tanaylab · aviezerl · Nov 12, 2025 · Nov 11, 2025 · Nov 11, 2025
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: naryn
 Title: Native Access Medical Record Retriever for High Yield Analytics
-Version: 2.6.30.9000
+Version: 2.6.31
 Authors@R: c(
     person("Misha", "Hoichman", , "misha@hoichman.com", role = "aut"),
     person("Aviezer", "Lifshitz", , "aviezer.lifshitz@weizmann.ac.il", role = c("aut", "cre")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,6 @@
-# naryn (development version)
+# naryn 2.6.31 
+
+* Removed non-API calls to `Rf_GetOption` in the C++ code.
 
 # naryn 2.6.30 
 

diff --git a/R/db.R b/R/db.R
@@ -63,7 +63,7 @@
 #' variables are added to the .naryn environment. These variables should not be
 #' modified by the user!
 #'
-#' \tabular{lll}{
+#' \tabular{ll}{
 #' .naryn$EMR_GROOT \tab First db dir of tracks in the order of connections \cr
 #' .naryn$EMR_UROOT \tab Last db dir of tracks in the order of connection (user dir) \cr
 #' .naryn$EMR_ROOTS \tab Vector of directories (db_dirs) \cr
@@ -208,7 +208,6 @@ emr_db.init_examples <- function(n_dbs = 1) {
 }
 
 
-
 #' Reloads database
 #'
 #' Reloads database
@@ -292,7 +291,6 @@ emr_db.subset <- function(src = "", fraction = NULL, complementary = NULL) {
 }
 
 
-
 #' Returns the ids that constitute the current ids subset
 #'
 #' Returns the ids that constitute the current ids subset.
@@ -312,7 +310,6 @@ emr_db.subset.ids <- function() {
 }
 
 
-
 #' Returns information about the current subset
 #'
 #' Returns information about the current subset.

diff --git a/R/extract.R b/R/extract.R
@@ -98,7 +98,6 @@ emr_cor <- function(..., cor.exprs = NULL, include.lowest = FALSE, right = TRUE,
 }
 
 
-
 #' Calculates distribution of track expressions
 #'
 #' Calculates distribution of track expressions' values over the given set of
@@ -300,7 +299,6 @@ emr_extract <- function(expr, tidy = FALSE, sort = FALSE, names = NULL, stime =
 }
 
 
-
 #' Returns ids coverage per track
 #'
 #' Returns ids coverage per track.
@@ -534,7 +532,6 @@ emr_ids_vals_coverage <- function(ids, tracks, stime = NULL, etime = NULL, filte
 }
 
 
-
 #' Calculates quantiles of a track expression
 #'
 #' Calculates quantiles of a track expression for the given percentiles.
@@ -576,7 +573,6 @@ emr_quantiles <- function(expr, percentiles = 0.5, stime = NULL, etime = NULL, i
 }
 
 
-
 #' Finds Id-Time points that match track expression
 #'
 #' Finds all patient-time pairs where track expression is 'TRUE'.
@@ -622,7 +618,6 @@ emr_screen <- function(expr, sort = FALSE, stime = NULL, etime = NULL, iterator
 }
 
 
-
 #' Calculates summary statistics of track expression
 #'
 #' Calculates summary statistics of track expression.

diff --git a/R/filter.R b/R/filter.R
@@ -226,7 +226,6 @@
 }
 
 
-
 #' Generate a default name for a naryn filter
 #'
 #' Generate a default name for a naryn filter
@@ -747,7 +746,6 @@ emr_filter.attr.expiration <- function(filter, expiration) {
 }
 
 
-
 #' Checks whether the named filter exists
 #'
 #' Checks whether the named filter exists.
@@ -829,7 +827,6 @@ emr_filters.info <- function(filter) {
 }
 
 
-
 #' Returns a list of named filters
 #'
 #' Returns a list of named filters.
@@ -876,7 +873,6 @@ emr_filter.ls <- function(pattern = "", ignore.case = FALSE, perl = FALSE, fixed
 }
 
 
-
 #' Deletes a named filter
 #'
 #' Deletes a named filter.

diff --git a/R/time.R b/R/time.R
@@ -30,7 +30,6 @@ emr_time2hour <- function(time) {
 }
 
 
-
 #' Converts time from internal format to a day of month
 #'
 #' Converts time from internal format to a day of month.
@@ -63,7 +62,6 @@ emr_time2dayofmonth <- function(time) {
 }
 
 
-
 #' Converts time from internal format to a month
 #'
 #' Converts time from internal format to a month.
@@ -96,7 +94,6 @@ emr_time2month <- function(time) {
 }
 
 
-
 #' Converts time from internal format to a year
 #'
 #' Converts time from internal format to a year.
@@ -128,7 +125,6 @@ emr_time2year <- function(time) {
 }
 
 
-
 #' Converts date and hour to internal time format
 #'
 #' Converts date and hour to internal time format.

diff --git a/R/track-attributes.R b/R/track-attributes.R
@@ -121,7 +121,6 @@ emr_track.attr.get <- function(track = NULL, attr = NULL) {
 }
 
 
-
 #' Deletes a track attribute
 #'
 #' Deletes a track attribute.
@@ -169,7 +168,6 @@ emr_track.attr.rm <- function(track, attr) {
 }
 
 
-
 #' Assigns a value to the track attribute
 #'
 #' Assigns a value to the track attribute.

diff --git a/R/track-vars.R b/R/track-vars.R
@@ -64,7 +64,6 @@ emr_track.var.get <- function(track, var) {
 }
 
 
-
 #' Returns a list of track variables for a track
 #'
 #' Returns a list of track variables for a track.
@@ -119,7 +118,6 @@ emr_track.var.ls <- function(track, pattern = "", ignore.case = FALSE, perl = FA
 }
 
 
-
 #' Deletes a track variable
 #'
 #' Deletes a track variable.
@@ -174,7 +172,6 @@ emr_track.var.rm <- function(track, var) {
 }
 
 
-
 #' Assigns value to a track variable
 #'
 #' Assigns value to a track variable.

diff --git a/R/track.R b/R/track.R
@@ -77,7 +77,6 @@
 }
 
 
-
 #' Adds new records to a track
 #'
 #' Adds new records to a track from a TAB-delimited file or a data frame.
@@ -239,7 +238,6 @@ emr_track.create <- function(track, space, categorical, expr, stime = NULL, etim
 }
 
 
-
 #' Checks whether the track exists
 #'
 #' Checks whether the track exists.
@@ -298,7 +296,6 @@ multiple_tracks_exist <- function(tracks, db_id = NULL) {
 }
 
 
-
 #' Returns track ids
 #'
 #' Returns the ids contained by the track.
@@ -327,7 +324,6 @@ emr_track.ids <- function(track) {
 }
 
 
-
 #' Imports a track from a file or data-frame
 #'
 #' Imports a track from a file or data-frame.
@@ -624,8 +620,6 @@ emr_track.logical.ls <- function(..., ignore.case = FALSE, perl = FALSE, fixed =
 }
 
 
-
-
 #' Moves (renames) a track
 #'
 #' Moves (renames) a track
@@ -714,7 +708,6 @@ emr_track.mv <- function(src, tgt, space = NULL) {
 }
 
 
-
 #' Returns track percentile of the values
 #'
 #' Returns track percentile of the values.
@@ -770,7 +763,6 @@ emr_track.percentile <- function(track, val, lower = TRUE) {
 }
 
 
-
 #' Gets or sets "read-only" property of a track
 #'
 #' Gets or sets "readonly" property of a track.

diff --git a/R/vtrack.R b/R/vtrack.R
@@ -422,7 +422,6 @@ emr_vtrack.create <- function(vtrack, src, func = NULL, params = NULL, keepref =
 }
 
 
-
 #' Get or set attributes of a virtual track
 #'
 #' Get or set attributes of a virtual track.
@@ -640,7 +639,6 @@ emr_vtrack.attr.filter <- function(vtrack, filter) {
 }
 
 
-
 #' Checks whether the virtual track exists
 #'
 #' Checks whether the virtual track exists.
@@ -671,7 +669,6 @@ emr_vtrack.exists <- function(vtrack) {
 }
 
 
-
 #' Returns the definition of a virtual track
 #'
 #' Returns the definition of a virtual track.
@@ -697,7 +694,6 @@ emr_vtrack.info <- function(vtrack) {
 }
 
 
-
 #' Returns a list of virtual track names
 #'
 #' Returns a list of virtual track names.
@@ -743,7 +739,6 @@ emr_vtrack.ls <- function(pattern = "", ignore.case = FALSE, perl = FALSE, fixed
 }
 
 
-
 #' Deletes a virtual track
 #'
 #' Deletes a virtual track.

diff --git a/R/zzz.R b/R/zzz.R
@@ -6,8 +6,7 @@
 .naryn$entries <- list()
 .naryn$entries_timestamp <- list()
 
-.onLoad <- function(lib, pkg) {
-}
+.onLoad <- function(lib, pkg) {}
 
 .onAttach <- function(lib, pkg) {
     Sys.umask("007")

diff --git a/cran-comments.md b/cran-comments.md
@@ -2,5 +2,4 @@
 
 0 errors | 0 warnings | 0 notes
 
-* Fixed *noRemap* additional issue.
-* Removed non-API calls to R: 'PRENV', 'PRVALUE', 'R_PromiseExpr'. 
+* Removed non-API calls to `Rf_GetOption`.
diff --git a/man/emr_db.connect.Rd b/man/emr_db.connect.Rd
diff --git a/src/NRTest.cpp b/src/NRTest.cpp
@@ -790,7 +790,7 @@ SEXP logical_track_vtrack(SEXP _track, SEXP envir){
 //         for (int i = 0; i < num_processes; ++i) {
 //             if (!g_naryn->launch_process()) { // kid process
 //                 if (g_naryn->debug()){
-//                     SEXP rvar = Rf_GetOption(Rf_install("emr_child_run_delay"), R_NilValue);
+//                     SEXP rvar = Rf_GetOption1(Rf_install("emr_child_run_delay"));
 //                     if (Rf_isReal(rvar) || Rf_isInteger(rvar))
 //                         sleep(Rf_asInteger(rvar));
 //                 }

diff --git a/src/naryn.cpp b/src/naryn.cpp
@@ -302,7 +302,7 @@ pid_t Naryn::launch_process()
         sigaction(SIGALRM, &s_old_sigalrm_act, NULL);
 		sigaction(SIGCHLD, &s_old_sigchld_act, NULL);
 
-		SEXP r_multitasking_stdout = Rf_GetOption(Rf_install("emr_multitasking_stdout"), R_NilValue);
+		SEXP r_multitasking_stdout = Rf_GetOption1(Rf_install("emr_multitasking_stdout"));
 
         int devnull;
         if ((devnull = open("/dev/null", O_RDWR)) == -1){
@@ -495,43 +495,43 @@ void Naryn::load_options()
 {
 	SEXP rvar;
 
-    rvar = Rf_GetOption(Rf_install("emr_debug"), R_NilValue);
+    rvar = Rf_GetOption1(Rf_install("emr_debug"));
     if (Rf_isLogical(rvar)){
         m_debug = Rf_asLogical(rvar);
     }
 
-    rvar = Rf_GetOption(Rf_install("emr_multitasking"), R_NilValue);
+    rvar = Rf_GetOption1(Rf_install("emr_multitasking"));
     if (Rf_isLogical(rvar)){
         m_multitasking_avail = Rf_asLogical(rvar);
     }
 
-    rvar = Rf_GetOption(Rf_install("emr_min.processes"), R_NilValue);
+    rvar = Rf_GetOption1(Rf_install("emr_min.processes"));
     if ((Rf_isReal(rvar) || Rf_isInteger(rvar)) && Rf_asInteger(rvar) >= 1){
         m_min_processes = Rf_asInteger(rvar);
     }
 
-    rvar = Rf_GetOption(Rf_install("emr_max.processes"), R_NilValue);
+    rvar = Rf_GetOption1(Rf_install("emr_max.processes"));
     if ((Rf_isReal(rvar) || Rf_isInteger(rvar)) && Rf_asInteger(rvar) >= 1){
         m_max_processes = Rf_asInteger(rvar);
     }
     m_max_processes = max(m_min_processes, m_max_processes);
 
-	rvar = Rf_GetOption(Rf_install("emr_max.data.size"), R_NilValue);
+	rvar = Rf_GetOption1(Rf_install("emr_max.data.size"));
 	if ((Rf_isReal(rvar) || Rf_isInteger(rvar)) && Rf_asReal(rvar) >= 1){
 		m_max_data_size = (uint64_t)Rf_asReal(rvar);
     }
 
-    rvar = Rf_GetOption(Rf_install("emr_eval.buf.size"), R_NilValue);
+    rvar = Rf_GetOption1(Rf_install("emr_eval.buf.size"));
     if ((Rf_isReal(rvar) || Rf_isInteger(rvar)) && Rf_asInteger(rvar) >= 1){
         m_eval_buf_size = Rf_asInteger(rvar);
     }
 
-	rvar = Rf_GetOption(Rf_install("emr_quantile.edge.data.size"), R_NilValue);
+	rvar = Rf_GetOption1(Rf_install("emr_quantile.edge.data.size"));
 	if ((Rf_isReal(rvar) || Rf_isInteger(rvar)) && Rf_asReal(rvar) >= 0){
 		m_quantile_edge_data_size = (uint64_t)Rf_asReal(rvar);
     }
 
-    rvar = Rf_GetOption(Rf_install("emr_warning.itr.no.filter.size"), R_NilValue);
+    rvar = Rf_GetOption1(Rf_install("emr_warning.itr.no.filter.size"));
     if ((Rf_isReal(rvar) || Rf_isInteger(rvar)) && Rf_asReal(rvar) >= 1){
         m_beat_itr_warning_size = (uint64_t)Rf_asReal(rvar);
     }

diff --git a/tests/testthat/test-logical_tracks.R b/tests/testthat/test-logical_tracks.R
@@ -85,7 +85,6 @@ test_that("emr_track.logical.create tracks works in batch mode length of values
 })
 
 
-
 test_that("emr_track.logical.create fails when track length do not equal names length", {
     expect_error(emr_track.logical.create(c("a", "b"), c("ph1")))
 })
-Original file line number
+Diff line change
@@ Expand Up / @@ -121,7 +121,6 @@ emr_track.attr.get <- function(track = NULL, attr = NULL) { @@
     }
     #' Deletes a track attribute
     #'
     #' Deletes a track attribute.
@@ Expand Down Expand Up / @@ -169,7 +168,6 @@ emr_track.attr.rm <- function(track, attr) { @@
     }
     #' Assigns a value to the track attribute
     #'
     #' Assigns a value to the track attribute.
@@ Expand Down @@