na.omit could not find function; S3 methods not loaded?

[dereckmezquita]

Error description

I am using data.table and R6 classes. I want to use data.table na.omit function on the data but I get the above error.

I suspect that it's because na.omit is an S3 that has not been loaded. Unfortunately I cannot figure out how to solve this since na.omit is not exported from data.table.

I really don't want to have to call library("data.table") to solve this. Any help or is this indeed a bug?

Here's a minimal example.

R6 class module:

box::use(R6)

#' @export
TestClass <- R6$R6Class(
    "TestClass",
    public = list(
        some_method = function(data) {
            return(na.omit(data))
        }
    )
)

main.R

box::use(dt = data.table)
box::use(./dev/`na-omit`/`r6-class`[ TestClass ])

DT = dt$data.table(
    x=c(1,NaN,NA,3),
    y=c(NA_integer_, 1:3),
    z=c("a", NA_character_, "b", "c")
)

test <- TestClass$new()

test$some_method(DT)

r$> test$some_method(DT)
Error in na.omit(data) : could not find function "na.omit"

R version

r$> version
               _                           
platform       aarch64-apple-darwin23.4.0  
arch           aarch64                     
os             darwin23.4.0                
system         aarch64, darwin23.4.0       
status                                     
major          4                           
minor          4.1                         
year           2024                        
month          06                          
day            14                          
svn rev        86737                       
language       R                           
version.string R version 4.4.1 (2024-06-14)
nickname       Race for Your Life  

r$> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin23.4.0
Running under: macOS Sonoma 14.4.1

Matrix products: default
BLAS:   /opt/homebrew/Cellar/openblas/0.3.27/lib/libopenblasp-r0.3.27.dylib 
LAPACK: /opt/homebrew/Cellar/r/4.4.1/lib/R/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

loaded via a namespace (and not attached):
 [1] compiler_4.4.1    R6_2.5.1          cli_3.6.3         tools_4.4.1      
 [5] yaml_2.3.10       box_1.2.0         data.table_1.15.4 jsonlite_1.8.8   
 [9] rlang_1.1.4       renv_1.0.7       

r$>

### ‘box’ version

1.2.0

[ArcadeAntics]

na.omit is part of package:stats, you'll have to add

box::use(
    stats[na.omit]
)

[dereckmezquita]

@ArcadeAntics yes indeed. However, data.table provides it's own version of na.omit which is an S3 method that applies to data.table objects. This version of na.omit is written in C and significantly faster.

https://rdatatable.gitlab.io/data.table/reference/na.omit.data.table.html

The issue is: I believe these are attached on package load event and thus not exported.

[klmr]

‘data.table’ does not provide its own na.omit function. Instead, it registers an S3 method for na.omit for classes of type data.table.

You can use it by calling na.omit from ‘stats’ normally:

box::use(
  dt = data.table,
  stats[na.omit],
)

trace(data.table:::na.omit.data.table, quote(message('called na.omit.data.table')))

na.omit(dt$data.table(x = 1 : 5))

This will print “called na.omit.data.table”, showing that we called the expected S3 method.

(Please see #80 for possible limitations when working with ‘data.table’ inside modules, since ‘data.table’ hard-codes support for packages and certain functionalities it contains may break when used in other contexts due limitations in its data.table-awareness detection. However, in general it should work.)

[dereckmezquita]

Okay thank you both then @klmr @ArcadeAntics!

I was wrong and had not understood how this works. Thank you for the trace example I'll be using that.