test

README.md

@@ -5,6 +5,10 @@ Source the cute_little_functions.R into R/RStudio to have the functions availabl
 
 WHAT'S NEW IN 
 
+v1.8:
+
+1) Updated for saferDev
+
 v1.7:
 
 1) Debugged

r_debugging_tools.R

 ################################################################
 ##                                                            ##
-##     R DEBUGGING TOOLS v1.7                                 ##
+##     R DEBUGGING TOOLS                                      ##
 ##                                                            ##
 ##     Gael A. Millot                                         ##
-##                                                            ##
-##     Compatible with R v4.0.2                               ##
+##     Bioinformatics and Biostatistics Hub                   ##
+##     Institut Pasteur Paris                                 ##
 ##                                                            ##
 ################################################################
 
@@ -109,24 +109,21 @@ cat(paste0("\n================\n\n"))
 str_arg_check_with_fun_check_dev <- '
 # AIM:
 # string that check:
-# which arguments have been checked using fun_check()
+# which arguments have been checked using saferDev::arg_check()
 # STRING
 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\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\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\nERROR: MISSING checked.arg.names OBJECT\nARGUMENTS MAY HAVE NOT BEEN CHECKED USING saferDev::arg_check()\n\n================\n\n"))
 }
-cat(paste0("\n\n================================\n\n", function.name.local," FUNCTION ARGUMENT CHECKING USING fun_check()\n\n================================\n"))
+cat(paste0("\n\n================================\n\n", function.name.local," FUNCTION ARGUMENT CHECKING USING saferDev::arg_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():\n", paste(checked.arg.names[duplicated(checked.arg.names)], collapse = "\n")))
+cat(paste0("\n================\nTHESE ARGUMENTS ARE DUPLICATED IN CHECK USING saferDev::arg_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():\n", paste(names(default.arg.list)[ ! names(default.arg.list) %in% checked.arg.names], collapse = "\n")))
+cat(paste0("\n================\nTHESE ARGUMENTS HAVE NOT BEEN CHECKED WITH saferDev::arg_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()"))
+cat(paste0("\n================\nALL THE ARGUMENTS HAVE BEEN CHECKED USING saferDev::arg_check()"))
 }
 cat(paste0("\n================\n\n"))
 # END STRING