptr, &irtrn); 
+      solout (naccpt+1, xold, x, y, nptr, &irtrn);
       if (irtrn < 0)
         {
           /* if (fileout) */
@@ -482,7 +482,7 @@ static int dopcor (int *nptr, FcnEqDiff fcn, double x, double* y, double xend,
             b10*k10[i] + b11*k2[i] + b12*k3[i];
           k5[i] = y[i] + h * k4[i];
         }
-     
+
       /* error estimation */
       err = 0.0;
       err2 = 0.0;
@@ -531,7 +531,7 @@ static int dopcor (int *nptr, FcnEqDiff fcn, double x, double* y, double xend,
           naccpt++;
           fcn (nptr, xph, k5, k4);
           nfcn++;
-      
+
           /* stiffness detection */
           if (!(naccpt % nstiff) || (iasti > 0))
             {
@@ -552,7 +552,7 @@ static int dopcor (int *nptr, FcnEqDiff fcn, double x, double* y, double xend,
                   iasti++;
                   if (iasti == 15)
                     {
-		      Rprintf (_("the problem seems to become stiff at x = %.16e\n"), x); 
+		      Rprintf (_("the problem seems to become stiff at x = %.16e\n"), x);
 		      xout = x;
 		      hout = h;
 		      return -4;
@@ -565,7 +565,7 @@ static int dopcor (int *nptr, FcnEqDiff fcn, double x, double* y, double xend,
                     iasti = 0;
                 }
             }
-       
+
           /* final preparation for dense output */
           if (iout == 2)
             {
@@ -654,7 +654,7 @@ static int dopcor (int *nptr, FcnEqDiff fcn, double x, double* y, double xend,
                   }
             }
 
-          memcpy (k1, k4, n * sizeof(double)); 
+          memcpy (k1, k4, n * sizeof(double));
           memcpy (y, k5, n * sizeof(double));
           xold = x;
           x = xph;

diff --git a/src/forder.cpp b/src/forder.cpp
@@ -1,9 +1,6 @@
 #define USE_FC_LEN_T
 #define STRICT_R_HEADERS
 #include "rxomp.h"
-#include <R.h>
-#include <Rversion.h>
-#include <Rinternals.h>
 #include <algorithm>
 #include "../inst/include/rxode2.h"
 #define min2( a , b )  ( (a) < (b) ? (a) : (b) )
@@ -93,7 +90,7 @@ extern "C" int getRxThreads(const int64_t n, const bool throttle) {
   // this is the main getter used by all parallel regions; they specify num_threads(n, true|false).
   // Keep this light, simple and robust. rxSetThreads() ensures 1 <= rxThreads <= omp_get_num_proc()
   // throttle introduced in 1.12.10 (see NEWS item); #4484
-  // throttle==true  : a number of iterations per thread (rxThrottle) is applied before a second thread is utilized 
+  // throttle==true  : a number of iterations per thread (rxThrottle) is applied before a second thread is utilized
   // throttle==false : parallel region is already pre-chunked such as in fread; e.g. two batches intended for two threads
   if (n<1) return 1; // 0 or negative could be deliberate in calling code for edge cases where loop is not intended to run at all
   int64_t ans = throttle ? 1+(n-1)/rxThrottle :  // 1 thread for n<=2, 2 thread for n<=4, etc

diff --git a/src/handle_evid.c b/src/handle_evid.c
@@ -3,20 +3,16 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <time.h>
-#include <R.h>
-#include <Rinternals.h>
-#include <Rmath.h> //Rmath includes math.
-#include <R_ext/Rdynload.h>
-#include "../inst/include/rxode2.h"
 #include "strncmp.h"
-#include <rxode2parseHandleEvid.h>
 #ifdef ENABLE_NLS
 #include <libintl.h>
 #define _(String) dgettext ("rxode2", String)
 /* replace pkg as appropriate */
 #else
 #define _(String) (String)
 #endif
+#include "../inst/include/rxode2.h"
+#include <rxode2parseHandleEvid.h>
 
 
 int handle_evidL(int evid, double *yp, double xout, int id, rx_solving_options_ind *ind) {

diff --git a/src/init.c b/src/init.c
@@ -3,14 +3,11 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <time.h>
-#include <R.h>
-#include <Rinternals.h>
 #include <stdlib.h> // for NULL
-#include <R_ext/Rdynload.h>
-#include "../inst/include/rxode2.h"
 #define __DOINIT__
 #include "cbindThetaOmega.h"
 //#include "seed.h"
+#include "../inst/include/rxode2.h"
 #include <rxode2parseGetTime.h>
 
 SEXP _rxHasOpenMp(void);

diff --git a/src/intdy.c b/src/intdy.c
@@ -1,7 +1,5 @@
 #define USE_FC_LEN_T
 #define STRICT_R_HEADERS
-#include <R.h>
-#include <Rinternals.h>
 #include <stdio.h>
 #include <math.h>
 #include "lsoda.h"
@@ -16,6 +14,10 @@
 #define _(String) (String)
 #endif
 
+#include <R.h>
+#include <Rinternals.h>
+
+
 void RSprintf(const char *format, ...);
 
 int intdy(struct lsoda_context_t * ctx, double t, int k, double *dky)
@@ -80,4 +82,3 @@ int intdy(struct lsoda_context_t * ctx, double t, int k, double *dky)
 		dky[i] *= r;
 	return 0;
 }				/* end intdy   */
-
diff --git a/src/lsoda.c b/src/lsoda.c
@@ -1,7 +1,5 @@
 #define USE_FC_LEN_T
 #define STRICT_R_HEADERS
-#include <R.h>
-#include <Rinternals.h>
 #ifdef ENABLE_NLS
 #include <libintl.h>
 #define _(String) dgettext ("rxode2", String)
@@ -10,6 +8,9 @@
 #define _(String) (String)
 #endif
 
+#include <R.h>
+#include <Rinternals.h>
+
 void RSprintf(const char *format, ...);
 
 /*
@@ -127,7 +128,7 @@ tam@wri.com
     ctx->state = -3 ;                           \
     return ctx->state;				\
   }
-  
+
 
 /* Terminate lsoda due to various error conditions. */
 #define softfailure(code, fmt,...) \

diff --git a/src/par_solve.cpp b/src/par_solve.cpp
@@ -4,17 +4,13 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <time.h>
-#include <R.h>
-#include <Rinternals.h>
 #include <string>
-#include <Rmath.h> //Rmath includes math.
-#include <R_ext/Rdynload.h>
-#include "../inst/include/rxode2.h"
 #include "strncmp.h"
-#include <rxode2parseHandleEvid.h>
-#include <rxode2parseGetTime.h>
 //#include "seed.h"
 #include <timsort.h>
+#include "../inst/include/rxode2.h"
+#include <rxode2parseHandleEvid.h>
+#include <rxode2parseGetTime.h>
 #define SORT gfx::timsort
 #define isSameTimeOp(xout, xp) (op->stiff == 0 ? isSameTimeDop(xout, xp) : isSameTime(xout, xp))
 // dop853 is same time

diff --git a/src/solsy.c b/src/solsy.c
@@ -1,13 +1,13 @@
 #define USE_FC_LEN_T
 #define STRICT_R_HEADERS
-#include <R.h>
-#include <Rinternals.h>
 #include "lsoda.h"
 #include "lsoda_internal.h"
 #include "common.h"
 #include <stdio.h>
 #include <stdlib.h>
 #include "blas.h"
+#include <R.h>
+#include <Rinternals.h>
 
 int solsy(struct lsoda_context_t * ctx, double *y)
 
@@ -32,4 +32,3 @@ int solsy(struct lsoda_context_t * ctx, double *y)
 	return 1;
 
 }
-