tidyr update cause failure when replacing na's.

[price0416]

In the line referenced below, an error results when using tidyr 1.2.0+.

annotateMaf/R/hotspot-annotate-maf.R

Line 96 in cb94e4b

tidyr::replace_na(list(start_residue = 0, end_residue = 0)) %>%

The error generates is as follows:
Error in vec_assign():
! Can't convert replace$start_residue to match type of data$start_residue .
Backtrace:
▆

1. └─global annotate_maf_with_hotspots(combined_maf)
2. └─annotateMaf::hotspot_annotate_maf(maf)

3. └─... %>% ...
   

4.   ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
   

5.   └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
   

6.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
   

7.       └─annotateMaf `_fseq`(`_lhs`)
   

8.         └─magrittr::freduce(value, `_function_list`)
   

9.           └─function_list[[i]](value)
   

10.             ├─tidyr::replace_na(., list(start_residue = 0, end_residue = 0))
    

11.             └─tidyr:::replace_na.data.frame(., list(start_residue = 0, end_residue = 0))
    

12.               └─vctrs::vec_assign(...)
    

13.                 └─vctrs `<fn>`()
    

14.                   └─vctrs::vec_default_cast(...)
    

15.                     └─vctrs::stop_incompatible_cast(...)
    

16.                       └─vctrs::stop_incompatible_type(...)
    

17.                         └─vctrs:::stop_incompatible(...)
    

18.                           └─vctrs:::stop_vctrs(...)
    

19.                             └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
    

The issue is caused by the following tidyr updates:
replace_na() no longer allows the type of data to change when the replacement is applied. replace will now always be cast to the type of data before the replacement is made. For example, this means that using a replacement value of 1.5 on an integer column is no longer allowed. Similarly, replacing missing values in a list-column must now be done with list("foo") rather than just "foo".

replace_na() no longer replaces empty atomic elements in list-columns (like integer(0)). The only value that is replaced in a list-column is NULL (#1168).

This might be fixed by casting start_residue and end_residue to double in the replace_na() call.