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")))



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