Hello
I worked on R environment of parsemsf package. I have no idea of this error.
Thank you in advance for your great help!
Best,
Yue
>library(parsemsf)
>area_table <- make_area_table("LD-CS-150113_OstromR_OR_AC2_enriched.msf")
Error: Can't subset columns that don't exist.
x Column `PEP` doesn't exist.
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning messages:
1: `chr_along()` is deprecated as of rlang 0.2.0.
This warning is displayed once per session.
2: `new_overscope()` is deprecated as of rlang 0.2.0.
Please use `new_data_mask()` instead.
This warning is displayed once per session.
3: `overscope_eval_next()` is deprecated as of rlang 0.2.0.
Please use `eval_tidy()` with a data mask instead.
This warning is displayed once per session.
4: `overscope_clean()` is deprecated as of rlang 0.2.0.
This warning is displayed once per session.
> rlang::last_error()
<error/vctrs_error_subscript_oob>
Can't subset columns that don't exist.
x Column `PEP` doesn't exist.
Backtrace:
1. parsemsf::quantitate(...)
4. parsemsf::make_area_table(reps[[i]])
5. parsemsf::make_pep_table(msf_file, min_conf, prot_regex, collapse)
7. dplyr:::select_.grouped_df(...)
8. dplyr:::select.grouped_df(.data, !!!dots)
9. dplyr:::.select_grouped_df(.data, !!!enquos(...), notify = TRUE)
10. tidyselect::vars_select(tbl_vars(.data), !!!enquos(...))
11. tidyselect:::eval_select_impl(...)
19. tidyselect:::vars_select_eval(...)
20. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
21. tidyselect:::eval_c(expr, data_mask, context_mask)
22. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
23. tidyselect:::walk_data_tree(new, data_mask, context_mask)
24. tidyselect:::as_indices_sel_impl(...)
25. tidyselect:::as_indices_impl(x, vars, strict = strict)
26. tidyselect:::chr_as_locations(x, vars)
27. vctrs::vec_as_location(x, n = length(vars), names = vars)
29. vctrs:::stop_subscript_oob(...)
30. vctrs:::stop_subscript(...)
Run `rlang::last_trace()` to see the full context.
> rlang::last_trace()
<error/vctrs_error_subscript_oob>
Can't subset columns that don't exist.
x Column `PEP` doesn't exist.
Backtrace:
█
1. ├─parsemsf::quantitate(...)
2. │ ├─`%>%`(...)
3. │ └─parsemsf::make_area_table(reps[[i]])
4. │ └─parsemsf::make_pep_table(msf_file, min_conf, prot_regex, collapse)
5. │ ├─dplyr::select_(pep_table, .dots = setNames(old_names, new_names))
6. │ └─dplyr:::select_.grouped_df(...)
7. │ └─dplyr:::select.grouped_df(.data, !!!dots)
8. │ └─dplyr:::.select_grouped_df(.data, !!!enquos(...), notify = TRUE)
9. │ └─tidyselect::vars_select(tbl_vars(.data), !!!enquos(...))
10. │ └─tidyselect:::eval_select_impl(...)
11. │ ├─tidyselect:::with_subscript_errors(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base:::doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─tidyselect:::instrument_base_errors(expr)
17. │ │ └─base::withCallingHandlers(...)
18. │ └─tidyselect:::vars_select_eval(...)
19. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
20. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
21. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
22. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
23. │ └─tidyselect:::as_indices_sel_impl(...)
24. │ └─tidyselect:::as_indices_impl(x, vars, strict = strict)
25. │ └─tidyselect:::chr_as_locations(x, vars)
26. │ └─vctrs::vec_as_location(x, n = length(vars), names = vars)
27. │ └─(function () ...
28. │ └─vctrs:::stop_subscript_oob(...)
29. │ └─vctrs:::stop_subscript(...)
30. └─dplyr::mutate_(., .dots = setNames(list(i), c("tech_rep")))