fix: replace non-API Rf_findVar with R_getVar/R_getVarEx

.Rbuildignore

@@ -20,4 +20,5 @@
 ^naryndb/$
 ^naryndb$
 ^AGENTS\.md$
-^.claude$
+^.claude$
+^\.Rd2pdf.*$

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.6.32
-Date: 2026-01-18 17:42:41 UTC
-SHA: 16c2625c7377a6838f2c28263e24519c86080763
+Version: 2.6.33
+Date: 2026-03-19 20:19:54 UTC
+SHA: 453a10849252e5883574039ce1056a753a965dec

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: naryn
 Title: Native Access Medical Record Retriever for High Yield Analytics
-Version: 2.6.32
+Version: 2.6.34
 Authors@R: c(
     person("Misha", "Hoichman", , "misha@hoichman.com", role = "aut"),
     person("Aviezer", "Lifshitz", , "aviezer.lifshitz@weizmann.ac.il", role = c("aut", "cre")),
@@ -55,4 +55,4 @@ Language: en-US
 LazyLoad: yes
 NeedsCompilation: yes
 OS_type: unix
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NEWS.md

@@ -1,3 +1,11 @@
+# naryn 2.6.34
+
+* Fixed CRAN pre-test warning about `pipe.Rd` documenting usage for re-exported `%>%`.
+
+# naryn 2.6.33
+
+* Replaced non-API C entry point `Rf_findVar` with `R_getVar`/`R_getVarEx` for R 4.6.0 compatibility.
+
 # naryn 2.6.32
 
 * Fixed C++20 deprecation warnings: removed `std::rel_ops` usage and fixed enum arithmetic.

R/utils-pipe.R

@@ -7,10 +7,6 @@
 #' @keywords internal
 #' @export
 #' @importFrom magrittr %>%
-#' @usage lhs \%>\% rhs
-#' @param lhs A value or the magrittr placeholder.
-#' @param rhs A function call using the magrittr semantics.
-#' @return The result of calling `rhs(lhs)`.
 NULL
 
 

cran-comments.md

@@ -2,5 +2,10 @@
 
 0 errors | 0 warnings | 0 notes
 
-* Fixed C++20 deprecation warnings: removed `std::rel_ops` usage and fixed deprecated enum arithmetic.
-* As was written in the previous submissions, the package implements a database that is based on shared memory files and therefore includes many unix-specific system calls. In addition, many parallel algorithms used in the package rely on the unix forking mechanism, therefore the package is not fully portable to Windows.
+## Changes
+
+* Replaced non-API C entry point `Rf_findVar` with `R_getVar`/`R_getVarEx`.
+
+## Note on portability
+
+The package implements a database that is based on shared memory files and therefore includes many unix-specific system calls. In addition, many parallel algorithms used in the package rely on the unix forking mechanism, therefore the package is not fully portable to Windows.

src/NRIteratorFilter.cpp

@@ -18,7 +18,7 @@ void NRIteratorFilter::init(SEXP filter, unsigned stime, unsigned etime)
     vector<SEXP> filters;
 
     // retrieve filter names (named filters are at a variable called EMR_FILTERS inside the .naryn environment)    
-    rprotect(emr_filters = Rf_findVar(Rf_install("EMR_FILTERS"), Rf_findVar(Rf_install(".naryn"), g_naryn->env())));
+    rprotect(emr_filters = R_getVarEx(Rf_install("EMR_FILTERS"), R_getVar(Rf_install(".naryn"), g_naryn->env(), (Rboolean)TRUE), (Rboolean)TRUE, R_NilValue));
 
     if (!Rf_isNull(emr_filters) && !Rf_isSymbol(emr_filters)) {        
 
@@ -183,7 +183,7 @@ EMRIteratorFilterItem *NRIteratorFilter::create_filter_item(vector<SEXP> &filter
             return filter;
         }
 
-        SEXP rval = Rf_findVar(Rf_install(str), g_naryn->env());
+        SEXP rval = R_getVarEx(Rf_install(str), g_naryn->env(), (Rboolean)TRUE, R_NilValue);
         bool success = false;
 
         EMRPoints points;

src/NRLogicalTrack.cpp

@@ -330,7 +330,7 @@ SEXP emr_expr_virtual_tracks(SEXP _expr, SEXP _envir) {
         vector<SEXP> vtracks;
 
         // retrieve virtual track names (virtual tracks are at a variable called EMR_VTRACKS in the .naryn environment)        
-        rprotect(emr_vtracks = Rf_findVar(Rf_install("EMR_VTRACKS"), Rf_findVar(Rf_install(".naryn"), g_naryn->env())));
+        rprotect(emr_vtracks = R_getVarEx(Rf_install("EMR_VTRACKS"), R_getVar(Rf_install(".naryn"), g_naryn->env(), (Rboolean)TRUE), (Rboolean)TRUE, R_NilValue));
 
         if (!Rf_isNull(emr_vtracks) && !Rf_isSymbol(emr_vtracks)) {
             if (!Rf_isVector(emr_vtracks)){

src/NRTrackExpressionScanner.cpp

@@ -109,7 +109,7 @@ void NRTrackExprScanner::define_r_vars(unsigned eval_buf_limit)
     for (unsigned i = 0; i < eval_buf_limit; ++i){
         m_itr_times[i] = 0;
     }
-    SEXP env = Rf_findVar(Rf_install(".GlobalEnv"), g_naryn->env());
+    SEXP env = R_getVar(Rf_install(".GlobalEnv"), g_naryn->env(), (Rboolean)TRUE);
     Rf_defineVar(Rf_install("EMR_TIME"), m_ritr_times, env);
 
     for (unsigned iexpr = 0; iexpr < m_track_exprs.size(); ++iexpr) {

src/NRTrackExpressionScanner.h

@@ -240,15 +240,15 @@ inline bool NRTrackExprScanner::eval_next()
                             m_track_exprs[iexpr].c_str(), Rf_length(m_eval_bufs[iexpr]), m_eval_buf_limit);
                 if (Rf_isReal(m_eval_bufs[iexpr])) {
                     if (m_valtype != REAL_T) {
-                        SEXP env = Rf_findVar(Rf_install(".GlobalEnv"), g_naryn->env());
+                        SEXP env = R_getVar(Rf_install(".GlobalEnv"), g_naryn->env(), (Rboolean)TRUE);
                         Rf_defineVar(Rf_install("EMR_ERROR_EXPR"), m_eval_bufs[iexpr], env);
                         verror("Expression \"%s\" does not produce a numeric result.\n"
                                 "The result of the last expression evaluation was saved in EMR_ERROR_EXPR variable.", m_track_exprs[iexpr].c_str());
                     }
                     m_eval_doubles[iexpr] = REAL(m_eval_bufs[iexpr]);
                 } else if (Rf_isLogical(m_eval_bufs[iexpr])) {
                     if (m_valtype != LOGICAL_T) {
-                        SEXP env = Rf_findVar(Rf_install(".GlobalEnv"), g_naryn->env());
+                        SEXP env = R_getVar(Rf_install(".GlobalEnv"), g_naryn->env(), (Rboolean)TRUE);
                         Rf_defineVar(Rf_install("EMR_ERROR_EXPR"), m_eval_bufs[iexpr], env);
                         verror("Expression \"%s\" does not produce a logical result.\n"
                                 "The result of the last expression evaluation was saved in EMR_ERROR_EXPR variable.", m_track_exprs[iexpr].c_str());

src/naryn.cpp

@@ -766,7 +766,7 @@ void runprotect_all()
 const char *get_groot(SEXP envir)
 {
 	// no need to protect the returned value
-	SEXP groot = Rf_findVar(Rf_install("GROOT"), envir);
+	SEXP groot = R_getVar(Rf_install("GROOT"), envir, (Rboolean)TRUE);
 
 	if (!Rf_isString(groot))
 		verror("GROOT variable does not exist");
@@ -777,7 +777,7 @@ const char *get_groot(SEXP envir)
 const char *get_glib_dir(SEXP envir)
 {
 	// no need to protect the returned value
-	SEXP glibdir = Rf_findVar(Rf_install(".GLIBDIR"), envir);
+	SEXP glibdir = R_getVar(Rf_install(".GLIBDIR"), envir, (Rboolean)TRUE);
 
 	if (!Rf_isString(glibdir))
 		verror(".GLIBDIR variable does not exist");

src/naryn.h

@@ -21,6 +21,25 @@
 #include <Rinternals.h>
 #include <Rinterface.h>
 
+// Backward-compatible shim for R < 4.5.0
+#include <Rversion.h>
+#if R_VERSION < R_Version(4, 5, 0)
+static inline SEXP R_getVar(SEXP sym, SEXP rho, Rboolean inherits) {
+    SEXP val = inherits ? Rf_findVar(sym, rho) : Rf_findVarInFrame(sym, rho);
+    if (val == R_UnboundValue)
+        Rf_error("object '%s' not found", CHAR(PRINTNAME(sym)));
+    MARK_NOT_MUTABLE(val);
+    return val;
+}
+static inline SEXP R_getVarEx(SEXP sym, SEXP rho, Rboolean inherits, SEXP ifnotfound) {
+    SEXP val = inherits ? Rf_findVar(sym, rho) : Rf_findVarInFrame(sym, rho);
+    if (val == R_UnboundValue)
+        return ifnotfound;
+    MARK_NOT_MUTABLE(val);
+    return val;
+}
+#endif
+
 #include "Thread.h"
 
 #ifdef length