Only update the batch file if something changes

Expanding on #6

R/grid.batchFunction.R

@@ -100,6 +100,7 @@ function(grid.input.Parameters, fName, yName, varlist, scriptName, remScriptName
 	#read outputs
 	while(count_done < length(cmd))
     {
+        count_done_prev = count_done
         count_done = 0
         count=1
      	while(count<=length(cmd))
@@ -126,9 +127,12 @@ function(grid.input.Parameters, fName, yName, varlist, scriptName, remScriptName
             		else
             			ret[[count]]=grid.input.Parameters#c(y, paste("result from parameters:",cmd[count]))
             		count_done = count_done + 1
-                    grid.input.Parameters = ret
-                    unlink(yName)
-                    save(list=c("grid.batch_done", "grid.input.Parameters"), file=yName)
+                    if ( count_done_prev != count_done ) {
+                        # Only update the file if something changed
+                        grid.input.Parameters = ret
+                        unlink(yName)
+                        save(list=c("grid.batch_done", "grid.input.Parameters"), file=yName)
+                    }
 
     			}
     			if(file.exists(paste(scriptName, "out",sep=""))){

inst/GridR/R-bootstrap.py

@@ -169,8 +169,12 @@ def installR(install_dir):
     # Ok, now move the R installation into the correct directory
     tmp_r_dir = os.path.join(tmp_dir, 'R')
     for rDir in os.listdir(tmp_r_dir):
-        shutil.rmtree(os.path.join(install_dir, rDir), ignore_errors=True)
-        shutil.move(os.path.join(tmp_r_dir, rDir), os.path.join(install_dir, rDir))
+        try:
+            shutil.rmtree(os.path.join(install_dir, rDir), ignore_errors=True)
+            shutil.move(os.path.join(tmp_r_dir, rDir), os.path.join(install_dir, rDir))
+        except OSError:
+            sys.stderr.write("Unable to move directory: %s, moving on..." % rDir)
+
     #shutil.move(os.path.join(tmp_dir, 'R'), install_dir)
     shutil.rmtree(tmp_dir)
 
@@ -245,19 +249,20 @@ def main():
             # Initialize to some time way in the past
             completed_date = datetime(1970, 1, 1)
             try:
-                completed_date = datetime.fromtimestamp(os.path.getmtime(os.path.join(r_dir, ".completed")))
+                completed_date = datetime.utcfromtimestamp(os.path.getmtime(os.path.join(r_dir, ".completed")))
 
             except OSError:
                 # If there's an OS error, then that typically means that the .completed file
                 # was removed (race condition).  We can just ignore it.
-                sys.stderr.write("The .completed file was deleted on us")
+                sys.stderr.write("The .completed file was deleted on us\n")
                 pass
 
             if completed_date < server_date:
-                sys.stderr.write("Completed time is before server time")
+                sys.stderr.write("Completed time is before server time\n")
                 sys.stderr.write(str(completed_date))
                 sys.stderr.write(str(server_date))
                 try:
+                    os.remove(os.path.join(r_dir, ".started"))
                     os.remove(os.path.join(r_dir, ".completed"))
                 except OSError:
                     pass