From 4231cec67f6d56e5d3bdbeec867890127b286560 Mon Sep 17 00:00:00 2001
From: Gael <Gael@WL20-0067.corp.pasteur.fr>
Date: Tue, 3 Nov 2020 20:24:21 +0100
Subject: [PATCH] release v1.5
---
README.md | 5 ++++
r_debugging_tools.R | 68 ++++++++++++++++++++++++++++-----------------
2 files changed, 48 insertions(+), 25 deletions(-)
diff --git a/README.md b/README.md
index 2a347a8..1f46c43 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,11 @@ Source the cute_little_functions.R into R/RStudio to have the functions availabl
WHAT'S NEW IN
+v1.5:
+
+1) Improved
+
+
v1.4:
1) Debugged
diff --git a/r_debugging_tools.R b/r_debugging_tools.R
index f9dd03d..1a5c54b 100644
--- a/r_debugging_tools.R
+++ b/r_debugging_tools.R
@@ -1,6 +1,6 @@
################################################################
## ##
-## R DEBUGGING TOOLS v1.4 ##
+## R DEBUGGING TOOLS v1.5 ##
## ##
## Gael A. Millot ##
## ##
@@ -17,15 +17,17 @@ str_basic_arg_check_dev <- '
# arguments without default values
# arguments with variable as default value (FORBIDDEN)
# STRING
-function.name <- as.list(match.call(expand.dots=FALSE))[[1]]
+function.name.local <- as.list(match.call(expand.dots=FALSE))[[1]]
default.arg.list <- formals(fun = sys.function(sys.parent(n = 2))) # list of all the arguments of the function with their default values (not the values of the user !). Use n = 2 when he string has to be evaluated by eval() inside a function. Use n=1 (default) if not evaluation. It seems that ls() as first line of the function provide the names of the arguments (empty, called, etc., or not)
+
arg.without.default.value.log <- sapply(default.arg.list, is.symbol) & sapply(sapply(default.arg.list, as.character), identical, "") # logical indicating argument without default values (these are typeof "symbol" and class "name" and empty character
name.or.empty.default.val.arg.log <- sapply(default.arg.list, FUN = "class") == "name"
+arg.with.fun.as.default.value.log <- sapply(default.arg.list, class) %in% c("function", "call") & ! name.or.empty.default.val.arg.log # arguments with function as default values
if(length(name.or.empty.default.val.arg.log) != length(arg.without.default.value.log)){
- stop(paste0("\n\n================\n\nINTERNAL ERROR IN str_basic_arg_check_dev IN ", function.name,". CODE MUST BE MODIFED\n\n================\n\n"))
+ stop(paste0("\n\n================\n\nINTERNAL ERROR IN str_basic_arg_check_dev IN ", function.name.local,". CODE MUST BE MODIFED\n\n================\n\n"))
}else if(any(name.or.empty.default.val.arg.log & ! arg.without.default.value.log)){
- cat(paste0("\n\n================\n\nALERT\nDEFAULT VALUE OF ARGUMENT OF ", function.name," MUST NOT BE A VARIABLE (POTENTIAL PROBLEM OF SCOPE)\nTHE CONCERNED ARGUMENTS ARE:\n", paste(names(formals(fun = sys.function(sys.parent(n = 2))))[name.or.empty.default.val.arg.log & ! arg.without.default.value.log], collapse = "\n"), "\n\n================\n\n"))
+ cat(paste0("\n\n================\n\nALERT\nDEFAULT VALUE OF ARGUMENT OF ", function.name.local," MUST NOT BE A VARIABLE (POTENTIAL PROBLEM OF SCOPE)\nTHE CONCERNED ARGUMENTS ARE:\n", paste(names(formals(fun = sys.function(sys.parent(n = 2))))[name.or.empty.default.val.arg.log & ! arg.without.default.value.log], collapse = "\n"), "\n\n================\n\n"))
}
if(any(arg.without.default.value.log)){
@@ -33,15 +35,26 @@ if(any(arg.without.default.value.log)){
}else{
arg.without.default.value <- NULL
}
+if(any(arg.with.fun.as.default.value.log)){
+ arg.with.fun.as.default.value <- default.arg.list[arg.with.fun.as.default.value.log]
+}else{
+ arg.with.fun.as.default.value <- NULL
+}
if(any( ! arg.without.default.value.log)){
- arg.with.default.value <- default.arg.list[ ! arg.without.default.value.log]
+ if( ! is.null(arg.with.fun.as.default.value)){
+ arg.with.default.value.log <- ( ! arg.without.default.value.log) & ( ! arg.with.fun.as.default.value.log) # remove also the # remove the functions from the default values
+ }else{
+ arg.with.default.value.log <- ( ! arg.without.default.value.log)
+ }
+ arg.with.default.value <- default.arg.list[arg.with.default.value.log]
}else{
arg.with.default.value <- NULL
}
-cat(paste0("\n\n================================\n\n", function.name," FUNCTION ARGUMENT CHECKING\n\n================================\n"))
+
+cat(paste0("\n\n================================\n\n", function.name.local," FUNCTION ARGUMENT CHECKING\n\n================================\n"))
cat(paste0("\n================\nARGUMENTS OF THE FUNCTION ARE (INCLUDING DEFAULT VALUES):\n\n"))
-print(default.arg.list)
+
if(any(arg.without.default.value.log)){ # argument names that are empty by default added now because null arguments will not be inserted thenafter
cat(paste0("\n================\nARGUMENTS WITHOUT DEFAULT VALUES ARE:\n", paste(names(arg.without.default.value)[arg.without.default.value.log], collapse= "\n")))
@@ -49,34 +62,39 @@ if(any(arg.without.default.value.log)){ # argument names that are empty by defau
cat(paste0("\n================\nNO ARGUMENTS WITHOUT DEFAULT VALUES"))
}
-if(any( ! arg.without.default.value.log)){
- if(any(sapply(arg.with.default.value, FUN = is.null))){
- cat(paste0("\n================\nNULL ARGUMENTS ARE:\n", paste(names(arg.with.default.value)[sapply(arg.with.default.value, FUN = is.null)], collapse= "\n")))
- }
+
+if(any(arg.with.fun.as.default.value.log)){ #
+ cat(paste0("\n================\nARGUMENTS WITH FUNCTION (CLASS function OR call) AS DEFAULT VALUE ARE:\n", paste(names(arg.with.fun.as.default.value), collapse= "\n")))
}else{
- cat(paste0("\n================\nNO NULL ARGUMENTS"))
+ cat(paste0("\n================\nNO ARGUMENTS WITH FUNCTION (CLASS function OR call) AS DEFAULT VALUE"))
}
+
tempo.na <- NULL
-if(any( ! arg.without.default.value.log)){
+if( ! is.null(arg.with.default.value)){
+ if(any(sapply(arg.with.default.value, FUN = is.null))){
+ cat(paste0("\n================\nARGUMENTS WITH NULL DEFAULT VALUE ARE:\n", paste(names(arg.with.default.value)[sapply(arg.with.default.value, FUN = is.null)], collapse= "\n")))
+ }else{
+ cat(paste0("\n================\nNO ARGUMENTS WITH NULL DEFAULT VALUE"))
+ }
if(any( ! sapply(arg.with.default.value, FUN = is.null))){
- cat(paste0("\n================\nNON NULL ARGUMENTS ARE:\n", paste(names(arg.with.default.value)[ ! sapply(arg.with.default.value, FUN = is.null)], collapse= "\n")))
+ cat(paste0("\n================\nARGUMENTS WITH NON-NULL DEFAULT VALUE ARE:\n", paste(names(arg.with.default.value)[ ! sapply(arg.with.default.value, FUN = is.null)], collapse= "\n")))
tempo <- arg.with.default.value[ ! sapply(arg.with.default.value, FUN = is.null)]
if(any(sapply(tempo, FUN = is.na))){
- tempo.na <- paste0("\n================\nNA ARGUMENTS ARE:\n", paste(names(tempo)[sapply(tempo, FUN = is.na)], collapse= "\n"))
+ tempo.na <- paste0("\n================\nARGUMENTS WITH NA DEFAULT VALUE ARE:\n", paste(names(tempo)[sapply(tempo, FUN = is.na)], collapse= "\n"))
}else{
- tempo.na <- paste0("\n================\nNO NA ARGUMENTS")
+ tempo.na <- paste0("\n================\nNO ARGUMENTS WITH NA DEFAULT VALUE")
}
}
}else{
- cat(paste0("\n================\nNO NON NULL ARGUMENTS"))
+ cat(paste0("\n================\nNO ARGUMENTS WITH NON-NULL DEFAULT VALUE"))
}
if(any( ! arg.without.default.value.log)){
if(any(sapply(arg.with.default.value, FUN = is.logical))){
- cat(paste0("\n================\nLOGICAL ARGUMENTS ARE:\n", paste(names(arg.with.default.value)[sapply(arg.with.default.value, FUN = is.logical)], collapse= "\n")))
+ cat(paste0("\n================\nARGUMENTS WITH LOGICAL DEFAULT VALUE ARE:\n", paste(names(arg.with.default.value)[sapply(arg.with.default.value, FUN = is.logical)], collapse= "\n")))
}
}else{
- cat(paste0("\n================\nNO LOGICAL ARGUMENTS"))
+ cat(paste0("\n================\nNO ARGUMENTS WITH LOGICAL DEFAULT VALUE"))
}
if(! is.null(tempo.na)){
@@ -92,20 +110,20 @@ str_arg_check_with_fun_check_dev <- '
# string that check:
# which arguments have been checked using fun_check()
# STRING
-function.name <- as.list(match.call(expand.dots=FALSE))[[1]]
+function.name.local <- as.list(match.call(expand.dots=FALSE))[[1]]
default.arg.list <- formals(fun = sys.function(sys.parent(n = 2))) # list of all the arguments of the function with their default values (not the values of the user !). Use n = 2 when he string has to be evaluated by eval() inside a function. Use n=1 (default) if not evaluation. It seems that ls() as first line of the function provide the names of the arguments (empty, called, etc., or not)
if( ! any(ls() %in% "checked.arg.names")){
- cat(paste0("\n\n================\n\nERROR: MISSING checked.arg.names OBJECT. ARGUMENTS MAY HAVE NOT BEEN CHECKED USING fun_check(). SEE THE fun_export_data() FUNCTION FOR THIS KIND OF CHECKING\n\n================\n\n"))
+ cat(paste0("\n\n================\n\nERROR: MISSING checked.arg.names OBJECT\nARGUMENTS MAY HAVE NOT BEEN CHECKED USING fun_check()\nSEE THE fun_export_data() FUNCTION FOR THIS KIND OF CHECKING\n\n================\n\n"))
}
if( ! find("fun_check") == ".GlobalEnv"){
- cat(paste0("\n\n================\n\nERROR: MISSING fun_check() FUNCTION IN THE GLOBAL ENVIRONMENT. ARGUMENTS MAY HAVE NOT BEEN CHECKED USING fun_check(). SEE THE fun_export_data() FUNCTION FOR THIS KIND OF CHECKING\n\n================\n\n"))
+ cat(paste0("\n\n================\n\nERROR: MISSING fun_check() FUNCTION IN THE GLOBAL ENVIRONMENT\nARGUMENTS MAY HAVE NOT BEEN CHECKED USING fun_check()\nSEE THE fun_export_data() FUNCTION FOR THIS KIND OF CHECKING\n\n================\n\n"))
}
-cat(paste0("\n\n================================\n\n", function.name," FUNCTION ARGUMENT CHECKING USING fun_check()\n\n================================\n"))
+cat(paste0("\n\n================================\n\n", function.name.local," FUNCTION ARGUMENT CHECKING USING fun_check()\n\n================================\n"))
if(any(duplicated(checked.arg.names))){ # for function debbuging
-cat(paste0("\n================\nTHESE ARGUMENTS ARE DUPLICATED IN CHECK USING fun_check(): ", paste(checked.arg.names[duplicated(checked.arg.names)], collapse = " ")))
+cat(paste0("\n================\nTHESE ARGUMENTS ARE DUPLICATED IN CHECK USING fun_check():\n", paste(checked.arg.names[duplicated(checked.arg.names)], collapse = "\n")))
}
if( any(! names(default.arg.list) %in% checked.arg.names)){ # check the correct number of args # for function debbuging # names(default.arg.list) can be replaced by formalArgs("name of the created function")
-cat(paste0("\n================\nTHESE ARGUMENTS HAVE NOT BEEN CHECKED WITH fun_check(): ", paste(names(default.arg.list)[ ! names(default.arg.list) %in% checked.arg.names], collapse = " ")))
+cat(paste0("\n================\nTHESE ARGUMENTS HAVE NOT BEEN CHECKED WITH fun_check():\n", paste(names(default.arg.list)[ ! names(default.arg.list) %in% checked.arg.names], collapse = "\n")))
}else{
cat(paste0("\n================\nALL THE ARGUMENTS HAVE BEEN CHECKED USING fun_check()"))
}
--
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