Change cores=1 so that it doesn't create parallel clusters

R/BandsPartition_TMLA.R

@@ -18,16 +18,7 @@ BandsPartition_TMLA <- function(evnVariables = NULL,
 
   #Development
   #Start Cluster
-  if (Sys.getenv("RSTUDIO") == "1" &&
-      !nzchar(Sys.getenv("RSTUDIO_TERM")) &&
-      Sys.info()["sysname"] == "Darwin" &&
-      as.numeric(gsub('[.]', '', getRversion())) >= 360) {
-    cl <- parallel::makeCluster(cores,outfile="", setup_strategy = "sequential")
-  }else{
-    cl <- parallel::makeCluster(cores,outfile="")
-  }
-  doParallel::registerDoParallel(cl)
-
+  cl <- start_cluster(cores)
 
   #Separate data by groups
   RecordsData <-
@@ -583,6 +574,6 @@ BandsPartition_TMLA <- function(evnVariables = NULL,
     sep = "\t",
     row.names = F
   )
-  parallel::stopCluster(cl)
+  stop_cluster(cl)
   return(FinalResult)
 }

R/BlockPartition_TMLA.R

@@ -42,15 +42,7 @@ BlockPartition_TMLA <- function(evnVariables = NULL,
   # BestGridList <- rep(list(NULL),length(RecordsData))
 
   #Start Cluster
-  if (Sys.getenv("RSTUDIO") == "1" &&
-      !nzchar(Sys.getenv("RSTUDIO_TERM")) &&
-      Sys.info()["sysname"] == "Darwin" &&
-      as.numeric(gsub('[.]', '', getRversion())) >= 360) {
-        cl <- parallel::makeCluster(cores,outfile="", setup_strategy = "sequential")
-      }else{
-        cl <- parallel::makeCluster(cores,outfile="")
-      }
-      doParallel::registerDoParallel(cl)
+  cl <- start_cluster(cores)
 
   # LOOP----
   results <-
@@ -598,7 +590,8 @@ BlockPartition_TMLA <- function(evnVariables = NULL,
       return(out)
     }
 
-  parallel::stopCluster(cl)
+  stop_cluster(cl)
+
   FinalResult <- dplyr::bind_rows(lapply(results, function(x) x[[1]]))
   FinalInfoGrid <- dplyr::bind_rows(lapply(results, function(x) x[[2]]))
 

R/Ensemble_TMLA.R

@@ -11,15 +11,7 @@ Ensemble_TMLA <- function(DirR,
                           cores,
                           ensemble_metric = NULL) {
   #Start Cluster----
-  if (Sys.getenv("RSTUDIO") == "1" &&
-      !nzchar(Sys.getenv("RSTUDIO_TERM")) &&
-      Sys.info()["sysname"] == "Darwin" &&
-      as.numeric(gsub('[.]', '', getRversion())) >= 360) {
-        cl <- parallel::makeCluster(cores,outfile="", setup_strategy = "sequential")
-      }else{
-        cl <- parallel::makeCluster(cores,outfile="")
-      }
-  doParallel::registerDoParallel(cl)
+  cl <- start_cluster(cores)
 
   #Create Folders----
   DirENS <- paste(DirR, "Ensemble", sep = "/")
@@ -629,5 +621,5 @@ Ensemble_TMLA <- function(DirR,
     col.names = T,
     row.names = F
   )
-  parallel::stopCluster(cl)
+  stop_cluster(cl)
 }

R/FitENM_Parallel_TMLA.R

@@ -26,17 +26,8 @@ FitENM_TMLA_Parallel <- function(RecordsData,
   Ti <- Sys.time()
   options(warn = -1)
 
-  #Start Cluster
-  # temporary parallel package debug for macOS systems
-  if (Sys.getenv("RSTUDIO") == "1" &&
-      !nzchar(Sys.getenv("RSTUDIO_TERM")) &&
-      Sys.info()["sysname"] == "Darwin" &&
-      as.numeric(gsub('[.]', '', getRversion())) >= 360) {
-        cl <- parallel::makeCluster(cores,outfile="", setup_strategy = "sequential")
-      }else{
-        cl <- parallel::makeCluster(cores,outfile="")
-      }
-  doParallel::registerDoParallel(cl)
+  #Start Cluster if necessary
+  cl <- start_cluster(cores)
 
   # Directory to save----
   folders <- paste(DirSave,"Algorithm",Algorithm,sep="/")
@@ -4058,5 +4049,5 @@ InfoModeling <- list(c("########################################################
   lapply(InfoModeling, write,
          paste(DirSave, "/InfoModeling.txt", sep=""), append=TRUE,
          ncolumns=20, sep='\t')
-  parallel::stopCluster(cl)
+  stop_cluster(cl)
 }

R/M_delimited_TMLA.R

@@ -76,15 +76,7 @@ M_delimited <- function(var,
       return(x)
     })
 
-    if (Sys.getenv("RSTUDIO") == "1" &&
-        !nzchar(Sys.getenv("RSTUDIO_TERM")) &&
-        Sys.info()["sysname"] == "Darwin" &&
-        as.numeric(gsub('[.]', '', getRversion())) >= 360) {
-          cl <- parallel::makeCluster(cores,outfile="", setup_strategy = "sequential")
-        }else{
-          cl <- parallel::makeCluster(cores,outfile="")
-        }
-    doParallel::registerDoParallel(cl)
+    cl <- start_cluster(cores)
     foreach(i = 1:length(M_list),
             .packages = c("raster")) %dopar% {
               if (Buffer_Opt == 2) {
@@ -105,7 +97,7 @@ M_delimited <- function(var,
                                   format = "GTiff",
                                   overwrite = T)
             }
-    parallel::stopCluster(cl)
+    stop_cluster(cl)
   }
 
   if (method == 'MASK') {
@@ -136,15 +128,7 @@ M_delimited <- function(var,
       x <- x[x != 0]
     })
 
-    if (Sys.getenv("RSTUDIO") == "1" &&
-        !nzchar(Sys.getenv("RSTUDIO_TERM")) &&
-        Sys.info()["sysname"] == "Darwin" &&
-        as.numeric(gsub('[.]', '', getRversion())) >= 360) {
-          cl <- parallel::makeCluster(cores,outfile="", setup_strategy = "sequential")
-        }else{
-          cl <- parallel::makeCluster(cores,outfile="")
-        }
-    doParallel::registerDoParallel(cl)
+    cl <- start_cluster(cores)
     foreach(i = 1:length(sp.Ecoregions),
             .packages = c("raster")) %dopar% {
               EcoregionSp <- EcoregionsFile
@@ -159,7 +143,7 @@ M_delimited <- function(var,
                 overwrite = T
               )
             }
-    parallel::stopCluster(cl)
+    stop_cluster(cl)
   }
 
   if (method == 'USER-DEFINED') {

R/cluster.R

@@ -0,0 +1,22 @@
+
+start_cluster <- function(cores) {
+  cl <- NULL
+  if (cores > 1) {
+    if (Sys.getenv("RSTUDIO") == "1" &&
+        !nzchar(Sys.getenv("RSTUDIO_TERM")) &&
+        Sys.info()["sysname"] == "Darwin" &&
+        as.numeric(gsub('[.]', '', getRversion())) >= 360) {
+      cl <- parallel::makeCluster(cores,outfile="", setup_strategy = "sequential")
+    }else{
+      cl <- parallel::makeCluster(cores,outfile="")
+    }
+    doParallel::registerDoParallel(cl)
+  }
+  return(cl)
+}
+
+stop_cluster <- function(cluster) {
+  if (!is.null(cluster)) {
+    parallel::stopCluster(cluster)
+  }
+}