@arisp99, here are some elements that might be helpful. Good luck!
I can reproduce the error
> read_file(cov_file)
Error:
Names repair functions can't return `NA` values.
Caused by error:
Names repair functions can't return `NA` values.
Backtrace:
1. miplicorn::read_file(cov_file)
4. vroom `<fn>`(`<col_spec>`, 123L, `<chr>`, `<quos>`, "unique")
6. tidyselect::vars_select(names(spec$cols), !!!col_select, .strict = FALSE)
7. tidyselect:::eval_select_impl(...)
15. tidyselect:::vars_select_eval(...)
16. tidyselect:::ensure_named(pos, vars, uniquely_named, allow_rename)
17. vctrs::vec_as_names(names(pos), repair = "check_unique")
18. vctrs `<fn>`()
19. vctrs:::validate_unique(names = names, arg = arg)
20. vctrs:::validate_minimal_names(names, n)
I am using Ubuntu but am not sure it's a specific OS thing, it's probably rather due to versions of some of the dependencies (e.g. vroom). I might be wrong, of course. A good tip by @krlmlr: https://twitter.com/krlmlr/status/1443076268551979010
PSA: Record your sessioninfo::session_info() or sessioninfo::package_info() for #rstats environments where you don't control for package versions. It helps a lot when things start to fail for no apparent reason.
You could switch from your remotes-based GHA workflow to a pak-based GHA workflow https://github.com/r-lib/actions/tree/master/examples as it should by default include session info in the log see e.g. https://github.com/ggseg/ggsegExtra/runs/3905677808?check_suite_focus=true#step:9:137
If you compare versions between the failing checks and your local environment, it might help? See a similar issue (same error message, but probably different exact cause).
In practice in your code
# Read in entire data set but select only columns we are interested in
data <- vroom::vroom(
file = .file,
col_names = FALSE,
col_select = c(1, col_select),
show_col_types = FALSE
)
are the lines failing. They do not fail if I set col_names to TRUE but I have no idea what I'm doing. I'd recommend checking your assumptions about the data at that stage, and maybe setting col_names to TRUE or changing the .name_repair argument in vroom::vroom (contrary to me you'll know what you are doing as you know what the data manipulation is supposed to do).