Merge pull request #1121 from jiajic/suite_dev

fix: dbMatrix method
drieslab · Mar 3, 2025 · 2397b88 · 2397b88
2 parents 576d3c6 + c0f9867
commit 2397b88
Showing 1 changed file with 28 additions and 25 deletions.
diff --git a/R/zzz.R b/R/zzz.R
@@ -45,33 +45,36 @@
 }
 
 .onLoad <- function(libname, pkgname) {
-    # extensible classunions --------------------------------------------#
     all_matrix <- c("matrix", "Matrix")
     update_matrix_sig <- FALSE
-    if (requireNamespace("DelayedArray", quietly = TRUE)) {
-        getClass("DelayedArray")
-        all_matrix <- c(all_matrix, "DelayedArray")
-        update_matrix_sig <- TRUE
-    }
-    if (requireNamespace("dbMatrix", quietly = TRUE)) {
-        getClass("dbMatrix")
-        all_matrix <- c(all_matrix, "dbMatrix")
-        update_matrix_sig <- TRUE
-    }
-
-    if (isTRUE(update_matrix_sig)) {
-        setClassUnion("allMatrix", members = all_matrix)
-    }
-    # methods extensions ------------------------------------------------#
 
-    if (requireNamespace("dbMatrix", quietly = TRUE)) {
-    setMethod("processData",
-        signature(x = "dbMatrix", param = "logNormParam"),
-        function(x, param) {
-            x[] <- dplyr::mutate(x[], x = x + param$offset)
-            # workaround for lack of @x slot
-            mymatrix <- log(mymatrix) / log(base)
+    # suppress known warnings about onload class and method extensions
+    suppressWarnings({
+        # extensible classunions --------------------------------------------#
+        if (requireNamespace("DelayedArray", quietly = TRUE)) {
+            getClass("DelayedArray")
+            all_matrix <- c(all_matrix, "DelayedArray")
+            update_matrix_sig <- TRUE
         }
-    )
-}
+        if (requireNamespace("dbMatrix", quietly = TRUE)) {
+            getClass("dbMatrix")
+            all_matrix <- c(all_matrix, "dbMatrix")
+            update_matrix_sig <- TRUE
+        }
+        # signature update
+        if (isTRUE(update_matrix_sig)) {
+            setClassUnion("allMatrix", members = all_matrix)
+        }
+        # methods extensions ------------------------------------------------#
+
+        if (requireNamespace("dbMatrix", quietly = TRUE)) {
+            setMethod("processData",
+                      signature(x = "dbMatrix", param = "logNormParam"),
+                      function(x, param) {
+                          x[] <- dplyr::mutate(x[], x = x + param$offset)
+                          log(x) / log(param$base)
+                      }
+            )
+        }
+    })
 }