testthat | An R 📦 to make testing 😀 | Testing library

I am trying to install factoextra, but I gets stuck during the CMake part, in particular with error like:

CMake Error: The source directory "/tmp/..." does not exist.

(same when I try to install its dependencies: nloptr, pbkrtest, lme4, car, rstatix, FactoMineR, ggpubr )

any idea?

thanks

ps:

• R version 4.0.0
• centos 7

last part of logs:

I've written an import function that gets a single file from an aws s3-bucket.

That function itself is a wrapper around aws.s3::s3read_using() which takes a reading function as its first argument.

Why do I wrap around aws.s3::s3read_using() ? Because I need to do some special error-handling and want the wrapping function to do some Recall() up to a limit... but that's a different story.

Now that i've successfully build and tested my wrapping function i want to do another wrapping arround that:

I want to iterate n times over my wrapper to bind the downloaded files together. I now have the difficulty to hand the 'reading_function' to the FUN argument of aws.s3::s3read_using().

I could do that by simply using ... - BUT! I want to make clear to the USER of my wrapping wrapper, that he needs to specify that argument.

So I've decided to use rlangs rlang::enexpr() to capture the argument and to hand it over to my first wrapper via !! - which in return captures that argument again with rlang::enexpr() and hands it over - finally - to aws.s3::s3read_using() via rlang::expr(aws.s3::s3read_using(FUN = !!reading_fn, object = s3_object))

That works perfectly fine and smooth. My Problem is with testing that function construct using testthat and mockery

Here is some broadly simplyfied code:

I'm writing unit tests using testthat to check some operations and these operations needs objects with srcref attribute. srcref attribute is added if during the package installation / building option keep.source was set to TRUE.

I see all my tests fail when using devtools::check() if those tests expect srcref attribute for object. This not happens when tests are performed interactively, i.e. using devtools:test(). What could I do to keep these tests, run it and make them pass using devtools::check()? I have tried devtools::check(args = "--with-keep.source") but this argument is not recognized.

I'm using rlang::pkg_env("my-package") to get objects with srcref attribute, so tests look like this:

I want to run all the tests and obtain the test results and produced warnings to programmatically create a markdown report showing test outcomes and potential warnings that occurred in the tested code.

But it seems there is no way to obtain or capture warnings during the test run! I understand that tests are executed in a closed environment, but is there really no way to let testthat provide me the thrown warnings?

In the following setup, the warn_list variable is always empty.

Three files for the minimal example:

./tests/testthat.R

I work for an org that has a number of internal packages that were created many years ago. These are in the form of package zip archives that were compiled on Windows on R 3.x. Therefore, they can't be installed on R 4.x, and can't be used on Macs or Linux either without being recompiled. So everyone in the entire org is stuck on R 3.6 until this is resolved. I don't have access to the original package source files. They are lost to time....

I want to take these packages, extract the code and data, and update them for modern best practices (roxygen, GitHub repos, testthat etc.). What is the best way of doing this? I have a fair amount of experience with package development. I have already tackled one. I started a new RStudio package project, and going function by function, copying the function code to a new script file, getting and reformatting the help from the help browser as roxygen docs. I've done the same for any internal hidden functions that i could find (via pkg_name::: mostly) , and also the internal datasets. That is all fairly straightforward, but very time consuming. It builds ok, but I haven't yet tested the actual functionality of the code.

I'm currently stuck because there are a couple of standardGeneric method functions for custom S4 class objects. I am completely unfamiliar with these and haven't been able to figure out how to copy them over. Viewing the source code they are wrapped in new() with "standardGeneric" as the first argument (plus a lot more obviously), as opposed to just being a simple function definition for all the other functions. Any help with how to recreate or copy these over would be very welcome.

But maybe I am going about this the wrong way in the first place. I haven't been able to find any helpful suggestions about how to "back engineer" R package source files from a compiled version.

Anyone any ideas?

According to Carl Boettiger in this thread, "...when tests fail. Like Solaris, some of these failures can occur when an upstream dependency installs on the platform but does not actually run." My code fails numerically on M1mac, but not on other platforms, while using stats::integrate on functions returning very small values.

Should I skip the test on M1mac (arm64)?

Since a few months, ggplot2 started to save png files with a transparent background. The code output in Rstudio and when saved as pdf looks great. It happens mainly with the use of themes when I omit the gray panel background. I tested it on my macbook with "Preview" and on a Windows Computer with the "foto viewer" there.

I have a dataset like the one below (actual dataset has 5M+ rows with no gaps), where I am trying to filter out rows where the sum of all numeric columns for the row itself and its previous and next rows is equal to zero.

N.B.

• Time is a dttm column in the actual data.
• Number of consecutive zeros can be more than 3 rows and in that case multiple rows will be filtered out.

I am writing some unit tests for an R package using testthat. I would like to compare two objects where not all the details need to match, but they must maintain equivalence with respect to a set of functions of interest.

For a simple example, I want to use something like