v4.2-4-6 fixed parallelization in BIOMOD_Projection

biomodhub · Aug 16, 2023 · e32acc4 · e32acc4
1 parent 7e0da31
commit e32acc4
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Showing 89 changed files with 119 additions and 106 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: biomod2
 Type: Package
 Title: Ensemble Platform for Species Distribution Modeling
-Version: 4.2-4-5
+Version: 4.2-4-6
 Date: 2023-06-15
 Authors@R: c(person("Wilfried", "Thuiller", role = c("aut")
                     , email = "[email protected]"),

diff --git a/R/BIOMOD_Projection.R b/R/BIOMOD_Projection.R
@@ -290,9 +290,10 @@ BIOMOD_Projection <- function(bm.mod,
       warning("Parallelisation with `foreach` is not available for Windows. Sorry.")
     }
   }
-
+  new.env.wrap <- wrap(new.env) # ensure parallel run compatibility
   proj <- foreach(mod.name = models.chosen) %dopar% {
     cat("\n\t> Projecting", mod.name, "...")
+    new.env <- unwrap(new.env.wrap) # ensure parallel run compatibility
     if (do.stack) {
       filename <- NULL
     } else {
@@ -301,7 +302,6 @@ BIOMOD_Projection <- function(bm.mod,
                                    ifelse(output.format == ".RData"
                                           , ".tif", output.format)))
     }
-
     mod <- get(BIOMOD_LoadModels(bm.out = bm.mod, full.name = mod.name))
     temp_workdir = NULL
     if (length(grep("MAXENT$", mod.name)) == 1) {
@@ -311,13 +311,15 @@ BIOMOD_Projection <- function(bm.mod,
                         filename = filename, omit.na = omit.na, 
                         temp_workdir = temp_workdir, seedval = seed.val, 
                         overwrite = TRUE, mod.name = mod.name)
+    cat("\n step 3",mod.name)
     if (do.stack) {
       if (proj_is_raster) {
         return(wrap(pred.tmp)) 
       } else {
         return(pred.tmp)
       }
     } else {
+      cat(filename)
       return(filename)
     }
   }

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/news.html b/docs/articles/news.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/reference/BIOMOD.ensemble.models.out.html b/docs/reference/BIOMOD.ensemble.models.out.html
diff --git a/docs/reference/BIOMOD.formated.data.PA.html b/docs/reference/BIOMOD.formated.data.PA.html
diff --git a/docs/reference/BIOMOD.formated.data.html b/docs/reference/BIOMOD.formated.data.html
diff --git a/docs/reference/BIOMOD.models.options.html b/docs/reference/BIOMOD.models.options.html
diff --git a/docs/reference/BIOMOD.models.out.html b/docs/reference/BIOMOD.models.out.html
diff --git a/docs/reference/BIOMOD.projection.out.html b/docs/reference/BIOMOD.projection.out.html
diff --git a/docs/reference/BIOMOD.stored.data.html b/docs/reference/BIOMOD.stored.data.html
diff --git a/docs/reference/BIOMOD_ConvertOldRun-deprecated.html b/docs/reference/BIOMOD_ConvertOldRun-deprecated.html
diff --git a/docs/reference/BIOMOD_CrossValidation-deprecated.html b/docs/reference/BIOMOD_CrossValidation-deprecated.html
diff --git a/docs/reference/BIOMOD_EnsembleForecasting.html b/docs/reference/BIOMOD_EnsembleForecasting.html
diff --git a/docs/reference/BIOMOD_EnsembleModeling.html b/docs/reference/BIOMOD_EnsembleModeling.html
diff --git a/docs/reference/BIOMOD_FormatingData.html b/docs/reference/BIOMOD_FormatingData.html
diff --git a/docs/reference/BIOMOD_LoadModels.html b/docs/reference/BIOMOD_LoadModels.html
diff --git a/docs/reference/BIOMOD_Modeling.html b/docs/reference/BIOMOD_Modeling.html
diff --git a/docs/reference/BIOMOD_ModelingOptions.html b/docs/reference/BIOMOD_ModelingOptions.html
diff --git a/docs/reference/BIOMOD_PresenceOnly.html b/docs/reference/BIOMOD_PresenceOnly.html