Fixed start_yael(); Fixed obsolete code and updated dependencies

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rave
 Type: Package
 Title: R Analysis and Visualization of 'ECOG/iEEG' Data
-Version: 1.0.5
+Version: 1.0.6
 Authors@R: c(
     person("Zhengjia", "Wang", email = "dipterix.wang@gmail.com", role = c("cph", "aut", "cre")),
     person("John", "Magnotti", role = c("aut")),
@@ -22,7 +22,7 @@ Language: en-US
 URL: https://rave.wiki,
     https://beauchamplab.github.io/rave/
 BugReports: https://github.com/beauchamplab/rave/issues
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Imports:
     utils,
     stats,

R/class-ExecEnvir.R

@@ -39,7 +39,12 @@ ExecEnvir <- R6::R6Class(
     outputs = NULL,
     update = NULL,
     tabsets = NULL,
-    executes = NULL
+    executes = NULL,
+
+    finalize = function(){
+      self$clean()
+      catgl(sprintf('[%s] Runtime Environment Removed.', self$module_env$module_id))
+    }
   ),
   public = list(
     #' @field .__rave_context__. context string for current instance, indicating
@@ -164,13 +169,6 @@ ExecEnvir <- R6::R6Class(
       }
     },
 
-    #' @description garbage collection
-    #' @return none
-    finalize = function(){
-      self$clean()
-      catgl(sprintf('[%s] Runtime Environment Removed.', self$module_env$module_id))
-    },
-
     #' @description print variables in different layers (environment)
     #' @return none
     info = function(){

R/class-RaveFinalizer.R

@@ -5,9 +5,7 @@ RaveFinalizer <- R6::R6Class(
   cloneable = FALSE,
   portable = TRUE,
   parent_env = ..setup_env,
-  public = list(
-    .fin = NULL,
-    files = NULL,
+  private = list(
     finalize = function(){
       if(is.function(self$.fin)){
         try({
@@ -20,7 +18,11 @@ RaveFinalizer <- R6::R6Class(
         lapply(self$files, unlink, recursive = TRUE)
       }
 
-    },
+    }
+  ),
+  public = list(
+    .fin = NULL,
+    files = NULL,
     initialize = function(fun){
       self$.fin <- fun
 

R/class-Subject.R

@@ -19,7 +19,11 @@ Subject <- R6::R6Class(
   classname = 'Subject',
   private = list(
     loaded = NULL,
-    subjectinfo = NULL
+    subjectinfo = NULL,
+
+    finalize = function(){
+      rm(list = ls(private$loaded), envir = private$loaded)
+    }
   ),
   public = list(
 
@@ -57,10 +61,6 @@ Subject <- R6::R6Class(
       self$info()
     },
 
-    #' @description called when garbage collected
-    finalize = function(){
-      rm(list = ls(private$loaded), envir = private$loaded)
-    },
 
     #' @description constructor
     #' @param project_name project name