Changes to get closer to compiling binary

nlmixr2 · Jul 11, 2024 · 587d2c2 · 587d2c2
1 parent f3de07d
commit 587d2c2
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Showing 32 changed files with 651 additions and 742 deletions.
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -192,8 +192,8 @@ etTransEvidIsObs <- function(isObsSexp) {
 #' @keywords internal
 #'
 #' @export
-etTransParse <- function(inData, mv, addCmt = FALSE, dropUnits = FALSE, allTimeVar = FALSE, keepDosingOnly = FALSE, combineDvid = NULL, keep = character(0), addlKeepsCov = FALSE, addlDropSs = TRUE, ssAtDoseTime = TRUE) {
-    .Call(`_rxode2_etTransParse`, inData, mv, addCmt, dropUnits, allTimeVar, keepDosingOnly, combineDvid, keep, addlKeepsCov, addlDropSs, ssAtDoseTime)
+etTrans <- function(inData, mv, addCmt = FALSE, dropUnits = FALSE, allTimeVar = FALSE, keepDosingOnly = FALSE, combineDvid = NULL, keep = character(0), addlKeepsCov = FALSE, addlDropSs = TRUE, ssAtDoseTime = TRUE) {
+    .Call(`_rxode2_etTrans`, inData, mv, addCmt, dropUnits, allTimeVar, keepDosingOnly, combineDvid, keep, addlKeepsCov, addlDropSs, ssAtDoseTime)
 }
 
 rxEtTransAsDataFrame_ <- function(inData1) {

diff --git a/inst/include/rxode2.h b/inst/include/rxode2.h
@@ -7,29 +7,14 @@
 #define rxLlikSaveSize 9
 
 #include <stdbool.h>
-#include <rxode2parse.h>
+#include "rxode2parse.h"
 #include <R.h>
 #include <Rinternals.h>
 #include <Rversion.h>
 #include <Rmath.h>
 #include <R_ext/Rdynload.h>
 
-#define rc_buf_read _rxode2_rc_buf_read
-#define sIniTo _rxode2_sIniTo
-#define sFree _rxode2_sFree
-#define sFreeIni _rxode2_sFreeIni
-#define sAppendN _rxode2_sAppendN
-#define sAppend _rxode2_sAppend
-#define sPrint _rxode2_sPrint
-#define lineIni _rxode2_lineIni
-#define lineFree _rxode2_lineFree
-#define addLine _rxode2_addLine
-#define curLineProp _rxode2_curLineProp
-#define curLineType _rxode2_curLineType
-#define doDot _rxode2_doDot
-#define doDot2 _rxode2_doDot2
-
-#include <rxode2parseSbuf.h>
+#include "rxode2parseSbuf.h"
 
 #include <float.h>
 #include <stdio.h>

diff --git a/inst/include/rxode2_control.h b/inst/include/rxode2_control.h
@@ -1,100 +1,5 @@
 #pragma once
 #ifndef __rxode2_control_H__
 #define __rxode2_control_H__
-#include <rxode2parse_control.h>
-#define Rxc_scale 0
-#define Rxc_method 1
-#define Rxc_atol 2
-#define Rxc_rtol 3
-#define Rxc_maxsteps 4
-#define Rxc_hmin 5
-#define Rxc_hmax 6
-#define Rxc_hini 7
-#define Rxc_maxordn 8
-#define Rxc_maxords 9
-#define Rxc_covsInterpolation 10
-#define Rxc_addCov 11
-#define Rxc_returnType 12
-#define Rxc_sigma 13
-#define Rxc_sigmaDf 14
-#define Rxc_nCoresRV 15
-#define Rxc_sigmaIsChol 16
-#define Rxc_sigmaSeparation 17
-#define Rxc_sigmaXform 18
-#define Rxc_nDisplayProgress 19
-#define Rxc_amountUnits 20
-#define Rxc_timeUnits 21
-#define Rxc_addDosing 22
-#define Rxc_stateTrim 23
-#define Rxc_updateObject 24
-#define Rxc_omega 25
-#define Rxc_omegaDf 26
-#define Rxc_omegaIsChol 27
-#define Rxc_omegaSeparation 28
-#define Rxc_omegaXform 29
-#define Rxc_nSub 30
-#define Rxc_thetaMat 31
-#define Rxc_thetaDf 32
-#define Rxc_thetaIsChol 33
-#define Rxc_nStud 34
-#define Rxc_dfSub 35
-#define Rxc_dfObs 36
-#define Rxc_seed 37
-#define Rxc_nsim 38
-#define Rxc_minSS 39
-#define Rxc_maxSS 40
-#define Rxc_strictSS 41
-#define Rxc_infSSstep 42
-#define Rxc_istateReset 43
-#define Rxc_subsetNonmem 44
-#define Rxc_hmaxSd 45
-#define Rxc_maxAtolRtolFactor 46
-#define Rxc_from 47
-#define Rxc_to 48
-#define Rxc_by 49
-#define Rxc_length_out 50
-#define Rxc_iCov 51
-#define Rxc_keep 52
-#define Rxc_keepF 53
-#define Rxc_drop 54
-#define Rxc_warnDrop 55
-#define Rxc_omegaLower 56
-#define Rxc_omegaUpper 57
-#define Rxc_sigmaLower 58
-#define Rxc_sigmaUpper 59
-#define Rxc_thetaLower 60
-#define Rxc_thetaUpper 61
-#define Rxc_indLinPhiM 62
-#define Rxc_indLinPhiTol 63
-#define Rxc_indLinMatExpType 64
-#define Rxc_indLinMatExpOrder 65
-#define Rxc_idFactor 66
-#define Rxc_mxhnil 67
-#define Rxc_hmxi 68
-#define Rxc_warnIdSort 69
-#define Rxc_ssAtol 70
-#define Rxc_ssRtol 71
-#define Rxc_safeZero 72
-#define Rxc_sumType 73
-#define Rxc_prodType 74
-#define Rxc_sensType 75
-#define Rxc_linDiff 76
-#define Rxc_linDiffCentral 77
-#define Rxc_resample 78
-#define Rxc_resampleID 79
-#define Rxc_maxwhile 80
-#define Rxc_cores 81
-#define Rxc_atolSens 82
-#define Rxc_rtolSens 83
-#define Rxc_ssAtolSens 84
-#define Rxc_ssRtolSens 85
-#define Rxc_simVariability 86
-#define Rxc_nLlikAlloc 87
-#define Rxc_useStdPow 88
-#define Rxc_naTimeHandle 89
-#define Rxc_addlKeepsCov 90
-#define Rxc_addlDropSs 91
-#define Rxc_ssAtDoseTime 92
-#define Rxc_ss2cancelAllPending 93
-#define Rxc__zeros 94
+#include "rxode2parse_control.h"
 #endif // __rxode2_control_H__
diff --git a/inst/include/rxode2parse.h b/inst/include/rxode2parse.h
@@ -37,40 +37,8 @@
 #include <stdio.h>
 #include <stdarg.h>
 
-#include "rxode2parse_control.h"
+#include "rxode2_control.h"
 #include <stdint.h>    // for uint64_t rather than unsigned long long
 
-#ifdef _isrxode2parse_
-#define max2( a , b )  ( (a) > (b) ? (a) : (b) )
-#define isSameTime(xout, xp) (fabs((xout)-(xp))  <= DBL_EPSILON*max2(fabs(xout),fabs(xp)))
-// use ~dop853 definition of same time
-#define isSameTimeDop(xout, xp) (0.1 * fabs((xout)-(xp)) <= fabs(xout) * 2.3E-16)
-#define _linCmtParse _rxode2parse_linCmtParse
-#define _rxode2_linCmtGen _rxode2parse_linCmtGen
-#define rc_buf_read _rxode2parse_rc_buf_read
-#define sIniTo _rxode2parse_sIniTo
-#define sFree _rxode2parse_sFree
-#define sFreeIni _rxode2parse_sFreeIni
-#define sAppendN _rxode2parse_sAppendN
-#define sAppend _rxode2parse_sAppend
-#define sPrint _rxode2parse_sPrint
-#define lineIni _rxode2parse_lineIni
-#define lineFree _rxode2parse_lineFree
-#define addLine _rxode2parse_addLine
-#define curLineProp _rxode2parse_curLineProp
-#define curLineType _rxode2parse_curLineType
-#define doDot _rxode2parse_doDot
-#define doDot2 _rxode2parse_doDot2
-#define _setSilentErr _rxode2parse__setSilentErr
-#define _isRstudio2 _rxode2parse_isRstudio2
-#define setSilentErr _rxode2parse_setSilentErr
-#define setRstudioPrint _rxode2parse_setRstudioPrint
-#define getSilentErr _rxode2parse_getSilentErr
-#define getRstudioPrint _rxode2parse_getRstudioPrint
-#define RSprintf _rxode2parse_RSprintf
-#define parseFree _rxode2parse_parseFree
-#define parseFreeLast _rxode2parse_parseFreeLast
-#define reset _rxode2parse_reset
-#endif
 #include "rxode2parseStruct.h"
 #endif
diff --git a/inst/include/rxode2parseConvertMethod.h b/inst/include/rxode2parseConvertMethod.h
diff --git a/inst/include/rxode2parseSbuf.h b/inst/include/rxode2parseSbuf.h
@@ -77,7 +77,6 @@ void addLine(vLines *sbb, const char *format, ...);
 void curLineProp(vLines *sbb, int propId);
 
 void curLineType(vLines *sbb, int propId);
-
 void doDot(sbuf *out, char *buf);
 
 void doDot2(sbuf *sb, sbuf *sbDt, char *buf);

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -284,9 +284,9 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// etTransParse
-List etTransParse(List inData, List mv, bool addCmt, bool dropUnits, bool allTimeVar, bool keepDosingOnly, Nullable<LogicalVector> combineDvid, CharacterVector keep, bool addlKeepsCov, bool addlDropSs, bool ssAtDoseTime);
-RcppExport SEXP _rxode2_etTransParse(SEXP inDataSEXP, SEXP mvSEXP, SEXP addCmtSEXP, SEXP dropUnitsSEXP, SEXP allTimeVarSEXP, SEXP keepDosingOnlySEXP, SEXP combineDvidSEXP, SEXP keepSEXP, SEXP addlKeepsCovSEXP, SEXP addlDropSsSEXP, SEXP ssAtDoseTimeSEXP) {
+// etTrans
+List etTrans(List inData, List mv, bool addCmt, bool dropUnits, bool allTimeVar, bool keepDosingOnly, Nullable<LogicalVector> combineDvid, CharacterVector keep, bool addlKeepsCov, bool addlDropSs, bool ssAtDoseTime);
+RcppExport SEXP _rxode2_etTrans(SEXP inDataSEXP, SEXP mvSEXP, SEXP addCmtSEXP, SEXP dropUnitsSEXP, SEXP allTimeVarSEXP, SEXP keepDosingOnlySEXP, SEXP combineDvidSEXP, SEXP keepSEXP, SEXP addlKeepsCovSEXP, SEXP addlDropSsSEXP, SEXP ssAtDoseTimeSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
@@ -301,7 +301,7 @@ BEGIN_RCPP
     Rcpp::traits::input_parameter< bool >::type addlKeepsCov(addlKeepsCovSEXP);
     Rcpp::traits::input_parameter< bool >::type addlDropSs(addlDropSsSEXP);
     Rcpp::traits::input_parameter< bool >::type ssAtDoseTime(ssAtDoseTimeSEXP);
-    rcpp_result_gen = Rcpp::wrap(etTransParse(inData, mv, addCmt, dropUnits, allTimeVar, keepDosingOnly, combineDvid, keep, addlKeepsCov, addlDropSs, ssAtDoseTime));
+    rcpp_result_gen = Rcpp::wrap(etTrans(inData, mv, addCmt, dropUnits, allTimeVar, keepDosingOnly, combineDvid, keep, addlKeepsCov, addlDropSs, ssAtDoseTime));
     return rcpp_result_gen;
 END_RCPP
 }

diff --git a/src/approx.c b/src/approx.c
@@ -6,8 +6,8 @@
 #include <stdio.h>
 #include <stdarg.h>
 #include "../inst/include/rxode2.h"
-#include <rxode2parseHandleEvid.h>
-#include <rxode2parseGetTime.h>
+#include "../inst/include/rxode2parseHandleEvid.h"
+#include "../inst/include/rxode2parseGetTime.h"
 
 #define safe_zero(a) ((a) == 0 ? DBL_EPSILON : (a))
 #define _as_zero(a) (fabs(a) < sqrt(DBL_EPSILON) ? 0.0 : a)

diff --git a/src/cbindThetaOmega.cpp b/src/cbindThetaOmega.cpp
@@ -2,7 +2,7 @@
 #define STRICT_R_HEADERS
 #include <Rcpp.h>
 #include <R.h>
-#include <rxode2parse.h>
+#include "../inst/include/rxode2parse.h"
 
 
 #ifdef ENABLE_NLS

diff --git a/src/codegen.c b/src/codegen.c
@@ -545,7 +545,7 @@ void writeSb(sbuf *sbb, FILE *fp){
 
 extern SEXP _goodFuns;
 
-SEXP _rxode2parse_codegen(SEXP c_file, SEXP prefix, SEXP libname,
+SEXP _rxode2_codegen(SEXP c_file, SEXP prefix, SEXP libname,
                           SEXP pMd5, SEXP timeId, SEXP mvLast,
                           SEXP goodFuns){
   _goodFuns = PROTECT(goodFuns); _rxode2parse_protected++;

diff --git a/src/codegen.h b/src/codegen.h
@@ -19,6 +19,7 @@
 #define _(String) (String)
 #endif
 #include "../inst/include/rxode2parse.h"
+#include "../inst/include/rxode2_control.h"
 #include "tran.h"
 #include "../inst/include/rxode2parseSbuf.h"
 
@@ -261,7 +262,7 @@ static inline void printCModelVars(const char *prefix) {
   sAppend(&sbOut, "extern SEXP %smodel_vars(void){\n  int pro=0;\n", prefix);
   sAppend(&sbOut, "  SEXP _mv = PROTECT(_rxGetModelLib(\"%smodel_vars\"));pro++;\n", prefix);
   sAppendN(&sbOut, "  if (!_rxIsCurrentC(_mv)){\n", 28);
-  sAppendN(&sbOut, "    SEXP hash    = PROTECT(allocVector(STRSXP, 1));pro++;\n", 58);
+  sAppendN(&sbOut, "    SEXP hash    = PROTECT(Rf_allocVector(STRSXP, 1));pro++;\n", 61);
   sAppend(&sbOut, "#define __doBuf__  snprintf(buf, __doBufN__, \"", _mv.o+1);
   int off=0;
   int off2 = 0;
@@ -355,7 +356,7 @@ void writeSb(sbuf *sbb, FILE *fp);
 	  CHAR(STRING_ELT(libname, 1)));					\
   writeSb(&sbOut, fpIO);
 
-SEXP _rxode2parse_codegen(SEXP c_file, SEXP prefix, SEXP libname,
+SEXP _rxode2_codegen(SEXP c_file, SEXP prefix, SEXP libname,
                           SEXP pMd5, SEXP timeId, SEXP mvLast, SEXP goodFuns);
 
 extern int fullPrint;