diff --git a/R/pkg/R/utils.R b/R/pkg/R/utils.R
index 65db9c21d9dbb..cef2fa9b47440 100644
--- a/R/pkg/R/utils.R
+++ b/R/pkg/R/utils.R
@@ -529,7 +529,10 @@ processClosure <- function(node, oldEnv, defVars, checkedFuncs, newEnv) {
         # Namespaces other than "SparkR" will not be searched.
         if (!isNamespace(func.env) ||
             (getNamespaceName(func.env) == "SparkR" &&
-               !(nodeChar %in% getNamespaceExports("SparkR")))) {
+               !(nodeChar %in% getNamespaceExports("SparkR")) &&
+                  # Note that generic S4 methods should not be set to the environment of
+                  # cleaned closure. It does not work with R 4.0.0+. See also SPARK-31918.
+                  nodeChar != "" && !methods::isGeneric(nodeChar, func.env))) {
           # Only include SparkR internals.
 
           # Set parameter 'inherits' to FALSE since we do not need to search in
diff --git a/R/pkg/tests/fulltests/test_context.R b/R/pkg/tests/fulltests/test_context.R
index 6be04b321e985..f86872d727a1d 100644
--- a/R/pkg/tests/fulltests/test_context.R
+++ b/R/pkg/tests/fulltests/test_context.R
@@ -26,7 +26,9 @@ test_that("Check masked functions", {
                      "colnames", "colnames<-", "intersect", "rank", "rbind", "sample", "subset",
                      "summary", "transform", "drop", "window", "as.data.frame", "union", "not")
   version <- packageVersion("base")
-  if (as.numeric(version$major) >= 3 && as.numeric(version$minor) >= 3) {
+  is33Above <- as.numeric(version$major) >= 3 && as.numeric(version$minor) >= 3
+  is40Above <- as.numeric(version$major) >= 4
+  if (is33Above || is40Above) {
     namesOfMasked <- c("endsWith", "startsWith", namesOfMasked)
   }
   masked <- conflicts(detail = TRUE)$`package:SparkR`
diff --git a/R/pkg/tests/fulltests/test_mllib_classification.R b/R/pkg/tests/fulltests/test_mllib_classification.R
index 9dd275a173089..5b49a013959df 100644
--- a/R/pkg/tests/fulltests/test_mllib_classification.R
+++ b/R/pkg/tests/fulltests/test_mllib_classification.R
@@ -34,7 +34,7 @@ test_that("spark.svmLinear", {
   summary <- summary(model)
 
   # test summary coefficients return matrix type
-  expect_true(class(summary$coefficients) == "matrix")
+  expect_true(any(class(summary$coefficients) == "matrix"))
   expect_true(class(summary$coefficients[, 1]) == "numeric")
 
   coefs <- summary$coefficients[, "Estimate"]
@@ -130,7 +130,7 @@ test_that("spark.logit", {
   summary <- summary(model)
 
   # test summary coefficients return matrix type
-  expect_true(class(summary$coefficients) == "matrix")
+  expect_true(any(class(summary$coefficients) == "matrix"))
   expect_true(class(summary$coefficients[, 1]) == "numeric")
 
   versicolorCoefsR <- c(1.52, 0.03, -0.53, 0.04, 0.00)
@@ -242,8 +242,8 @@ test_that("spark.logit", {
   # Test binomial logistic regression against two classes with upperBoundsOnCoefficients
   # and upperBoundsOnIntercepts
   u <- matrix(c(1.0, 0.0, 1.0, 0.0), nrow = 1, ncol = 4)
-  model <- spark.logit(training, Species ~ ., upperBoundsOnCoefficients = u,
-                       upperBoundsOnIntercepts = 1.0)
+  model <- suppressWarnings(spark.logit(training, Species ~ ., upperBoundsOnCoefficients = u,
+                                        upperBoundsOnIntercepts = 1.0))
   summary <- summary(model)
   coefsR <- c(-11.13331, 1.00000, 0.00000, 1.00000, 0.00000)
   coefs <- summary$coefficients[, "Estimate"]
@@ -255,8 +255,8 @@ test_that("spark.logit", {
   # Test binomial logistic regression against two classes with lowerBoundsOnCoefficients
   # and lowerBoundsOnIntercepts
   l <- matrix(c(0.0, -1.0, 0.0, -1.0), nrow = 1, ncol = 4)
-  model <- spark.logit(training, Species ~ ., lowerBoundsOnCoefficients = l,
-                       lowerBoundsOnIntercepts = 0.0)
+  model <- suppressWarnings(spark.logit(training, Species ~ ., lowerBoundsOnCoefficients = l,
+                                        lowerBoundsOnIntercepts = 0.0))
   summary <- summary(model)
   coefsR <- c(0, 0, -1, 0, 1.902192)
   coefs <- summary$coefficients[, "Estimate"]
@@ -268,9 +268,9 @@ test_that("spark.logit", {
   # Test multinomial logistic regression with lowerBoundsOnCoefficients
   # and lowerBoundsOnIntercepts
   l <- matrix(c(0.0, -1.0, 0.0, -1.0, 0.0, -1.0, 0.0, -1.0), nrow = 2, ncol = 4)
-  model <- spark.logit(training, Species ~ ., family = "multinomial",
-                       lowerBoundsOnCoefficients = l,
-                       lowerBoundsOnIntercepts = as.array(c(0.0, 0.0)))
+  model <- suppressWarnings(spark.logit(training, Species ~ ., family = "multinomial",
+                                        lowerBoundsOnCoefficients = l,
+                                        lowerBoundsOnIntercepts = as.array(c(0.0, 0.0))))
   summary <- summary(model)
   versicolorCoefsR <- c(42.639465, 7.258104, 14.330814, 16.298243, 11.716429)
   virginicaCoefsR <- c(0.0002970796, 4.79274, 7.65047, 25.72793, 30.0021)
diff --git a/R/pkg/tests/fulltests/test_mllib_clustering.R b/R/pkg/tests/fulltests/test_mllib_clustering.R
index 028ad574b8134..f180aeea28150 100644
--- a/R/pkg/tests/fulltests/test_mllib_clustering.R
+++ b/R/pkg/tests/fulltests/test_mllib_clustering.R
@@ -171,7 +171,7 @@ test_that("spark.kmeans", {
   expect_equal(sort(collect(distinct(select(cluster, "prediction")))$prediction), c(0, 1))
 
   # test summary coefficients return matrix type
-  expect_true(class(summary.model$coefficients) == "matrix")
+  expect_true(any(class(summary.model$coefficients) == "matrix"))
   expect_true(class(summary.model$coefficients[1, ]) == "numeric")
 
   # Test model save/load
diff --git a/R/pkg/tests/fulltests/test_mllib_regression.R b/R/pkg/tests/fulltests/test_mllib_regression.R
index 0f2a62b7229ca..b281cd6235ef0 100644
--- a/R/pkg/tests/fulltests/test_mllib_regression.R
+++ b/R/pkg/tests/fulltests/test_mllib_regression.R
@@ -116,7 +116,7 @@ test_that("spark.glm summary", {
   rStats <- summary(glm(Sepal.Width ~ Sepal.Length + Species, data = dataset))
 
   # test summary coefficients return matrix type
-  expect_true(class(stats$coefficients) == "matrix")
+  expect_true(any(class(stats$coefficients) == "matrix"))
   expect_true(class(stats$coefficients[, 1]) == "numeric")
 
   coefs <- stats$coefficients