expect_error_or_warning in testthat? - r

I have some particularly finicky code that behaves differently on different platforms, but also behaves differently if run under valgrind ... right now I know that it
gives a warning if run on 32-bit Linux not under valgrind
gives an error if run elsewhere or on 32-bit Linux with R -d valgrind
The code below works (sorry for the lack of reproducible example, you can probably see that it would be pretty hard to write one) if I'm not running under valgrind, but under valgrind it fails because we get an error rather than a warning.
if (sessionInfo()$platform=="i686-pc-linux-gnu (32-bit)") {
expect_warning(update(g0, .~. +year), "failed to converge")
} else {
expect_error(update(g0, .~. +year), "pwrssUpdate did not converge in")
}
I would like an expect_warning_or_error() function; I suppose I could make one by hacking together the guts of expect_error and expect_warning, which don't look too complicated, but I welcome other suggestions.
Alternatively, I could figure out how to detect whether I am running under valgrind or not (seems harder).
A sort-of reproducible example:
library(testthat)
for (i in c("warning","stop")) {
expect_warning(get(i)("foo"))
expect_error(get(i)("foo"))
}

My solution, hacked together from gives_warning() and throws_error(). I'm not sure it's completely idiomatic/robust ...
gives_error_or_warning <- function (regexp = NULL, all = FALSE, ...)
{
function(expr) {
res <- try(evaluate_promise(expr),silent=TRUE)
no_error <- !inherits(res, "try-error")
if (no_error) {
warnings <- res$warnings
if (!is.null(regexp) && length(warnings) > 0) {
return(matches(regexp, all = FALSE, ...)(warnings))
} else {
return(expectation(length(warnings) > 0, "no warnings or errors given",
paste0(length(warnings), " warnings created")))
}
}
if (!is.null(regexp)) {
return(matches(regexp, ...)(res))
}
else {
expectation(TRUE, "no error thrown", "threw an error")
}
}
}

#Ben I may be misunderstanding but it comes to mind here that if you want to know if something errored/warned or not you could use tryCatch. If this is not what you want or you were hoping for a more testthat approach feel free to say, "You're way of the mark" but add an emoticon like :-) and it will make everything better.
First I make a temperamental function to mimic what you describe. Then I make an is.bad function and just look for errors or warnings (don't worry about OS as this behavior is hard to predict). Then I wrap with expect_true or expect_false:
temperamental <- function(x) {
if (missing(x)){
ifelse(sample(c(TRUE, FALSE), 1), stop("Robot attack"), warning("Beware of bots!"))
} else {
x
}
}
temperamental()
temperamental(5)
is.bad <- function(code) {
isTRUE(tryCatch(code,
error = function(c) TRUE,
warning = function(c) TRUE
))
}
expect_true(is.bad(temperamental()))
expect_false(is.bad(temperamental(5)))

I had the same problem and after reading the source for both functions I found a good solution. Actually is very simple, you only need to add a small if statement in the code from expect_error.
This is the code from expect_error
function (object, regexp = NULL, ..., info = NULL, label = NULL)
{
lab <- make_label(object, label)
error <- tryCatch({
object
NULL
}, error = function(e) {
e
})
if (identical(regexp, NA)) {
expect(is.null(error), sprintf("%s threw an error.\n%s",
lab, error$message), info = info)
}
else if (is.null(regexp) || is.null(error)) {
expect(!is.null(error), sprintf("%s did not throw an error.",
lab), info = info)
}
else {
expect_match(error$message, regexp, ..., info = info)
}
invisible(NULL)
}
Adding an if statement before the return value you check if an error was not thrown and check for warnings (remember to add the all argument to the new function). The new function code is this:
expect_error_or_warning <- function (object, regexp = NULL, ..., info = NULL, label = NULL, all = FALSE)
{
lab <- testthat:::make_label(object, label)
error <- tryCatch({
object
NULL
}, error = function(e) {
e
})
if (identical(regexp, NA)) {
expect(is.null(error), sprintf("%s threw an error.\n%s",
lab, error$message), info = info)
} else if (is.null(regexp) || is.null(error)) {
expect(!is.null(error), sprintf("%s did not throw an error.",
lab), info = info)
} else {
expect_match(error$message, regexp, ..., info = info)
}
if(is.null(error)){
expect_warning(object = object, regexp = regexp, ..., all = all, info = info, label = label)
}
invisible(NULL)
}
This code is very robust and easy to maintain. If you are writing a package and can't use functions that aren't exported (:::) you can bring the code from make_label to the function, is only one line.

Related

Solving syntax mistake in R

I am trying to run the code below with the if else statement in R :
if (check_element=="TRUE") {
sqlUpdate(uat_conn, tps00176, "integration.tps00176")
}
else {
sqlSave(uat_conn, tps00176, tablename = "integration.tps00176",rownames=TRUE,addPK=TRUE ,safer=TRUE,
varTypes = c(
"citizen"="varchar(5)",
"time"="integer",
"values"="integer"))
}
Before I run this code, else is underlined with red color with the message
unexpected token else
So can someone help me how to solve this problem and find an error in the syntax?

Set default answer tu `menu` after a given amount of time

In R, is it possible to create a function that sets a default answer after some defined amount of time for menu (or to create something that works like that)?
My best not-working idea is to try using {future}.
Example
library(future)
plan(multisession(workers = 2))
zero_after_s <- function(s) Sys.sleep(s)
zero_after_t_menu <- function(
choices, graphics = FALSE, title = NULL, t = 0
) {
if (t == 0) {
menu(choices, graphics, title)
} else {
time_passed <- future(zero_after_s(t))
while (!resolved(time_passed)) {
return(menu(choices, graphics, title))
}
0
}
}
switch(
zero_after_t_menu(c("List letters", "List LETTERS"), t = 5) + 1,
cat("Nothing done (maybe t seconds passed without answers)\n"),
letters,
LETTERS
)
This cannon work because while will cycle and check its argument only when its body finishes the cycle, i.e., the user has answered to menu. I put this just as a tentative idea of a solution.
I try to call menu from the future (it seems more promising), but I cannot interact with it anymore (obviously), and anyway, it throws an error because menu cannot be used non-interactively :-)
zero_after_t_menu <- function(
choices, graphics = FALSE, title = NULL, t = 0
) {
if (t == 0) {
menu(choices, graphics, title)
} else {
res %<-% future(menu(choices, graphics, title), earlySignal = TRUE)
Sys.sleep(t)
if (resolved(res)) res else 0
}
}
Any ideas or suggestions?
Thank you,
Corrado.
PS: my actual use case is a loop across some (many) files to be (slowly) preprocessed. Under some conditions, I would like to have the opportunity to select what to do. Still, given that it is a very long execution, during nights or not-monitoring time, I would like a safe default selection (e.g., "skip that iteration for the future") to be made automatically to permit the loop to go on without my supervision.

Parallization of different instances in a R6class

I am asking for help to design a specific R6class and especially to design a run method to would run processes in parallel. Note that all of the code example listed below have not been tested and most likely contain errors. They are just here to help convey how I am thinking about implementing the parallelization of the jobs within my R6Class.
I built a R6class type of object called Input that is a wrapper for a simulation platform. The goal of the class is to ease the writing of individual set of paramers for inputs to the simulation platform. It might look like
input = Input$new()
input$set_parameter_x(...)
input$set_parameter_y(...)
I would like the class to be able to directly run the simulations (with the run method) and do so with a defined number of threads but I am not sure how to best achieve that goal. Note that each process started by run is single threaded. However, I would like that each process started by run can run in parallel of call to method run made from a different instance of the class Input. Something like
input_1$run(executable = "/path/to/executable", maxNbThreads = 4)
input_2$run(executable = "/path/to/executable", maxNbThreads = 4)
input_3$run(executable = "/path/to/executable", maxNbThreads = 4)
input_4$run(executable = "/path/to/executable", maxNbThreads = 4)
would all run in parallel. I don't know much about paralization in R (hence my question) but of course one could do
foreach (input_index = 1:nbInputs) %dopar%
{
require(myPackage)
input = Input$new()
input$set_parameter_x(...)
input$set_parameter_y(...)
input$run(executable = "/path/to/executable", maxNbThreads = 1)
}
instead but I'd wish that the work of parallelizing the processes would be taken into account by the R6class Input and not by the user of this class.
I am thinking about having a vector called runningThreads shared among all instances of the class (a static attribute of the class) using an environment (as explained here). runningThreads would contain the pid's of the currently running jobs. Then, everytime the run method is called, the user would specify the maximal number of threads (maxNbThreads) and, in a while loop it would remove from runningThreads the pid's of jobs that are not active anymore until the length of runningThreads is shorter than the argument maxNbThreads provided to run. run would then run the job and add its pid to runningThreads. The public method run (and private methods hat run would call) might look something like
isAThreadAvailable = function(maxNbThreads)
{
for (thread_index in 1:length(private$runningThreads))
{
thread = private$runningThreads[thread_index]
if (!isThreadRunning(thread))
{
private$runningThreads = private$runningThreads[-thread_index]
}
}
return (length(private$runningThreads) < maxNbThreads)
}
isThreadRunning = function(thread)
{
return (system(paste("kill -0", pid), intern=TRUE))
}
run = function(exec = defaultExecutable, maxNbThreads = 1, sleepTimeInSec = 2)
{
stopifnot(maxNbThreads > 0)
if (maxNbThreads == 1)
{
# Then just run it and wait for it to end
system(paste(exec, paste(private$data, collapse=" ")))
} else
{
while (!isAThreadAvailable(maxNbThreads))
{
Sys.sleep(sleepTimeInSec)
}
newThread = system(paste(exec, paste(private$data, collapse=" "), "&; echo !#"), intern=TRUE)
private$runningThreads = c(private$runningThreads, newThread)
}
}
Does it sound like a good method? There are probably packages that could ease the building my R6class. Would you be so kind as to point me to these packages and maybe show a small example of how it could be used for my run method in my R6Class?
Thanks to the package processx that #HongOoi mentionned in a comment I could implement what I needed. I did in a very similar style as I designed before but the processx package made everything so much easier.
Here is the code for the run method
isAThreadAvailable = function(maxNbThreads)
{
while (private$shared$isOtherProcessCheckingThreads)
{
Sys.sleep(0.001)
}
private$shared$isOtherProcessCheckingThreads = TRUE
thread_index = 1
while (thread_index <= length(private$shared$runningThreads))
{
thread = private$shared$runningThreads[[thread_index]]
if (!thread$is_alive())
{
private$shared$runningThreads = private$shared$runningThreads[-thread_index]
} else
{
thread_index = thread_index + 1
}
}
r = length(private$shared$runningThreads) < maxNbThreads
private$shared$isOtherProcessCheckingThreads = FALSE
return(r)
},
run = function(exec = "SimBit", maxNbThreads = 1, sleepTimeInSec = 1, waitEndOfThread = FALSE)
{
stopifnot(maxNbThreads > 0)
stopifnot(sleepTimeInSec >= 0)
while (!self$isAThreadAvailable(maxNbThreads))
{
Sys.sleep(sleepTimeInSec)
}
newThread = processx::process$new(exec, paste(private$data, collapse=" "))
private$shared$runningThreads = c(private$shared$runningThreads, newThread)
if (waitEndOfThread)
{
while (newThread$is_alive())
{
Sys.sleep(sleepTimeInSec)
}
}
}

Something like a Scala Option / Optional in R?

Is there something in R (either a package or base idiom) that is like an Option as found in Scala and other languages (see tag optional for details). Specifically, I'm looking for the following features some object that can:
signify the absence of a value but easily
hold attributes
return a default value in the face of having no contained value without requiring that the result of the default value be calculated unless it is actually needed
I'm sure there are a lot of other nice characteristics of Options that I haven't fully recognized as I'm relatively new to the idiom. Any answer that can provide more than the above listed features gets bonus points, especially if the additional features can be described well.
I tried writing a poor substitute using an R6 class (below). Anything that works better or is more idiomatically aligned with R would be greatly appreciated.
library(R6)
Option <- R6Class("Option",
public = list(
initialize = function(value=NULL) {
self$value <- value
}
,get = function() {
return(self$value)
}
,set = function(value) {
self$value <- value
return(value)
}
,getOrElse = function(...) {
if(self$isDefined()) {
return(self$value)
} else {
return(eval(...))
}
}
,isDefined = function() {
return(!all(is.null(self$value)) && !all(is.na(self$value)))
}
, value = NULL
)
,private = list()
,active = list()
) #end Option
Example:
bob <- Option$new()
bob$isDefined() == FALSE
bob$getOrElse("a") == "a"
bob$getOrElse({Sys.sleep(2);"b"})=="b"
bob$set(value = "a")
bob$isDefined() == TRUE
bob$getOrElse({Sys.sleep(2);"b"})=="a"

How to make a test fail with the testthat package?

I have a test for which if the prerequisites are not met (e.g., missing file or something) I would like to make it fail.
Just for clarification, here's an example I'd like to do:
test_that("...", {
if ( ... precondition to execute the test is not met... ) {
expect_true(FALSE) # Make it fail without going further
}
expect_that( ... real test here ...)
})
Now my question is: Is there any fail()-like expectation in the testthat package or I have to write expect_true(FALSE) all the time?
There isn't a fail function in testthat at the moment. I think you want something like
fail <- function(message = "Failure has been forced.", info = NULL, label = NULL)
{
expect_that(
NULL,
function(message)
{
expectation(FALSE, message)
},
info,
label
)
}
Usage is, for example,
test_that("!!!", fail())
Failure is not an option...
Try using stop:
test_that("testingsomething", {
if(file.exists("foo.txt")){
stop("foo.txt already exists")
}
foo = writeFreshVersion("foo.txt")
expect_true(file.exists("foo.txt"))
}
)

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