Removed non-API calls to R: 'PRENV', 'PRVALUE', 'R_PromiseExpr'.

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.6.26
-Date: 2024-01-14 19:09:33 UTC
-SHA: 2c56e06dccf3c5d22dbbd12e4dc746887ff0c28a
+Version: 2.6.30
+Date: 2024-09-27 08:34:48 UTC
+SHA: f465f7137992d8df2e04d2dfa10365e421076390

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: naryn
 Title: Native Access Medical Record Retriever for High Yield Analytics
-Version: 2.6.29
+Version: 2.6.30
 Authors@R: c(
     person("Misha", "Hoichman", , "[email protected]", role = "aut"),
     person("Aviezer", "Lifshitz", , "[email protected]", role = c("aut", "cre")),
@@ -54,4 +54,4 @@ Language: en-US
 LazyLoad: yes
 NeedsCompilation: yes
 OS_type: unix
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

NEWS.md

@@ -1,11 +1,15 @@
+# naryn 2.6.30 
+
+* Removed non-API calls to R in the C++ code.
+
 # naryn 2.6.29 
 
 * Fixed *noRemap* additional issue by adding `Rf_` prefix in the c++ code.
 
 # naryn 2.6.28 
 
 * Fix: `emr_track.mv` did not move track attributes. 
-* "exists" virtual track function without parameters now checks for existance of any value.
+* "exists" virtual track function without parameters now checks for existence of any value.
 
 # naryn 2.6.27
 

cran-comments.md

@@ -3,3 +3,4 @@
 0 errors | 0 warnings | 0 notes
 
 * Fixed *noRemap* additional issue.
+* Removed non-API calls to R: 'PRENV', 'PRVALUE', 'R_PromiseExpr'. 

inst/WORDLIST

@@ -14,10 +14,11 @@ MAXTIME
 MINID
 MINTIME
 Makevars
+Mendelson
 NA's
-NaN
 PARAM
 PKGDIR
+POSIXct
 Postmyocardial
 Pre
 Prefetch
@@ -68,6 +69,7 @@ mylist
 naryndb
 ndarray
 ness
+noRemap
 numpy
 param
 params

src/NRIdTimeInterval.cpp

@@ -9,10 +9,10 @@ void NRIdTimeIntervals::convert_rid_time_intervals(SEXP rintervs, EMRIdTimeInter
     intervs->clear();
 
     if (TYPEOF(rintervs) == PROMSXP) {
-        if (PRENV(rintervs) == R_NilValue)
-            rintervs = PRVALUE(rintervs);
+        if (NARYN_PRENV(rintervs) == R_NilValue)
+            rintervs = NARYN_PRVALUE(rintervs);
         else
-            rintervs = eval_in_R(R_PromiseExpr(rintervs), PRENV(rintervs));
+            rintervs = eval_in_R(NARYN_PREXPR(rintervs), NARYN_PRENV(rintervs));
     }
 
     if (!Rf_isVector(rintervs))

src/NRIdTimeInterval.h

@@ -16,6 +16,7 @@
 #undef error
 #endif
 
+#include "naryn.h"
 #include "EMRIdTimeInterval.h"
 
 using namespace std;

src/NRPoint.cpp

@@ -93,10 +93,10 @@ void NRPoint::convert_rpoints(SEXP rpoints, vector<EMRPoint> *points, const char
     points->clear();
 
     if (TYPEOF(rpoints) == PROMSXP) {
-        if (PRENV(rpoints) == R_NilValue)
-            rpoints = PRVALUE(rpoints);
+        if (NARYN_PRENV(rpoints) == R_NilValue)
+            rpoints = NARYN_PRVALUE(rpoints);
         else
-            rpoints = eval_in_R(R_PromiseExpr(rpoints), PRENV(rpoints));
+            rpoints = eval_in_R(NARYN_PREXPR(rpoints), NARYN_PRENV(rpoints));
     }
 
     if (!Rf_isVector(rpoints))
@@ -193,10 +193,10 @@ void NRPoint::convert_rids(SEXP rids, vector<unsigned> *ids, const char *error_m
     ids->clear();
 
     if (TYPEOF(rids) == PROMSXP) {
-        if (PRENV(rids) == R_NilValue)
-            rids = PRVALUE(rids);
+        if (NARYN_PRENV(rids) == R_NilValue)
+            rids = NARYN_PRVALUE(rids);
         else
-            rids = eval_in_R(R_PromiseExpr(rids), PRENV(rids));
+            rids = eval_in_R(NARYN_PREXPR(rids), NARYN_PRENV(rids));
     }
 
     if (!Rf_isVector(rids))

src/NRPoint.h

@@ -3,6 +3,7 @@
 
 #include "EMRPoint.h"
 #include "EMRTrack.h"
+#include "naryn.h"
 #include <cstdint>
 
 struct NRPoint {
@@ -33,10 +34,10 @@ template<class T>
 void NRPoint::convert_rpoints_vals(SEXP rsrc, EMRTrackData<T> &data, const char *error_msg_prefix)
 {
     if (TYPEOF(rsrc) == PROMSXP) {
-        if (PRENV(rsrc) == R_NilValue)
-            rsrc = PRVALUE(rsrc);
+        if (NARYN_PRENV(rsrc) == R_NilValue)
+            rsrc = NARYN_PRVALUE(rsrc);
         else
-            rsrc = eval_in_R(R_PromiseExpr(rsrc), PRENV(rsrc));
+            rsrc = eval_in_R(NARYN_PREXPR(rsrc), NARYN_PRENV(rsrc));
     }
 
     SEXP colnames = Rf_getAttrib(rsrc, R_NamesSymbol);

src/NRTimeInterval.cpp

@@ -8,10 +8,10 @@ void NRTimeIntervals::convert_rtime_intervals(SEXP rintervs, EMRTimeIntervals *i
     intervs->clear();
 
     if (TYPEOF(rintervs) == PROMSXP) {
-        if (PRENV(rintervs) == R_NilValue)
-            rintervs = PRVALUE(rintervs);
+        if (NARYN_PRENV(rintervs) == R_NilValue)
+            rintervs = NARYN_PRVALUE(rintervs);
         else
-            rintervs = eval_in_R(R_PromiseExpr(rintervs), PRENV(rintervs));
+            rintervs = eval_in_R(NARYN_PREXPR(rintervs), NARYN_PRENV(rintervs));
     }
 
     if (!Rf_isVector(rintervs))

src/NRTimeInterval.h

@@ -16,6 +16,7 @@
 #undef error
 #endif
 
+#include "naryn.h"
 #include "EMRTimeInterval.h"
 #include "EMRTimeStamp.h"
 

src/NRTrackExpressionVars.cpp

@@ -239,10 +239,10 @@ void NRTrackExpressionVars::add_vtrack_var(const string &vtrack, SEXP rvtrack, b
         static const char *COL_NAMES[NUM_COLS] = { "id1", "id2", "time.shift" };
 
         if (TYPEOF(rid_map) == PROMSXP) {
-            if (PRENV(rid_map) == R_NilValue)
-                rid_map = PRVALUE(rid_map);
+            if (NARYN_PRENV(rid_map) == R_NilValue)
+                rid_map = NARYN_PRVALUE(rid_map);
             else
-                rid_map = eval_in_R(R_PromiseExpr(rid_map), PRENV(rid_map));
+                rid_map = eval_in_R(NARYN_PREXPR(rid_map), NARYN_PRENV(rid_map));
         }
 
         if (!Rf_isVector(rid_map) || Rf_xlength(rid_map) < NUM_COLS - 1)

src/NRVtrack.cpp

@@ -123,10 +123,10 @@ SEXP emr_check_vtrack_attr_id_map(SEXP _id_map, SEXP _envir) {
             NRTrackExpressionVars::IdMap id_map;
 
             if (TYPEOF(_id_map) == PROMSXP) {
-                if (PRENV(_id_map) == R_NilValue)
-                    _id_map = PRVALUE(_id_map);
+                if (NARYN_PRENV(_id_map) == R_NilValue)
+                    _id_map = NARYN_PRVALUE(_id_map);
                 else
-                    _id_map = eval_in_R(R_PromiseExpr(_id_map), PRENV(_id_map));
+                    _id_map = eval_in_R(NARYN_PREXPR(_id_map), NARYN_PRENV(_id_map));
             }
 
             if (!Rf_isVector(_id_map) || Rf_xlength(_id_map) < NUM_COLS - 1)

src/naryn.h

@@ -38,6 +38,10 @@
     #define RNARYN
 #endif
 
+#define NARYN_PRENV(x) TAG(x)
+#define NARYN_PRVALUE(x) CAR(x)
+#define NARYN_PREXPR(x) R_BytecodeExpr(CDR(x))
+
 using namespace std;
 
 // should be used instead of R_CheckUserInterrupt. Throws exception if the command is interrupted.