Package {saferDev}

Type:	Package
Title:	Function and Pipeline Development
Version:	1.0.0
Date:	2026-06-02
Encoding:	UTF-8
Maintainer:	Gael Millot <gael.millot@pasteur.fr>
Description:	Set of functions that perform checks according to the safer-r project recommendations for R function development (see https://github.com/safer-r). This includes checking argument values, ensuring correct specification of all mandatory arguments for embedded functions, as well as their explicit package namespace qualification, among other things.
URL:	<https://github.com/safer-r/saferDev>, <https://safer-r.github.io/saferDev/>
License:	GPL-3
RoxygenNote:	7.3.3
Imports:	ggplot2
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0)
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2026-06-02 16:14:25 UTC; gmillot
Author:	Haiding Wang [ctb], Yushi Han [ctb], Mia Legras [ctb], Gael Millot [cre, aut, ctb]
Repository:	CRAN
Date/Publication:	2026-06-08 18:10:03 UTC

Function for All Arguments Here

Description

Get the $MISSING_ARG_NAMES, $MISSING_ARGS and $NEW of all_args_here().

Usage

.all_args_here_fill(
  arg_full,
  arg_full_names,
  tempo_split,
  three_dots_log,
  i2,
  col1_i2,
  col2_i2,
  arg_user_setting_x,
  warn,
  warn_count,
  lib_path,
  error_text
)

Arguments

Details

Warnings:

• requires saferDev::arg_check.

• In the safer Backbone section "######## check of the required functions from the required packages", add also saferDev::arg_check when checking for the presence of .all_args_here_fill.

Value

A list:

• col6: the $MISSING_ARG_NAMES.

• col7: the $MISSING_ARGS.

• col8: the $STATUS.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Base Operator Check

Description

Check if critical operators of R are not present in other packages or in the global env.

Usage

.base_op_check(error_text)

Arguments

Value

An error message if at least one of the checked operator is present in the R scope, nothing otherwise.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Colons Check Message

Description

Create the message for the colons_check() function.

Usage

.colons_check_message(
  list_fun,
  list_fun_pos,
  line_nb,
  ini,
  arg_user_setting2,
  text,
  internal_fun_names,
  lib_path,
  error_text
)

Arguments

Details

Warnings:

• requires saferDev::arg_check, .noclean_functions.

• In main safer functions, in the section "######## check of the required functions from the required packages", add also these 2 functions when checking for the presence of .colons_check_message.

Value

A list:

• output.cat: the message (string).

• colon_not_here: logical vector. Does list_fun contain function names without :: or ::: ?

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Extract All Function Names

Description

Extract all function names.

Usage

.extract_all_fun_names(text, pattern, lib_path, error_text)

Arguments

Details

Warnings:

• requires saferDev::arg_check.

• In the safer Backbone section "######## check of the required functions from the required packages", add also saferDev::arg_check when checking for the presence of .extract_all_fun_names.

Value

List containing:

• string: the function names without parenthesis.

• pos: position of the first character of the function names in the input string

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Function Arguments Position

Description

Return the positions of 1st letter of the first function name in a string, as well as its own opening and closing parenthesis, as well as positions of all the internal parenthesis (inside the own parenthesis).

Usage

.fun_args_pos(text, pattern, lib_path, error_text)

Arguments

Details

Warnings:

• The tested string must be cleaned form brackets between quotes. Use .in_quotes_replacement() for that.

• Quotes in strings are escaped, so that position of ( in \"a( is 3, not 4.

• requires saferDev::arg_check.

• In the safer Backbone section "######## check of the required functions from the required packages", add also saferDev::arg_check when checking for the presence of .fun_args_pos.

Value

A list containing positions:

• begin_fun: position of the 1st letter of the first function name in the tested string.

• begin: position of the opening "(" of the first function.

• end: position of the closing ")" of the first function.

• middle_bracket_pos: list of the positions of each couple of brackets in the middle of the begin and end positions. In each compartment, the first number is the position of ( and the second the position of ). NULL if no inside brackets.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Functions Detection

Description

Detect all the functions names inside a function.

Usage

.functions_detect(x, skipped_base, arg_user_setting2, lib_path, error_text)

Arguments

Details

Does not check if the functions inside the code exist.

Use the regex pattern "([a-zA-Z]|\.[a-zA-Z._])[a-zA-Z0-9._]*\s*\(" to detect a function in the code.

The result in all_basic_funs are all the functions in base::c("package:stats", "package:graphics", "package:grDevices", "package:utils", "package:datasets", "package:methods", "Autoloads", "package:base").

Warnings:

• Requires saferDev::arg_check, .extract_all_fun_names, .has_odd_number_of_quotes.

• In the safer Backbone section "######## check of the required functions from the required packages", add also these 3 functions when checking for the presence of .functions_detect.

Value

A list:

• code: vector of strings of the code of the tested function.

• all_basic_funs: vector or strings of names of all the basic R functions.

• fun_names: list of names of all the functions, not considering base::c("function", "if", "for", "while", "repeat"). Compartment names indicate the code line number of the functions in code.

• fun_names_pos: list of position of the first character of each fun_names. Compartment names indicate the code line number of the functions in code.

• code_line_nb: vector of integers of the code line numbers of code for each non empty compartment of fun_names and fun_names_pos.

• internal_fun_names: vector of string of names of internal functions in the code of the tested function.

• arg_user_setting: list of argument user settings of the tested function.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Has Odd Number of Quotes

Description

Determine if a string has a odd number of quotes.

Usage

.has_odd_number_of_quotes(input_string, pattern, lib_path, error_text)

Arguments

Details

The function considers any present ⁠'⁠ (pattern = "'\''") or ⁠"⁠ (pattern = '"'). Meaning that it does not treat special situation, like escape quotes \", or situation like this "'". All these must be removed from the input_string if necessary, using for instance: input_string <- gsub( x = input_string, pattern = '"\'"', replacement = ' ')

Warnings:

• requires saferDev::arg_check.

• In the safer Backbone section "######## check of the required functions from the required packages", add also saferDev::arg_check when checking for the presence of .has_odd_number_of_quotes.

Value

TRUE or FALSE.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Replacement Inside Parenthesis

Description

Parse a string and replace any pattern present between brackets () by another pattern.

Usage

.in_parenthesis_replacement(
  string,
  pattern,
  no_regex_pattern,
  replacement,
  perl,
  open_pos,
  close_pos,
  lib_path,
  error_text
)

Arguments

Details

Warnings:

• Must be very simple pattern, like "\(".

• requires saferDev::arg_check.

• In the safer Backbone section "######## check of the required functions from the required packages", add also saferDev::arg_check when checking for the presence of .in_parenthesis_replacement.

Value

A list containing:

• string: the input string with all pattern replaced by the replacement pattern.

• pos: the positions of the 1st character of the replaced pattern. NULL if no replaced pattern. In that case, string is identical to the input string

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Replacement Inside Quotes

Description

Parse a string and replace any pattern inside simple or double quotes by another replacement pattern and get the position of replacements.

Usage

.in_quotes_replacement(
  string,
  pattern,
  no_regex_pattern,
  replacement,
  perl,
  lib_path,
  error_text
)

Arguments

Details

The function works first by replacing in the code: 1) the three consecutive characters '"' or '"' by three spaces, 2) "\"'" and '\'"' by four spaces and 3) escape quotes like \" or \' by two spaces, before looking for the pattern inside quotes.

Warnings:

• Must be very simple pattern, like "\(".

• requires saferDev::arg_check, .has_odd_number_of_quotes.

• In the safer Backbone section "######## check of the required functions from the required packages", add also these 2 functions when checking for the presence of .in_quotes_replacement.

Value

A list containing:

• string: The input string with all pattern replaced by the replacement pattern.

• pos: vector of the positions of the 1st character of the replaced pattern. NULL if no replaced pattern. In that case, string is identical to the input string.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

No-Clean Functions

Description

Indicate if function names are inside quotes or after $.

Usage

.noclean_functions(col1, col2, col3, ini, lib_path, error_text)

Arguments

Details

Warnings:

• requires saferDev::arg_check, .has_odd_number_of_quotes.

• In the safer Backbone section "######## check of the required functions from the required packages", add also these 2 functions when checking for the presence of .noclean_functions.

Value

A logical vector indicating if function names of col2 are inside quotes or after $ (TRUE) in ini or not (FALSE). Can be length 0.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Package and Function Check

Description

Check if 1) required functions are present in required packages and 2) required packages are installed locally. Simplified version of saferDev::is_function_here(), used as internal function for the other functions of the saferDev package.

Usage

.pack_and_function_check(fun, lib_path, error_text)

Arguments

Value

An error message if at least one of the checked packages is missing in lib_path, or if at least one of the checked functions is missing in the required package, nothing otherwise.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

All Arguments Here

Description

Verify that all the functions used inside a function are written with all their arguments. For instance: base::paste0(letters[1:2], collapse = NULL, recycle0 = FALSE) and not paste0(letters[1:2]).

Usage

all_args_here(
  x,
  export = FALSE,
  out_path = ".",
  df_name = "res.tsv",
  overwrite = FALSE,
  safer_check = TRUE,
  lib_path = NULL,
  error_text = ""
)

Arguments

Details

More precisely, all_args_here() verifies that all the strings before an opening bracket ( are written with all their arguments. Thus, it cannot check function names written without brackets, like in the FUN argument of some functions, e.g., sapply(1:3, FUN = as.character).

The Perl regex used to detect a function name is: "([a-zA-Z]|\.[a-zA-Z._])[a-zA-Z0-9._]*\s*\(".

Currently, all_args_here() cannot detect functions written between quotes, like "+"() or "rownames<-"(x, "a").

Function names preceded by $ are not considered.

The following R functions are skipped: function, if, for, while, repeat and else.

Most of the time, all_args_here() does not check inside comments, but some unexpected writing could dupe all_args_here(). Please, report here if it is the case.

The returned line numbers are indicative, depending on which source is checked. For instance, saferDev::report (compiled) has not the same line numbers as its source file. Notably, compiled functions do not have comments anymore, compared to the same source function sourced into the working environment. In addition, the counting starts at the "<- function" line, i.e., without counting the #' header lines potentially present in source files.

The function works first by replacing in the code: 1) the three consecutive characters '"' or '"' by three spaces, 2) "\"'" and '\'"' by four spaces and 3) escape quotes like \" or \' by two spaces.

See more examples here.

Warnings:

1. The following R functions are also skipped (as indicated by "SKIPPED" in the DEF_ARGS column of the returned data frame): as.environment(). Click to see the explanation.

2. Some functions, like rownames(), have different arguments depending on whether something is assigned to it (e.g., rownames(x) <- "a") or not. The all_args_here() function always proposes the arguments defined in the help page without assignment, meaning that it cannot detect the assignment. A way to bypass this is to use the "exact" writing of the function. For instance, base::"rownames<-"(x, "a") instead of using base::rownames(x) <- "a", and use getAnywhere("rownames<-") to see the arguments of the function.

3. The function could not properly work if any comma is present in default argument values. Please, report here if it is the case.

4. Proposals in the STATUS column are only suggestions, as it is difficult to anticipate all the exceptions with arguments writing.

Value

A data frame indicating the missing arguments or a message saying that everything seems fine. If export argument is TRUE, then the data frame is exported as res.tsv instead of being returned. Column descriptions:

• $LINE_NB: the line number in the function code (starting at the "<- function" line, i.e., without counting the #' header lines).

• $FUN_NAME: the function name.

• $FUN_ARGS: the written arguments of FUN_NAME. "NOT_CONSIDERED" means that the function is between quotes or after $.

• $FUN_POS: the position of the first character of the function name in the $LINE_NB line.

• $DEF_ARGS: the defaults arguments of FUN_NAME. "NO_ARGS" means that the function has no arguments. "INTERNAL_FUNCTION" means that the function has been created inside the checked function. "SKIPPED" means that the function is not analyzed for the reason indicated in the "details" section.

• $MISSING_ARG_NAMES: the missing argument names in FUN_ARGS.

• $MISSING_ARGS: the missing arguments with their values in FUN_ARGS.

• $STATUS: either "GOOD", meaning that all the arguments are already written, or a new proposal of arguments writing, or indicates if some arguments are not fully written (abbreviation is discouraged), or nothing.

An additional message "EVERYTHING SEEMS CLEAN" if the STATUS column is only made of "" and "GOOD".

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Examples

# Warning: these examples may not work well when using the "Run examples" link 
# because of a particular environment. Please, copy-paste in a local environment.
# See also https://safer-r.github.io/saferDev/articles/all_args_here.html
## Not run: 
# Example that returns an error
saferDev::all_args_here(mean) # Example that returns an error
source("https://raw.githubusercontent.com/safer-r/saferDev/main/dev/other/test2.R")
saferDev::all_args_here(test2) # the checked function must be executable

## End(Not run)

FUN2 <- function(x, y){
    middle_bracket2 <- base::do.call(
        what = base::c, 
        args = code_for_col, 
        quote = FALSE, 
        envir = base::parent.frame()
    )
}
saferDev::all_args_here(FUN2, safer_check = FALSE)

## Not run: 
# Example that creates a file/folder in the working directory
source("https://raw.githubusercontent.com/safer-r/.github/refs/heads/main/profile/backbone.R")
saferDev::all_args_here(BACKBONE, export = TRUE, safer_check = FALSE)

## End(Not run)

Argument Check

Description

Check expected values of an argument of functions: class, type, mode, length, restricted values panel, kind of numeric values (in addition to the distinction between 'integer' and 'double')? Proportion only? Inf values authorized? negative values authorized? Integers of type 'double'?

Usage

arg_check(
  data,
  class = NULL,
  typeof = NULL,
  mode = NULL,
  length = NULL,
  prop = FALSE,
  double_as_integer_allowed = FALSE,
  options = NULL,
  all_options_in_data = FALSE,
  na_contain = FALSE,
  neg_values = TRUE,
  inf_values = TRUE,
  print = FALSE,
  data_name = NULL,
  data_arg = TRUE,
  safer_check = TRUE,
  lib_path = NULL,
  error_text = ""
)

Arguments

Details

If options == NULL, then at least class or type or mode or length argument must be non-null.

If options is non-null, then class, type and mode must be NULL, and length can be NULL or specified.

The function tests what is written in its arguments, even if what is written is incoherent. For instance, arg_check(data = factor(1), class = "factor", mode = "character") will return a problem, whatever the object tested in the data argument, because no object can be class "factor" and mode "character" (factors are class "factor" and mode "numeric"). Of note, the length of object of class "environment" is always 0.

If the tested object is NULL, then the function will always return a checking problem.

The class argument is a simplified version of class(data):

• "vector" tests objects of class "numeric", "integer", "character", "logical", "complex" or "expression" (no error if class(data) returns one of these values).

• "matrix" tests objects of class "matrix" for R < 4.0.0 and c(""matrix", "array"") otherwise.

• "ggplot2" tests objects of class c("gg", "ggplot") for R < 4.5 and c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg") otherwise.

• "ggplot2" tests objects of class "ggplot_built" for R < 4.5 and c("ggplot2::ggplot_built", "ggplot_built", "ggplot2::gg", "S7_object") otherwise.

Regarding typeof, the value "object" comes from the fact that if an object has type OBJSXP and has the S4 object flag set (IS_S4_OBJECT(x) is true), typeof() returns "S4". If an object has type OBJSXP without the S4 flag set, typeof() returns "object".

Value

A list containing:

• problem: logical. Is there any problem detected?

• text: message indicating the details of the problem, or the absence of problem.

• object.name: value of the data_name argument (i.e., name of the checked object if provided, NULL otherwise).

Author(s)

Gael Millot

Haiding Wang

Yushi Han

See Also

match.arg.

Examples

# Warning: these examples may not work well when using the "Run examples" link 
# because of a particular environment. Please, copy-paste in a local environment.
# See also https://safer-r.github.io/saferDev/articles/arg_check.html
test <- matrix(1:3)
## Not run: 
# Example that returns an error
saferDev::arg_check(data = test, print = TRUE, class = "vector", mode = "numeric")

## End(Not run)
saferDev::arg_check(data = test, print = TRUE, class = "matrix", mode = "numeric")
saferDev::arg_check(
    data = test, 
    print = TRUE, 
    class = "matrix", 
    mode = "numeric", 
    error_text = " using saferDev::arg_check()"
)

Colons Check

Description

Verify that all the functions used inside a function are preceded by a package attribution. For instance: base::mean() and not mean(), or saferDev:::.base_op_check() and not .base_op_check(). Warning: does not check that the package is the good one. Use all_args_here() for that.

Usage

colons_check(x, safer_check = TRUE, lib_path = NULL, error_text = "")

Arguments

Details

The result is used to modify the code inside the tested function like this: <PACKAGE>::<FUNCTION> (or <PACKAGE>:::<FUNCTION> for function names starting by a dot).

More precisely, colons_check() verifies that all the strings before an opening bracket ( are preceded by ::.

::: are not checked per se, because incorrect writing, like saferDev::.colons_check_message() returns an error when executing the tested function, and because base:::sum() is as ok as base::sum(). In the same manner, more than three colons are not checked because it returns an error when executing the tested function.

Warning: colons_check() cannot check function names written without brackets, like in the FUN argument of some functions, e.g., sapply(1:3, FUN = as.character).

The Perl regex used to detect a function name is: "([a-zA-Z]|\.[a-zA-Z._])[a-zA-Z0-9._]*\s*\(".

Currently, colons_check() cannot detect functions written between quotes, like "+"() or "rownames<-"(x, "a").

Function names preceded by $ are not considered.

The following R functions are skipped: "function", "if", "for", "while", "repeat" and "else".

Most of the time, colons_check() does not check inside comments, but some unexpected writing could dupe colons_check(). Please, report here if it is the case.

The returned line numbers are indicative, depending on which source is checked. For instance, saferDev::report (compiled) has not the same line numbers as its source file (source file). Notably, compiled functions do not have comments anymore, compared to the same source function sourced into the working environment. In addition, the counting starts at the "<- function" line, i.e., without counting the #' header lines potentially present in source files.

Of note, during package creation, the devtools::check() command tells which functions where wrongly attributed to package. Example:

checking dependencies in R code ... WARNING
  '::' or ':::' import not declared from: 'sbase'
  Missing or unexported objects:
    'base::dev.off' 'base::graphics.off' 'base::hcl' 'base::par' 'base::read.table' 'saferGG::report'

Value

A table-like text message indicating the missing :: or ::: or a message saying that everything seems fine.

Table-like: column 1, the line number in the function code (starting at the "<- function" line, i.e., without counting the #' header lines); column 2, the function name; column 3, the code preceding the function name.

With missing :: or :::, the message also indicates if internal functions are created inside the checked function code, since these functions cannot have :: or :::.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

Examples

# Warning: these examples may not work well when using the "Run examples" link 
# because of a particular environment. Please, copy-paste in a local environment.
# See also https://safer-r.github.io/saferDev/articles/colons_check.html
saferDev::colons_check(mean)
saferDev::colons_check(colons_check)
source("https://raw.githubusercontent.com/safer-r/saferDev/main/dev/other/test.R")
saferDev::colons_check(test)

Environment Check

Description

Verify that object names in the environment defined by the pos parameter are identical or not to object names in the above environments (following R Scope). This can be used to verify that names used for objects inside a function or in the working environment do not override names of objects already present in the above R environments, following the R scope.

Usage

env_check(
  pos = 1,
  name = NULL,
  safer_check = TRUE,
  lib_path = NULL,
  error_text = ""
)

Arguments

Value

A character string indicating the object names of the tested environment that match object names in the above environments, following the R scope, or NULL if no match.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

See Also

exists.

Examples

# Warning: these examples may not work well when using the "Run examples" link 
# because of a particular environment. Please, copy-paste in a local environment.
# See also https://safer-r.github.io/saferDev/articles/env_check.html
# Examples in the working environment
# creation of the object mean with value 1 in the .GlobalEnv environment, 
# knowing that the mean() function also exists in the environment base, above .GlobalEnv:
mean <- 1 
# creation of the object t.test with value 1 in the .GlobalEnv environment, 
# knowing that the t.test() function also exists in the environment stats, above .GlobalEnv:
t.test <- 1 
search() # current R scope (order of the successive R environments).
utils::find("mean") # where the objects with the name "mean" are present.
utils::find("t.test") # where the objects with the name "mean" are present.
# test if any object name of the global environment are above environments:
a <- saferDev::env_check(pos = 1) 
a # output string.
cat(a)
# test if any object of the stats environment (one step above .GlobalEnv) 
# are in upper environments of stats. Returns NULL since no object names of 
# stats are in upper environments:
saferDev::env_check(pos = 2) 
rm(mean)
rm(t.test)

# Examples inside a function
# saferDev::env_check() checks if the object names inside the fun1 function 
# exist in the .GlobalEnv environment and above:
fun1 <- function() {
  t.test <- 0
  mean <- 5
  saferDev::env_check(pos = 1)
}
a <- fun1()
cat(a) # Warning: cat(fun1()) creates an additional layer of environment.
# saferDev::env_check() checks if the object names inside the environment one step above fun2(), 
# here .GlobalEnv, exist in the upper environments of .GlobalEnv:
fun2 <- function() {
  sum <- 0
  saferDev::env_check(pos = 2)
}
fun2()
# Warning: cat(fun2()) does not return NULL, because the environment tested is not 
# anymore .GlobalEnv but inside cat().
a <- fun2() 
cat(a) # nothing displayed because fun2() returns NULL
# With the name of the function fun3 indicated in the message:
fun3 <- function() {
  t.test <- 0
  mean <- 5
  saferDev::env_check(pos = 1, name = "fun3")
}
a <- fun3() 
cat(a)
# Alternative way:
# sys.calls() gives the name of the imbricated functions and 
# sys.calls()[[length(sys.calls())]] the name of the function one step above.
fun4 <- function() {
  t.test <- 0
  mean <- 5
  name <- as.character(sys.calls()[[length(sys.calls())]])
  saferDev::env_check(pos = 1, name = name)
}
a <- fun4() 
cat(a)
# A way to have the name of the tested environment according to test.pos value:
fun7 <- function() {
  min <- "VALUE"
  fun8 <- function() {
    test.pos <- 1 # value 1 tests the fun8 env, 2 tests the fun7 env.
    range <- "VALUE"
    name <- if(length(sys.calls()) >= test.pos) {
      as.character(sys.calls()[[length(sys.calls()) + 1 - test.pos]])
    } else {
      search()[(1:length(search()))[test.pos - length(sys.calls())]]
    }
    saferDev::env_check(pos = test.pos, name = name) 
  }
  fun8()
}
a <- fun7() 
cat(a)

Get Message

Description

Evaluate an instruction written between "" and return the first of the error message, or the last of the warning or standard (non error non warning) messages if ever exist.

Using argument print_no = FALSE, return NULL if nothing reported, which is convenient in some cases.

Usage

get_message(
  data,
  kind = "error",
  header = TRUE,
  print_no = FALSE,
  text = NULL,
  env = NULL,
  safer_check = TRUE,
  lib_path = NULL,
  error_text = ""
)

Arguments

Details

Warnings:

• Only the first error or last warning/standard message is returned.

• Always use the env argument when get_message() is used inside functions.

• The function does not prevent printing, for instance if print() or show() is used inside the instruction tested. To prevent that, use tempo <- utils::capture.output(error <- get_message(data = "arg_check(data = 'a', class = mean, neg_values = FALSE, print = TRUE)")). The return of get_message() is assigned into error and the printed messages are captured by utils::capture.output() and assigned into tempo. See the examples.

The env argument is used as value for the envir argument of the base::eval() function.

Value

The function returns the error, warning, or standard message, as a single character string, depending on what has been selected using the kind argument and if such message exists.

NULL if no selected message returned and the print_no argument is FALSE.

The following message if no selected message returned and the print_no argument is TRUE: "NO (ERROR|WARNING|STANDARD) MESSAGE REPORTED".

The following message if 1) the kind argument is "warning" or "message" while an error message is returned and 2) the print_no argument is TRUE: "NO POTENTIAL (WARNING|STANDARD) MESSAGE BECAUSE OF ERROR MESSAGE REPORTED".

Author(s)

Gael Millot

Haiding Wang

Yushi Han

See Also

try.

Examples

# Warning: these examples may not work well when using the "Run examples" link 
# because of a particular environment. Please, copy-paste in a local environment.
# See also https://safer-r.github.io/saferDev/articles/get_message.html

# Report error message by default. Here no error to report:
saferDev::get_message(data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)")

# Warning message to report:
saferDev::get_message(data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)", kind = "warning")

# No standard message to report:
saferDev::get_message(data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)", kind = "message", 
print_no = TRUE, text = "IN A")

# Standard message cannot be caught because wilcox.test() returns an error message:
saferDev::get_message(data = "wilcox.test()", kind = "message", print_no = TRUE, text = "IN A")

# Text added in warning message to report:
saferDev::get_message(data = "wilcox.test()", kind = "error", print_no = TRUE, text = "IN A")

# No error message to report with text added:
saferDev::get_message(data = "sum(1)", kind = "error", print_no = TRUE, text = "IN A")

# No error message to report with text added:
saferDev::get_message(data = "message('ahah')", kind = "error", print_no = TRUE, text = "IN A")

# Standard message reported with text added:
saferDev::get_message(data = "message('ahah')", kind = "message", print_no = TRUE, text = "IN A")

# Messages from ggplot2 functions caugth:
saferDev::get_message(data = "ggplot2::ggplot(data = data.frame(X = 1:10, stringsAsFactors = TRUE), 
mapping = ggplot2::aes(x = X)) + ggplot2::geom_histogram()", kind = "message", 
print_no = TRUE, text = "IN INSTRUCTION 1")

Is Function Here

Description

Check if required functions are present in installed packages. This controls the potential modifications of package contents.

Usage

is_function_here(fun, safer_check = TRUE, lib_path = NULL, error_text = "")

Arguments

Value

An error message if at least one of the checked packages is missing in lib_path, or if at least one of the checked functions is missing in the required package, nothing otherwise.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

See Also

exists and findFunction

Examples

# Warning: these examples may not work well when using the "Run examples" link 
# because of a particular environment. Please, copy-paste in a local environment.
# See also https://safer-r.github.io/saferDev/articles/is_function_here.html
## Not run: 
# Example that returns an error
saferDev::is_function_here(fun = "ggplot2::notgood", error_text = " INSIDE P1::F1")
saferDev::is_function_here(fun = c("ggplot2::geom_point", "grid::gpar"))
saferDev::is_function_here(fun = "c")

## End(Not run)
saferDev::is_function_here(fun = "base::c", error_text = " INSIDE P1::F1")

Is Package Here

Description

Check if required packages are installed locally.

Usage

is_package_here(
  req_package,
  safer_check = TRUE,
  lib_path = NULL,
  error_text = ""
)

Arguments

Value

An error message if at least one of the checked packages is missing in lib_path, nothing otherwise.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

See Also

require.

Examples

# Warning: these examples may not work well when using the "Run examples" link 
# because of a particular environment. Please, copy-paste in a local environment.
# See also https://safer-r.github.io/saferDev/articles/is_package_here.html
## Not run: 
# Example that returns an error
is_package_here(req_package = "nopackage", error_text = " INSIDE P1::F1")
# Example that returns an error
is_package_here(req_package = "ggplot2", lib_path = "NOTGOOD")

## End(Not run)
is_package_here(req_package = "ggplot2")

Report

Description

Print a character string or a data object into a same output file. Convenient for log file generation.

Usage

report(
  data,
  output = "log.txt",
  path,
  append = FALSE,
  rownames_kept = FALSE,
  vector_cat = FALSE,
  noquote = TRUE,
  sep = 2,
  safer_check = TRUE,
  lib_path = NULL,
  error_text = ""
)

Arguments

Value

Nothing (implementation of an existing file) or a text file.

Author(s)

Gael Millot

Haiding Wang

Yushi Han

See Also

capture.output.

Examples

# Warning: these examples may not work well when using the "Run examples" link 
# because of a particular environment. Please, copy-paste in a local environment.
# See also https://safer-r.github.io/saferDev/articles/report.html
## Not run: 
# Example that creates a file/folder in the working directory
saferDev::report(data = "THE FOLLOWING VECTOR IS:\n", output = "results.txt", path = ".", 
append = TRUE, sep = 1)
saferDev::report(data = 1:3, output = "results.txt", path = ".", append = TRUE, 
rownames_kept = FALSE, vector_cat = FALSE, noquote = FALSE, sep = 2)
saferDev::report(data = "THE FOLLOWING MATRIX IS:\n", output = "results.txt", path = ".", 
append = TRUE, sep = 1)
saferDev::report(data = matrix(1:5), output = "results.txt", path = ".", append = TRUE, 
rownames_kept = FALSE, vector_cat = FALSE, noquote = FALSE, sep = 5)
saferDev::report(data = "THE FOLLOWING DATA FRAME IS:\n", output = "results.txt", path = ".", 
append = TRUE, sep = 1)
saferDev::report(data = data.frame(A = 1:8, B = letters[1:8]), output = "results.txt", path = ".", 
append = TRUE, rownames_kept = FALSE, vector_cat = FALSE, noquote = FALSE, sep = 1)

## End(Not run)