Brief description of the problem
I have an R script that is sourcing a custom function. The custom function contains a loop that manipulates a data frame and returns the manipulated version of the data frame. I am using the slice() function to select particular rows of the data frame e.g.
test_alpha_1 <- as.data.frame(TCR_chains) %>%
slice(row_inner) %>%
select(TRAV, TRAJ, TRAC, CDR3alpha, CDR3alpha_nt) %>%
as.character()
row_inner is a numeric
My code works completely fine when I run it locally on my computer and also when I run it on the head node of the server, but when I run it in a pipeline, I get the following error. However this error only occurs for 9/12 of my samples:
Error: `env` must be an environment
Backtrace:
█
1. ├─rmarkdown::render(...)
2. │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
3. │ └─knitr:::process_file(text, output)
4. │ ├─base::withCallingHandlers(...)
5. │ ├─knitr:::process_group(group)
6. │ └─knitr:::process_group.block(group)
7. │ └─knitr:::call_block(x)
8. │ └─knitr:::block_exec(params)
9. │ └─knitr:::eng_r(options)
10. │ ├─knitr:::in_dir(...)
11. │ └─knitr:::evaluate(...)
12. │ └─evaluate::evaluate(...)
13. │ └─evaluate:::evaluate_call(...)
14. │ ├─evaluate:::timing_fn(...)
15. │ ├─base:::handle(...)
16. │ ├─base::withCallingHandlers(...)
17. │ ├─base::withVisible(eval(expr, envir, enclos))
18. │ └─base::eval(expr, envir, enclos)
19. │ └─base::eval(expr, envir, enclos)
20. ├─global::alpha_beta_nt_clonotypes(TCR_chains)
21. │ └─`%>%`(...)
22. ├─dplyr::select(., TRAV_2, TRAJ_2, TRAC_2, CDR3alpha_2, CDR3alpha_nt_2)
23. ├─dplyr::slice(., row_inner)
24. └─dplyr:::slice.data.frame(., row_inner)
25. └─dplyr:::slice_rows(.data, ...)
26. └─rlang::enquos(...)
27. └─rlang:::endots(...)
28. └─rlang:::map(...)
29. └─base::lapply(.x, .f, ...)
30. └─rlang:::FUN(X[[i]], ...)
31. └─rlang::splice(...)
Execution halted
Looking at the code for the slice() function, I have noticed this piece of code within slice_rows():
mask <- DataMask$new(.data, caller_env())
I am wondering whether the error may be something to do with the caller_env() part. I am happy to share my scripts privately if it helps.
Many thanks,
Lucy
Conda environment:
# Name Version Build Channel
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