[chore] Condition the use of shared memory to the check of SharedObject package being installed

Author: AndiMunteanu

R/stability-1-dim-reduction.R

@@ -273,14 +273,14 @@ assess_feature_stability <- function(data_matrix,
 
         if (graph_reduction_type == "PCA") {
             needed_vars <- c(needed_vars, "shared_neigh_matrix")
-            if (ncores > 1) {
+            if (ncores > 1 && is_package_installed("SharedObject")) {
                 shared_neigh_matrix <- SharedObject::share(neigh_matrix)
             } else {
                 shared_neigh_matrix <- neigh_matrix
             }
         } else {
             needed_vars <- c(needed_vars, "shared_embedding")
-            if (ncores > 1) {
+            if (ncores > 1 && is_package_installed("SharedObject")) {
                 shared_embedding <- SharedObject::share(embedding)
             } else {
                 shared_embedding <- embedding
@@ -395,10 +395,12 @@ assess_feature_stability <- function(data_matrix,
             cluster_results
         }
 
-        if (graph_reduction_type == "PCA") {
-            shared_neigh_matrix <- SharedObject::unshare(neigh_matrix)
-        } else {
-            shared_embedding <- SharedObject::unshare(embedding)
+        if (is_package_installed("SharedObject")) {
+            if (graph_reduction_type == "PCA") {
+                shared_neigh_matrix <- SharedObject::unshare(neigh_matrix)
+            } else {
+                shared_embedding <- SharedObject::unshare(embedding)
+            }
         }
 
         set.seed(42) # to match Seurat's default

R/stability-2-graph-construction.R

@@ -17,10 +17,10 @@ get_nn_conn_comps_umap <- function(embedding,
     umap_arguments[["n_neighbors"]] <- min(umap_arguments[["n_neighbors"]], ncells - 1)
 
     nn_conn_comps_list <- list()
-    if (ncores == 1) {
-        shared_embedding <- embedding
-    } else {
+    if (ncores > 1 && is_package_installed("SharedObject")) {
         shared_embedding <- SharedObject::share(embedding)
+    } else {
+        shared_embedding <- embedding
     }
 
     if (length(n_neigh_sequence) > 1) {
@@ -87,7 +87,7 @@ get_nn_conn_comps_umap <- function(embedding,
         n_comps
     }
 
-    if (ncores > 1) {
+    if (ncores > 1 && is_package_installed("SharedObject")) {
         shared_embedding <- SharedObject::unshare(embedding)
     }
 
@@ -116,10 +116,10 @@ get_nn_conn_comps_pca <- function(embedding,
         k = max(n_neigh_sequence)
     )$nn.idx
 
-    if (ncores == 1) {
-        shared_nn2_res <- nn2_res
-    } else {
+    if (ncores > 1 && is_package_installed("SharedObject")) {
         shared_nn2_res <- SharedObject::share(nn2_res)
+    } else {
+        shared_nn2_res <- nn2_res
     }
 
     if (length(n_neigh_sequence) > 1) {
@@ -151,7 +151,7 @@ get_nn_conn_comps_pca <- function(embedding,
         )
     }
 
-    if (ncores > 1) {
+    if (ncores > 1 && is_package_installed("SharedObject")) {
         shared_nn2_res <- SharedObject::unshare(nn2_res)
     }
 
@@ -568,7 +568,7 @@ assess_nn_stability_pca <- function(embedding,
         k = max(n_neigh_sequence)
     )$nn.idx
 
-    if (ncores > 1) {
+    if (ncores > 1 && is_package_installed("SharedObject")) {
         shared_nn2_res <- SharedObject::share(nn2_res)
     } else {
         shared_nn2_res <- nn2_res
@@ -610,7 +610,7 @@ assess_nn_stability_pca <- function(embedding,
 
     names(neigh_matrices) <- as.character(n_neigh_sequence)
 
-    if (ncores > 1) {
+    if (ncores > 1 && is_package_installed("SharedObject")) {
         shared_nn2_res <- SharedObject::unshare(nn2_res)
         rm(shared_nn2_res)
     }
@@ -625,7 +625,7 @@ assess_nn_stability_pca <- function(embedding,
     for (n_neigh in as.character(n_neigh_sequence)) {
         partitions_list[[paste("PCA", "snn", sep = "_")]][[n_neigh]] <- list()
 
-        if (ncores > 1) {
+        if (ncores > 1 && is_package_installed("SharedObject")) {
             shared_neigh_matrix <- SharedObject::share(neigh_matrices[[n_neigh]])
         } else {
             shared_neigh_matrix <- neigh_matrices[[n_neigh]]
@@ -773,7 +773,7 @@ assess_nn_stability_umap <- function(embedding,
     ncells <- nrow(embedding)
     umap_arguments <- process_umap_arguments(umap_arguments, ncells)
 
-    if (ncores > 1) {
+    if (ncores > 1 && is_package_installed("SharedObject")) {
         shared_embedding <- SharedObject::share(embedding)
     } else {
         shared_embedding <- embedding
@@ -879,7 +879,7 @@ assess_nn_stability_umap <- function(embedding,
         return(seed_result)
     }
 
-    if (ncores > 1) {
+    if (ncores > 1 && is_package_installed("SharedObject")) {
         shared_embedding <- SharedObject::unshare(embedding)
     }
 

R/stability-3-graph-clustering.R

@@ -184,7 +184,7 @@ assess_clustering_stability <- function(graph_adjacency_matrix,
     # additional arguments used by the clustering method
 
     # if (min(algorithm) < 4) {
-    if (ncores > 1) {
+    if (ncores > 1 && is_package_installed("SharedObject")) {
         graph_adjacency_matrix_shared <- SharedObject::share(graph_adjacency_matrix)
     } else {
         graph_adjacency_matrix_shared <- graph_adjacency_matrix
@@ -337,7 +337,7 @@ assess_clustering_stability <- function(graph_adjacency_matrix,
 
     on.exit(
         {
-            if (ncores > 1) {
+            if (ncores > 1 && is_package_installed("SharedObject")) {
                 graph_adjacency_matrix_shared <- SharedObject::unshare(graph_adjacency_matrix)
                 rm(graph_adjacency_matrix_shared)
             }