From 3a973d0172ee41e165271fd3f4fbd763c3680c6b Mon Sep 17 00:00:00 2001
From: Hollos Roland <hollorol@gmail.com>
Date: Thu, 24 Sep 2020 17:36:06 +0200
Subject: [PATCH] some bugfixing

---
 RBBGCMuso/R/calibrateMuso.R | 20 +++++++++++++-------
 calibrateMuso.R             |  6 +++---
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/RBBGCMuso/R/calibrateMuso.R b/RBBGCMuso/R/calibrateMuso.R
index 0deefa5..2ac1992 100644
--- a/RBBGCMuso/R/calibrateMuso.R
+++ b/RBBGCMuso/R/calibrateMuso.R
@@ -16,10 +16,10 @@ calibrateMuso <- function(measuredData, parameters = NULL, startDate = NULL,
                      maxLikelihoodEpc=TRUE,
                      pbUpdate = setTxtProgressBar, method="GLUE",lg = FALSE, w=NULL, ...){
 
-
-    file.remove(list.files(path = settings$inputLoc, pattern="progress.txt", recursive = TRUE))
-    file.remove(list.files(path = settings$inputLoc, pattern="preservedCalib.csv", recursive = TRUE))
-    unlink("thread",recursive=TRUE)
+    future::plan(future::multisession)
+    file.remove(list.files(path = settings$inputLoc, pattern="progress.txt", recursive = TRUE, full.names=TRUE))
+    file.remove(list.files(path = settings$inputLoc, pattern="preservedCalib.csv", recursive = TRUE, full.names=TRUE))
+    unlink(file.path(settings$inputLoc,"thread"),recursive=TRUE)
 
     #   ____                _         _   _                        _     
     #  / ___|_ __ ___  __ _| |_ ___  | |_| |__  _ __ ___  __ _  __| |___ 
@@ -94,9 +94,15 @@ calibrateMuso <- function(measuredData, parameters = NULL, startDate = NULL,
     while(progress < iterations){
         Sys.sleep(1)
         progress <- tryCatch(getProgress(), error=function(e){progress})
-        pbUpdate(pb,as.numeric(progress))
+        if(is.null(pb)){
+            pbUpdate(as.numeric(progress))
+        } else {
+            pbUpdate(pb,as.numeric(progress))
+        }
+    }
+    if(!is.null(pb)){
+        close(pb)
     }
-    close(pb)
 
     #   ____                _     _            
     #  / ___|___  _ __ ___ | |__ (_)_ __   ___ 
@@ -164,7 +170,7 @@ calibrateMuso <- function(measuredData, parameters = NULL, startDate = NULL,
 
 copyToThreadDirs <- function(prefix="thread", numcores=parallel::detectCores()-1, runDir="."){
     dir.create(file.path(runDir,prefix), showWarnings=TRUE)
-    fileNames <- grep("^thread.*", list.files(runDir), value=TRUE, invert=TRUE)
+    fileNames <- grep("^thread.*", list.files(runDir,full.names=TRUE), value=TRUE, invert=TRUE)
     invisible(sapply(1:numcores,function(corenum){
                 threadDir <- file.path(runDir,prefix,paste0(prefix,"_",corenum))
                 dir.create(threadDir, showWarnings=FALSE)
diff --git a/calibrateMuso.R b/calibrateMuso.R
index 46c46e8..8df08d0 100644
--- a/calibrateMuso.R
+++ b/calibrateMuso.R
@@ -21,7 +21,6 @@ calibrateMuso <- function(measuredData, parameters = NULL, startDate = NULL,
     #  \____|_|  \___|\__,_|\__\___|  \__|_| |_|_|  \___|\__,_|\__,_|___/
                                                                        
     
-
     copyToThreadDirs(thread_prefix, numcores = numcores, runDir = settings$inputLoc)
 
     #  ____                _   _                        _     
@@ -33,7 +32,7 @@ calibrateMuso <- function(measuredData, parameters = NULL, startDate = NULL,
     threadCount <- distributeCores(iterations, numCores) 
 
     fut <- lapply(1:numCores, function(i) {
-         # future({
+         future({
              musoSingleThread(measuredData, parameters, startDate,
                               endDate, formatString,
                               dataVar, outLoc,
@@ -42,7 +41,7 @@ calibrateMuso <- function(measuredData, parameters = NULL, startDate = NULL,
                               skipSpinup, plotName,
                               modifyOriginal, likelihood, uncertainity,
                               naVal, postProcString, i)
-         # })
+         })
     })
 
     # __        ___           _       _                                         
@@ -96,6 +95,7 @@ calibrateMuso <- function(measuredData, parameters = NULL, startDate = NULL,
 }
 
 copyToThreadDirs <- function(prefix="thread", numcores=parallel::detectCores()-1, runDir="."){
+    browser()
     dir.create(file.path(runDir,prefix), showWarnings=TRUE)
     fileNames <- grep("^thread.*", list.files(runDir), value=TRUE, invert=TRUE)
     invisible(sapply(1:numcores,function(corenum){