@@ -1,8 +1,8 @@

 # Title: .Rprofile

 # Author: Frédéric CHEVALIER <f15.chevalier@gmail.com>

-# Version: 1.0

+# Version: 1.1

 # Created in: 2014-07-06

-# Modified in: 2020-03-01

+# Modified in: 2020-08-27

@@ -19,6 +19,7 @@

 # Versions #

 #==========#

+# v1.1 - 2020-08-27: reconnect_X11 function added / repo link updated

 # v1.0 - 2020-03-01: library path set / specific library path depending on the environment / section executed in non interactive mode / repo link updated

 # v0.4 - 2016-10-02: hour display on prompt simplified / auto-update of terminal column value for display added

 # v0.3 - 2014-11-03: less function added

@@ -50,7 +51,7 @@ if (! .startup$is.root && ! .startup$is.conda) {

 if (interactive()) {

 # Don't ask me for my CRAN mirror every time

-options("repos" = c(CRAN = "https://cran.revolutionanalytics.com"))

+options("repos" = c(CRAN = "https://cloud.r-project.org/"))

 #===========#

@@ -130,6 +131,15 @@ addTaskCallback(.startup$updatePrompt)

     file.show(file, delete.file = TRUE)

 }

+# Reconnect to X11

+.startup$reconnect_X11 <- function(port) {

+    if (missing(port)) {

+        port <- system("xauth list | grep $(hostname) | tail -1 | awk '{print $1}' | sed \"s/.*://\"", intern = TRUE)

+    }

+    Sys.setenv(DISPLAY = paste0("localhost:", port, ".0"))

+}

+

+

 #=========#

@@ -1,8 +1,8 @@

 # Title: .Rprofile

 # Author: Frédéric CHEVALIER <f15.chevalier@gmail.com>

-# Version: 0.4

+# Version: 1.0

 # Created in: 2014-07-06

-# Modified in: 2016-10-02

+# Modified in: 2020-03-01

@@ -10,7 +10,7 @@

 # Comments #

 #==========#

-# ~/.Rprodile: executed by R for interactive shells.

+# ~/.Rprofile: executed by R for interactive shells.

 # see http://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html

@@ -19,6 +19,7 @@

 # Versions #

 #==========#

+# v1.0 - 2020-03-01: library path set / specific library path depending on the environment / section executed in non interactive mode / repo link updated

 # v0.4 - 2016-10-02: hour display on prompt simplified / auto-update of terminal column value for display added

 # v0.3 - 2014-11-03: less function added

 # v0.2 - 2014-10-21: bug correction about width of terminal

@@ -31,15 +32,25 @@

 # User specific options #

 #=======================#

-# Test if it is an interactive session

-if (interactive()) {

-

-# Create a new invisible environment for all the functions to go in so it doesn't clutter your workspace

+# Create a new invisible environment for all the objects and functions to go in so it doesn't clutter the workspace

 .startup <- new.env()

-# Don't ask me for my CRAN mirror every time

-options("repos" = c(CRAN = "http://cran.revolutionanalytics.com"))

+# Determine environment

+.startup$is.root  <- system("id -u", intern=TRUE) == 0

+.startup$is.conda <- nchar(Sys.getenv("CONDA_PREFIX")) > 0

+

+# Specific package folder in user global environment only

+if (! .startup$is.root && ! .startup$is.conda) {

+    .startup$mylib <- paste0("~/.R-libs/", version$major, ".", version$minor)

+    if (! dir.exists(.startup$mylib)) {dir.create(.startup$mylib, recursive=TRUE)}

+    .libPaths(.startup$mylib)

+}

+

+# Test if it is an interactive session and run the downstream code

+if (interactive()) {

+# Don't ask me for my CRAN mirror every time

+options("repos" = c(CRAN = "https://cran.revolutionanalytics.com"))

 #===========#

@@ -81,7 +92,7 @@ require(utils, quietly = TRUE)

 # All functions executed when exiting R

 .Last <- function() {

-    if (! any(commandArgs() == '--no-readline')) {

+    if (! any(commandArgs() == '--no-readline') && ! .startup$is.root) {

         require(utils, quietly=TRUE)

         #timestamp(quiet=TRUE)

         try(savehistory(Sys.getenv("R_HISTFILE")))

@@ -116,7 +127,7 @@ addTaskCallback(.startup$updatePrompt)

     file <- tempfile()

     sink(file); on.exit(sink())

     print(x)

-    file.show(file, delete.file = T)

+    file.show(file, delete.file = TRUE)

 }

@@ -126,7 +137,7 @@ addTaskCallback(.startup$updatePrompt)

 #=========#

 # Moving (bash-like command)

-.startup$cd <- setwd

+.startup$cd  <- setwd

 .startup$pwd <- getwd

@@ -1,8 +1,8 @@

 # Title: .Rprofile

 # Author: Frédéric CHEVALIER <f15.chevalier@gmail.com>

-# Version: 0.3

+# Version: 0.4

 # Created in: 2014-07-06

-# Modified in: 2014-11-03

+# Modified in: 2016-10-02

@@ -19,6 +19,7 @@

 # Versions #

 #==========#

+# v0.4 - 2016-10-02: hour display on prompt simplified / auto-update of terminal column value for display added

 # v0.3 - 2014-11-03: less function added

 # v0.2 - 2014-10-21: bug correction about width of terminal

 # v0.1 - 2014-08-06: bug correction about interactivity (curly brackets missing)

@@ -39,10 +40,6 @@ if (interactive()) {

 # Don't ask me for my CRAN mirror every time

 options("repos" = c(CRAN = "http://cran.revolutionanalytics.com"))

-# Enlarge columns display in R terminal

-# source: http://stackoverflow.com/questions/1172485/how-to-increase-the-number-of-columns-using-r-in-linux

-options(width=as.integer(system("stty -a | head -n 1 | awk '{print $7}' | sed 's/;//'", intern=TRUE)))

-

 #===========#

@@ -94,21 +91,20 @@ require(utils, quietly = TRUE)

 # Prompt showing current clock

 # source: http://stackoverflow.com/questions/4222476/r-display-a-time-clock-in-the-r-command-line

+# Don't use Tcl/Tk beacuse starting X11 leading to R crash when X11 connection is killed

 myprompt <- "%H:%M R> "

-if (capabilities()[["tcltk"]] && require(tcltk2, quietly=TRUE)) {

-    # First way

-    .startup$updatePrompt <- function(...) {options(prompt=format(Sys.time(),myprompt))}

-    tclTaskSchedule(1000, .startup$updatePrompt(), id = "ticktock", redo = TRUE)

-    .startup$updatePrompt()

-}  else {

-    # Second way: working except when error message (no time update)

-    .startup$updatePrompt <- function(..., quietly=FALSE) {

-        options(prompt=format(Sys.time(),myprompt)) 

-        if (quietly == FALSE) {return(TRUE)}

-    }

-    addTaskCallback(.startup$updatePrompt)

-    .startup$updatePrompt(quietly=TRUE)

+.startup$updatePrompt <- function(..., quietly=FALSE) {

+    # Update time

+    options(prompt=format(Sys.time(),myprompt))

+

+    # Update terminal column value for display in R terminal

+    # source: http://stackoverflow.com/questions/1172485/how-to-increase-the-number-of-columns-using-r-in-linux

+    options(width=as.integer(system("stty -a | head -n 1 | awk '{print $7}' | sed 's/;//'", intern=TRUE)))

+

+    if (quietly == FALSE) {return(TRUE)}

 }

+addTaskCallback(.startup$updatePrompt)

+.startup$updatePrompt(quietly=TRUE)

 # Exit

@@ -1,8 +1,8 @@

 # Title: .Rprofile

 # Author: Frédéric CHEVALIER <f15.chevalier@gmail.com>

-# Version: 0.2

+# Version: 0.3

 # Created in: 2014-07-06

-# Modified in: 2014-10-21

+# Modified in: 2014-11-03

@@ -19,6 +19,7 @@

 # Versions #

 #==========#

+# v0.3 - 2014-11-03: less function added

 # v0.2 - 2014-10-21: bug correction about width of terminal

 # v0.1 - 2014-08-06: bug correction about interactivity (curly brackets missing)

 # v0.0 - 2014-07-06: creation

@@ -113,6 +114,15 @@ if (capabilities()[["tcltk"]] && require(tcltk2, quietly=TRUE)) {

 # Exit

 .startup$bye <- function () {q("no")}

+# Less emulation

+# source: http://stackoverflow.com/questions/3503811/is-there-an-r-equivalent-to-the-bash-command-more

+.startup$less <- function(x) {

+    file <- tempfile()

+    sink(file); on.exit(sink())

+    print(x)

+    file.show(file, delete.file = T)

+}

+

 #=========#

@@ -1,8 +1,8 @@

 # Title: .Rprofile

 # Author: Frédéric CHEVALIER <f15.chevalier@gmail.com>

-# Version: 0.1

+# Version: 0.2

 # Created in: 2014-07-06

-# Modified in: 2014-08-06

+# Modified in: 2014-10-21

@@ -19,6 +19,7 @@

 # Versions #

 #==========#

+# v0.2 - 2014-10-21: bug correction about width of terminal

 # v0.1 - 2014-08-06: bug correction about interactivity (curly brackets missing)

 # v0.0 - 2014-07-06: creation

@@ -37,6 +38,10 @@ if (interactive()) {

 # Don't ask me for my CRAN mirror every time

 options("repos" = c(CRAN = "http://cran.revolutionanalytics.com"))

+# Enlarge columns display in R terminal

+# source: http://stackoverflow.com/questions/1172485/how-to-increase-the-number-of-columns-using-r-in-linux

+options(width=as.integer(system("stty -a | head -n 1 | awk '{print $7}' | sed 's/;//'", intern=TRUE)))

+

 #===========#

@@ -73,13 +78,6 @@ require(utils, quietly = TRUE)

 		cat("\n")

     }

-	# Enlarge columns display in R terminal

-	# source: http://stackoverflow.com/questions/1172485/how-to-increase-the-number-of-columns-using-r-in-linux

-	wideScreen <- function(howWide=Sys.getenv("COLUMNS")) {

-		options(width=as.integer(howWide))

-	wideScreen()

-	}

-

 }

@@ -1,8 +1,8 @@

 # Title: .Rprofile

 # Author: Frédéric CHEVALIER <f15.chevalier@gmail.com>

-# Version: 0.0

+# Version: 0.1

 # Created in: 2014-07-06

-# Modified in:

+# Modified in: 2014-08-06

@@ -19,6 +19,7 @@

 # Versions #

 #==========#

+# v0.1 - 2014-08-06: bug correction about interactivity (curly brackets missing)

 # v0.0 - 2014-07-06: creation

@@ -28,7 +29,7 @@

 #=======================#

 # Test if it is an interactive session

-if(interactive())

+if (interactive()) {

 # Create a new invisible environment for all the functions to go in so it doesn't clutter your workspace

 .startup <- new.env()

@@ -56,11 +57,11 @@ require(utils, quietly = TRUE)

 	# Add colors to prompt

 	options(colorout.anyterm = TRUE)

-    if(! .startup$is.installed("colorout")) {

-        cat("If you want colored prompt, you should install the colorout package.\nLink: http://www.lepem.ufc.br/jaa/colorout.html\n\n")

-    } else {

-        library('colorout')

-    	setOutputColors256(

+	if(! .startup$is.installed("colorout")) {

+		cat("If you want colored prompt, you should install the colorout package.\nLink: http://www.lepem.ufc.br/jaa/colorout.html\n\n")

+	} else {

+		library('colorout')

+		setOutputColors256(

 	    	normal = 40,

 		    number = 214,

     		string = 85,

@@ -69,13 +70,13 @@ require(utils, quietly = TRUE)

     		error = c(1, 0, 1),

 	    	warn = c(1, 0, 100)

     	)

-	    cat("\n")

+		cat("\n")

     }

-    # Enlarge columns display in R terminal

+	# Enlarge columns display in R terminal

 	# source: http://stackoverflow.com/questions/1172485/how-to-increase-the-number-of-columns-using-r-in-linux

 	wideScreen <- function(howWide=Sys.getenv("COLUMNS")) {

-	     options(width=as.integer(howWide))

+		options(width=as.integer(howWide))

 	wideScreen()

 	}

@@ -127,3 +128,5 @@ if (capabilities()[["tcltk"]] && require(tcltk2, quietly=TRUE)) {

 # Attach all the variables above

 attach(.startup)

+

+} # End of interactive statement

new file mode 100644

@@ -0,0 +1,129 @@

+# Title: .Rprofile

+# Author: Frédéric CHEVALIER <f15.chevalier@gmail.com>

+# Version: 0.0

+# Created in: 2014-07-06

+# Modified in:

+

+

+

+#==========#

+# Comments #

+#==========#

+

+# ~/.Rprodile: executed by R for interactive shells.

+# see http://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html

+

+

+

+#==========#

+# Versions #

+#==========#

+

+# v0.0 - 2014-07-06: creation

+

+

+

+#=======================#

+# User specific options #

+#=======================#

+

+# Test if it is an interactive session

+if(interactive())

+

+# Create a new invisible environment for all the functions to go in so it doesn't clutter your workspace

+.startup <- new.env()

+

+# Don't ask me for my CRAN mirror every time

+options("repos" = c(CRAN = "http://cran.revolutionanalytics.com"))

+

+

+

+#===========#

+# Functions #

+#===========#

+

+# Check if pacakge is installed

+# source: http://r.789695.n4.nabble.com/test-if-a-package-is-installed-td1750671.html

+require(utils, quietly = TRUE)

+.startup$is.installed <- function(mypkg) {is.element(mypkg, installed.packages()[,1])}

+

+

+# All functions executed when starting R

+.First <- function() {

+        

+	# First message

+	cat("   Welcome to R!\n\n")

+	

+	# Add colors to prompt

+	options(colorout.anyterm = TRUE)

+    if(! .startup$is.installed("colorout")) {

+        cat("If you want colored prompt, you should install the colorout package.\nLink: http://www.lepem.ufc.br/jaa/colorout.html\n\n")

+    } else {

+        library('colorout')

+    	setOutputColors256(

+	    	normal = 40,

+		    number = 214,

+    		string = 85,

+	    	const = 35,

+		    stderror = 45,

+    		error = c(1, 0, 1),

+	    	warn = c(1, 0, 100)

+    	)

+	    cat("\n")

+    }

+	

+    # Enlarge columns display in R terminal

+	# source: http://stackoverflow.com/questions/1172485/how-to-increase-the-number-of-columns-using-r-in-linux

+	wideScreen <- function(howWide=Sys.getenv("COLUMNS")) {

+	     options(width=as.integer(howWide))

+	wideScreen()

+	}

+

+}

+

+

+# All functions executed when exiting R

+.Last <- function() {

+    if (! any(commandArgs() == '--no-readline')) {

+        require(utils, quietly=TRUE)

+        #timestamp(quiet=TRUE)

+        try(savehistory(Sys.getenv("R_HISTFILE")))

+     }

+}

+

+

+# Prompt showing current clock

+# source: http://stackoverflow.com/questions/4222476/r-display-a-time-clock-in-the-r-command-line

+myprompt <- "%H:%M R> "

+if (capabilities()[["tcltk"]] && require(tcltk2, quietly=TRUE)) {

+    # First way

+    .startup$updatePrompt <- function(...) {options(prompt=format(Sys.time(),myprompt))}

+    tclTaskSchedule(1000, .startup$updatePrompt(), id = "ticktock", redo = TRUE)

+    .startup$updatePrompt()

+}  else {

+    # Second way: working except when error message (no time update)

+    .startup$updatePrompt <- function(..., quietly=FALSE) {

+        options(prompt=format(Sys.time(),myprompt)) 

+        if (quietly == FALSE) {return(TRUE)}

+    }

+    addTaskCallback(.startup$updatePrompt)

+    .startup$updatePrompt(quietly=TRUE)

+}

+

+

+# Exit

+.startup$bye <- function () {q("no")}

+

+

+

+#=========#

+# Aliases #

+#=========#

+

+# Moving (bash-like command)

+.startup$cd <- setwd

+.startup$pwd <- getwd

+

+

+# Attach all the variables above

+attach(.startup)