R CMD check fails, devtools::test() works fine

Question

Sometimes R CMD check fails when all your test run fine when you run the manually (or using devtools::test()).

I ran into one of such issues as well, when I wanted to compare results from bootstrapping using the boot package. I went into a rabbit hole looking for issues caused by parallel computation (done by boot) and Random Number Generators (RNGs).

These were all not the answers.

Answer 1

In the end, the issue was trivial. I used base::sort() to create the levels of a factor. (To ensure that they would always align, even if the data was in a different order)

The problem is, that the default sort method depends on the locale of your system. And R CMD check uses a different locale than my interactive session.

The issue resided in this: R interactively used:LC_COLLATE=en_US.UTF-8; R CMD check used: LC_COLLATE=C;

In the details of base::sort this is mentioned:

Except for method ‘"radix"’, the sort order for character vectors
will depend on the collating sequence of the locale in use: 
see ‘Comparison’.  The sort order for factors is the order of their 
levels (which is particularly appropriate for ordered factors).

I now resolved the issue by specifying the radix sort method.

Now, all works fine.