New MSConvert version

LipidMatch_Flow.bat

@@ -2,5 +2,6 @@
 
 UF SECIM LipidMatch Flow Beta Version 1.0
 2018-05-30: new lipidomics libraries
+2018-07-20: add all required R libraries for R-3.3.3
 
 Start "" ".\LipidMatch_Flow\LipidMatch_Batch.exe"

LipidMatch_Flow/LipidMatch_Distribution/LIPIDMATCH_PARAMETERS.csv

@@ -11,5 +11,5 @@ Comments Column (row ID. Should be numeric,1,Must be changed to match your data
 MZ Column (in feature table),2,Must be changed to match your data format
 RT Column (in feature table),3,Must be changed to match your data format
 row numeric data starts (in feature table),2,Must be changed to match your data format
-Directory of Inputs,C:/Users/Jeremy/Desktop/Tamil_Test/LipidMatch_Run/,Directory
-Directory of Libraries,C:/Users/Jeremy/Desktop/Desktop/Instrumentation/Software/MSms/LipidMatch_Workflow/LipidMatch_Flow_Versions/LipidMatch_Flow_Portable/LipidMatch_Flow/LipidMatch_Distribution/LipidMatch_Libraries/,Directory
+Directory of Inputs,C:/aatemp_test/WorkDir10/LipidMatch_Run/,Directory
+Directory of Libraries,C:/Users/Yang/Google Drive/SECIM_Remote/VS_Projects/LipidMatch_Flow_Portable/LipidMatch_Batch/LipidMatch_Distribution/LipidMatch_Libraries/,Directory

LipidMatch_Flow/LipidMatch_Distribution/LIPIDMATCH_PARAMETERS_Agilent_QTOF_6530.csv

@@ -11,5 +11,5 @@ Comments Column (row ID. Should be numeric,1,Must be changed to match your data
 MZ Column (in feature table),2,Must be changed to match your data format
 RT Column (in feature table),3,Must be changed to match your data format
 row numeric data starts (in feature table),2,Must be changed to match your data format
-Directory of Inputs,C:/Users/Jeremy/Desktop/Demo_LM2/LipidMatch_Run/,Directory
-Directory of Libraries,C:/Users/Jeremy/Desktop/Desktop/Instrumentation/Software/MSms/LipidMatch_Workflow/LipidMatch_Flow_Versions/LipidMatch_Flow_Portable/LipidMatch_Flow/LipidMatch_Distribution/LipidMatch_Libraries/,Directory
+Directory of Inputs,C:/Users/Jeremy/Desktop/Desktop/Instrumentation/Software/MSms/LipidMatch/2017_8_05_LipidMatch_Distribution/ExampleData/,Directory
+Directory of Libraries,C:/Users/Jeremy/Desktop/Desktop/Instrumentation/Software/MSms/LipidMatch/2017_8_05_LipidMatch_Distribution/LipidMatch_Libraries_Test/,Directory

LipidMatch_Flow/LipidMatch_Distribution/LipidMatch.r

@@ -51,14 +51,13 @@ ManuallyInputVariables <- FALSE
 
 
 #Checks for updates, installs packagaes: "installr" "stringr" "sqldf" "gWidgets" "gWidgetstcltk" and "compiler"
-if(!require(installr)) {
-  install.packages("installr"); install.packages("stringr"); require(installr)}
-library(installr)
-
-if("sqldf" %in% rownames(installed.packages()) == FALSE) {install.packages("sqldf")}
+#if(!require(installr)) {
+#  install.packages("installr",  repos = c(CRAN = "http://cran.rstudio.com")); install.packages("stringr", repos = c(CRAN = "http://cran.rstudio.com")); require(installr)}
+#library(installr)
+if("sqldf" %in% rownames(installed.packages()) == FALSE) {install.packages("sqldf",  repos = c(CRAN = "http://cran.rstudio.com"))}
 # if("compiler" %in% rownames(installed.packages()) == FALSE) {install.packages("compiler")}
-if("gWidgets" %in% rownames(installed.packages()) == FALSE) {install.packages("gWidgets")}
-if("gWidgetstcltk" %in% rownames(installed.packages()) == FALSE) {install.packages("gWidgetstcltk")}
+if("gWidgets" %in% rownames(installed.packages()) == FALSE) {install.packages("gWidgets",  repos = c(CRAN = "http://cran.rstudio.com"))}
+if("gWidgetstcltk" %in% rownames(installed.packages()) == FALSE) {install.packages("gWidgetstcltk",  repos = c(CRAN = "http://cran.rstudio.com"))}
 require(gWidgets)
 require(gWidgetstcltk)
 options(guiToolkit="tcltk")