tempo.cat <- paste0("ERROR IN ", function.name, ": fun ARGUMENT IS NOT CLASS \"function\" BUT: ", paste(class(get(fun)), collapse = "\n"))
if( ! exists(fun)){
tempo.cat <- paste0("ERROR IN ", function.name, ": CHARACTER STRING IN fun ARGUMENT DOES NOT EXIST IN THE R WORKING ENVIRONMENT: ", paste(fun, collapse = "\n"))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
tempo <- fun_check(data = arg, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
args <- names(formals(get(fun)))
if( ! all(arg %in% args)){
tempo.cat <- paste0("ERROR IN ", function.name, ": SOME OF THE STRINGS IN arg ARE NOT ARGUMENTS OF fun\nfun ARGUMENTS: ", paste(args, collapse = " "),"\nPROBLEMATIC STRINGS IN arg: ", paste(arg[ ! arg %in% args], collapse = " "))
}else if( ! all(class(get(fun)) == "function")){
tempo.cat <- paste0("ERROR IN ", function.name, ": fun ARGUMENT IS NOT CLASS \"function\" BUT: ", paste(class(get(fun)), collapse = "\n"))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
tempo <- fun_check(data = arg, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = val, class = "list", fun.name = function.name) ; eval(ee)
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end primary argument checking
# second round of checking and data preparation
args <- names(formals(get(fun)))
if( ! all(arg %in% args)){
tempo.cat <- paste0("ERROR IN ", function.name, ": SOME OF THE STRINGS IN arg ARE NOT ARGUMENTS OF fun\nfun ARGUMENTS: ", paste(args, collapse = " "),"\nPROBLEMATIC STRINGS IN arg: ", paste(arg[ ! arg %in% args], collapse = " "))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
if( ! is.null(thread.nb) & is.null(res.path)){
tempo.cat <- paste0("ERROR IN ", function.name, ": res.path ARGUMENT MUST BE SPECIFIED IF thread.nb ARGUMENT IS NOT NULL")
data <- rbind(data, as.character(sapply(eval(parse(text = arg.values)), FUN = "paste", collapse = " ")), stringsAsFactors = FALSE) # each colum is a test
tempo.try.error <- fun_get_message(data = eval(parse(text = fun.test2)), kind = "error", header = FALSE, env = get(env.name)) # data argument needs a character string but eval(parse(text = fun.test2)) provides it (eval parse replace the i1, i2, etc., by the correct values, meaning that only val is required in the env.name environment)
tempo.try.warning <- fun_get_message(data = eval(parse(text = fun.test2)), kind = "warning", header = FALSE, env = get(env.name), print.no = TRUE) # data argument needs a character string but eval(parse(text = fun.test2)) provides it (eval parse replace the i1, i2, etc., by the correct values, meaning that only val is required in the env.name environment)
pdf(file = NULL) # send plots into a NULL file, no pdf file created
window.nb <- dev.cur()
warn.options.ini <- options()$warn
# last warning cannot be used because suppressWarnings() does not modify last.warning present in the base evironment (created at first warning in a new R session), or warnings() # to reset the warning history : unlockBinding("last.warning", baseenv()) ; assign("last.warning", NULL, envir = baseenv())
options(warn = 1) # 1 print all the warnings, 2 put messages and warnings as error but print only the first one in some cases
output <- NULL
tempo.error <- try(suppressMessages(suppressWarnings(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))), silent = TRUE) # get error message, not warning or messages
W <<- w # send to the above env, i.e., the inside of the fun.warning.capture function
invokeRestart("muffleWarning") # here w.handler() muffles all the warnings. See http://romainfrancois.blog.free.fr/index.php?post/2009/05/20/Disable-specific-warnings to muffle specific warnings and print others
}
output <- list(
value = withCallingHandlers(tryCatch(expr, error = function(e){e}), warning = w.handler),
warning = W
value = withCallingHandlers(tryCatch(expr, error = function(e){e}), warning = w.handler), # BEWARE: w.handler is a function written without (), like in other functions with FUN argument
# warn.options.ini <- options()$warn ; options(warn = 1) ; tempo.warn <- utils::capture.output({tempo <- suppressMessages(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))}, type = "message") ; options(warn = warn.options.ini) # this recover warnings not messages and not errors but does not work in all enviroments
tempo.message <- utils::capture.output({
tempo <- suppressMessages(suppressWarnings(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env})))
if(any(class(tempo) %in% c("gg", "ggplot"))){
...
...
@@ -9242,20 +9236,19 @@ tempo <- ggplot2::ggplot_build(tempo)
tempo <- suppressWarnings(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))
}
}, type = "message") # recover messages not warnings and not errors
if(length(tempo.warn) > 0){ # if something is returned by capture.ouptput() (only in this env) with a length more than 1
if(kind == "warning" & ! is.null(tempo.warn)){
if(length(tempo.warn) > 0){ # to avoid character(0)
if( ! any(sapply(tempo.warn, FUN = "grepl", pattern = "() FUNCTION:$"))){
tempo.warn <- paste(unique(tempo.warn), collapse = "\n") # if FALSE, means that the tested data is a special function. If TRUE, means that the data is a standard function. In that case, the output of capture.output() is two strings per warning messages: if several warning messages -> identical first string, which is removed in next messages by unique()
}else{
tempo.warn <- paste(tempo.warn, collapse = "\n")
}
if(header == TRUE){
if(any(grepl(x = tempo.warn, pattern = "(converted from warning)"))){# warning message converted to error
