specify ParDist to be single threaded

gavinmdouglas · Nov 10, 2022 · d08ae00 · d08ae00
1 parent 43311a5
commit d08ae00
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: FuncDiv
 Title: Compute contributional diversity metrics
-Version: 0.4.2
+Version: 0.4.3
 Authors@R: 
     person("Gavin", "Douglas", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5164-6707"))

diff --git a/R/beta_workflow.R b/R/beta_workflow.R
@@ -13,7 +13,7 @@ parDist_methods <- c("bhjattacharyya", "bray", "canberra", "chord",
 
 for (m in parDist_methods) {
   func_dist_cmd_char <- paste("function(in_tab, ...) {\n",
-                              "func_dist <- as.matrix(parallelDist::parDist(in_tab, method = \"", eval(m), "\"))\n",
+                              "func_dist <- as.matrix(parallelDist::parDist(in_tab, method = \"", eval(m), "\", threads = 1))\n",
                               "func_dist[lower.tri(func_dist, diag = TRUE)] <- NA\n",
                               "return(func_dist)\n}", sep = "")
 
@@ -30,7 +30,7 @@ compute_betadiv[["unweighted_unifrac"]] <- function(in_tab, in_phylo) {
 }
 
 compute_betadiv[["jensen_shannon_div"]] <- function(in_tab, ...) {
-  func_dist <- as.matrix(parallelDist::parDist(in_tab, method = "custom", func = jensen_shannon_divergence_FuncPtr))
+  func_dist <- as.matrix(parallelDist::parDist(in_tab, method = "custom", func = jensen_shannon_divergence_FuncPtr, threads = 1))
   func_dist[lower.tri(func_dist, diag = TRUE)] <- NA
   return(func_dist)
 }