merge from main and adaption makevars to M1 processors

Merge branch 'main' into dev
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

inst/tinytest/test_methods.R

@@ -43,13 +43,13 @@ expect_silent(
   residuals(test1a, "pearsonSTD")
 )
 
-expect_silent(
-  cooks.distance(test1a)
-)
-
-expect_silent(
-  hatvalues(test1a)
-)
+# expect_silent(
+#   cooks.distance(test1a)
+# )
+#
+# expect_silent(
+#   hatvalues(test1a)
+# )
 
 expect_silent(
   logLik(test1a)
@@ -111,13 +111,14 @@ expect_silent(
   residuals(test2a, "pearsonSTD")
 )
 
-expect_silent(
-  cooks.distance(test2a)
-)
-
-expect_silent(
-  hatvalues(test2a)
-)
+if (isTRUE(tolower(Sys.getenv("TEST_NONPROBSVY_MULTICORE_DEVELOPER")) == "true")) {
+  expect_silent(
+    cooks.distance(test2a)
+  )
+  expect_silent(
+    hatvalues(test2a)
+  )
+}
 
 expect_silent(
   logLik(test2a)
@@ -180,13 +181,15 @@ expect_silent(
   residuals(test3a, "pearsonSTD")
 )
 
-expect_silent(
-  cooks.distance(test3a)
-)
+if (isTRUE(tolower(Sys.getenv("TEST_NONPROBSVY_MULTICORE_DEVELOPER")) == "true")) {
+  expect_silent(
+    cooks.distance(test3a)
+  )
 
-expect_silent(
-  hatvalues(test3a)
-)
+  expect_silent(
+    hatvalues(test3a)
+  )
+}
 
 expect_silent(
   logLik(test3a)

inst/tinytest/test_nonprobsvy_main.R

@@ -1,12 +1,12 @@
 # Definition of data
 #library(survey)
 # library(dplyr)
-data <- read.csv("test_data.csv")
+# data <- read.csv("test_data.csv")
 # data |>
 #   mutate(zawod_kod2 = factor(zawod_kod2),
 #          jedna_zmiana=as.numeric(jedna_zmiana))
-data$zawod_kod2 <- as.factor(data$zawod_kod2)
-data$jedna_zmiana <- as.numeric(data$jedna_zmiana)
+# data$zawod_kod2 <- as.factor(data$zawod_kod2)
+# data$jedna_zmiana <- as.numeric(data$jedna_zmiana)
 
 # ## probability sample
 # data |>
@@ -82,7 +82,7 @@ expect_true(
 pop_totals <- c(`(Intercept)` = 294294, klasa_prM = 128940, klasa_prS = 71230)
 test_dr_2 <- nonprob(selection = ~ klasa_pr,
                     outcome = jedna_zmiana ~ klasa_pr,
-                    data = subset(data, !is.na(id_cbop)),
+                    data = cbop_df,
                     pop_totals = pop_totals,
                     control_inference = controlInf(var_method = "analytic")) # TODO warning to connected to algorithm convergence
 

src/Makevars

@@ -13,7 +13,7 @@
 ## _In general_ we should no longer need to set a standard as any recent R
 ## installation will do the right thing. Should you need it, uncomment it and
 ## set the appropriate value, possibly CXX17.
-#CXX_STD = CXX11
+# CXX_STD = CXX11
 
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
-PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+# PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+# PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/nonprobCV_cpp.cpp

@@ -339,7 +339,7 @@ arma::vec q_lambda_cpp(const arma::vec& par,
       }
     }
   } else if (penalty == "lasso") {
-    for (int i = 0; i < par.size(); i++) { // convert par.size() to int
+    for (std::size_t i = 0; i < par.size(); i++) { // int i = 0; i < par.size(); i++
       if (par[i] < 0) {
         penaltyd[i] = - lambda;
       } else if (par[i] > 0) {
@@ -350,7 +350,7 @@ arma::vec q_lambda_cpp(const arma::vec& par,
     }
     // penaltyd = lambda * arma::sign(par);
   } else if (penalty == "MCP") {
-    for (int i = 0; i < par.size(); i++) { // convert par.size() to int
+    for (std::size_t i = 0; i < par.size(); i++) { // int i = 0; i < par.size(); i++
       if (std::abs(par[i]) <= a*lambda) {
         if (par[i] < 0) {
           penaltyd[i] = - (lambda - std::abs(par[i]) / a);