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diff --git a/run.txt b/run.txt
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-
-## specify libraries
-libs = list("gWidgets","gWidgetstcltk","markdown","plyr")
-
-## install libraries
-# sapply(libs, biocLite) 
-# install.packages("gWidgets", repos='http://cran.us.r-project.org')
-# install.packages("gWidgetstcltk", repos='http://cran.us.r-project.org')
-# install.packages("markdown", repos='http://cran.us.r-project.org')
-# install.packages("plyr", repos='http://cran.us.r-project.org')
-
-
-## load libraries
-print("Loading libraries...")
-sapply(libs, function(x) do.call("library", list(x))) 
-
-options(warn = 2)
-
-# path = "C:\\Users\\Christian Tischer\\Dropbox\\R\\HTM\\HTM_Explorer\\HTM_Explorer";setwd(path);source("run.R");
-# path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R"); 
-# path = "\\almf\\almf\\software\\scripts\\R\\HTM_Explorer";setwd(path);source("run.R");
-# path = "Y:\\R\\HTM_Explorer";setwd(path);source("run.R");
-# path = "/g/almf/software/scripts/R/HTM_Explorer";setwd(path);source("run.R");
-
-
-
-## source code
-#setwd(path);source("install.R"); 
-
-source("classes.R")
-
-print("Checking htm object...")
-if(exists("htm")) {
-  print("  Found htm object; left it as it was; only restarting the GUI.")
-} else {
-  print("  No htm object found; initialising...")
-  htm <<- htmMake()
-}
-
-htmPath = getwd()
-
-## create the package:
-# package.skeleton(name="htmTool",path=path, code_files=c("classes.R","gui.R","plots.R","functions.R","install.R"))
-
-guiToolkit("tcltk")
-
-source("plots.R")
-source("functions.R")
-source("gui.R")
-
-## make package
-## - you can simply delete all files in the man directory to get through "check"
-## - check has options to ignore certain issues
-
-# R CMD build
-# R CMD check  
-# R CMD INSTALL
-
-
-## only "export" functions that you want the user to see; 
-## also only for those you need to write documenation
-
-
-## Roxygen