mutate error when downloading dorothea

[roskcl]

Hello,

I am trying to download the dorothea database on R 4.2.2 but I am getting the following error. Could you please let me know how I can solve it? It was working before.

Thank you very much!

Best.

net <- get_dorothea(organism='mouse', levels=c('A', 'B', 'C')) Error in mutate(): ℹ In argument: n_references = ifelse(...). Caused by error in map(): ℹ In index: 1. Caused by error in .f(): ! Arguments in ... must be passed by position, not name. ✖ Problematic argument: • outsep = outsep Run rlang::last_error() to see where the error occurred.

rlang::last_error() <error/dplyr:::mutate_error> Error in mutate(): ℹ In argument: n_references = ifelse(...). Caused by error in map(): ℹ In index: 1.

Backtrace:

1. decoupleR::get_dorothea(...)
2. purrr (local) <fn>(<rlb_rr__>)

3. cli::cli_abort(...) Caused by error in .f(): ! Arguments in ... must be passed by position, not name. ✖ Problematic argument: • outsep = outsep

   Backtrace:

4. decoupleR::get_dorothea(...)
5. purrr::map(., method, ...)
6. purrr:::map_("list", .x, .f, ..., .progress = .progress)
7. dplyr (local) .f(.x[[i]], ...) Run rlang::last_trace() to see the full context.

rlang::last_trace() <error/dplyr:::mutate_error> Error in mutate(): ℹ In argument: n_references = ifelse(...). Caused by error in map(): ℹ In index: 1.

Backtrace: ▆

1. ├─decoupleR::get_dorothea(...)
2. │ ├─... %>% ...
3. │ └─OmnipathR::import_dorothea_interactions(...)
4. │ └─OmnipathR:::import_omnipath(...)
5. │ └─result %<>% count_references
6. ├─dplyr::select(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr::mutate(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::distinct(...)
11. ├─dplyr::select(...)
12. ├─OmnipathR:::count_references(.)
13. │ └─data %>% ...
14. ├─dplyr::mutate(...)
15. ├─dplyr:::mutate.data.frame(...)
16. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
17. │ ├─base::withCallingHandlers(...)
18. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
19. │ └─mask$eval_all_mutate(quo)
20. │ └─dplyr (local) eval()
21. ├─base::ifelse(...)
22. ├─OmnipathR:::strip_resource_labels(., inplace = FALSE, method = n_distinct)
23. │ └─OmnipathR:::split_unique_join(...)
24. │ └─OmnipathR:::split_apply(x = x, method = method, sep = sep, outsep = outsep)
25. │ └─x %>% strsplit(sep) %>% map(method, ...) %>% unlist()
26. ├─base::unlist(.)
27. ├─purrr::map(., method, ...)
28. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
29. │ ├─purrr:::with_indexed_errors(...)
30. │ │ └─base::withCallingHandlers(...)
31. │ ├─purrr:::call_with_cleanup(...)
32. │ └─dplyr (local) .f(.x[[i]], ...)
33. │ └─rlang::check_dots_unnamed()
34. │ └─rlang:::action_dots(...)
35. │ ├─base (local) try_dots(...)
36. │ └─rlang (local) action(...)
37. │ └─rlang:::signal_abort(cnd, .file)
38. │ └─base::signalCondition(cnd)
39. ├─purrr (local) <fn>(<rlb_rr__>)
40. │ └─cli::cli_abort(...)
41. │ └─rlang::abort(...)
42. │ └─rlang:::signal_abort(cnd, .file)
43. │ └─base::signalCondition(cnd)
44. └─dplyr (local) <fn>(<prrr_rr_>)

45. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Caused by error in .f(): ! Arguments in ... must be passed by position, not name. ✖ Problematic argument: • outsep = outsep

    Backtrace: ▆

46. ├─decoupleR::get_dorothea(...)
47. │ ├─... %>% ...
48. │ └─OmnipathR::import_dorothea_interactions(...)
49. │ └─OmnipathR:::import_omnipath(...)
50. │ └─result %<>% count_references
51. ├─dplyr::select(...)
52. ├─dplyr::mutate(...)
53. ├─dplyr::mutate(...)
54. ├─dplyr::mutate(...)
55. ├─dplyr::distinct(...)
56. ├─dplyr::select(...)
57. ├─OmnipathR:::count_references(.)
58. │ └─data %>% ...
59. ├─dplyr::mutate(...)
60. ├─dplyr:::mutate.data.frame(...)
61. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
62. │ ├─base::withCallingHandlers(...)
63. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
64. │ └─mask$eval_all_mutate(quo)
65. │ └─dplyr (local) eval()
66. ├─base::ifelse(...)
67. ├─OmnipathR:::strip_resource_labels(., inplace = FALSE, method = n_distinct)
68. │ └─OmnipathR:::split_unique_join(...)
69. │ └─OmnipathR:::split_apply(x = x, method = method, sep = sep, outsep = outsep)
70. │ └─x %>% strsplit(sep) %>% map(method, ...) %>% unlist()
71. ├─base::unlist(.)
72. └─purrr::map(., method, ...)
73. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
74. ├─purrr:::with_indexed_errors(...)
75. │ └─base::withCallingHandlers(...)
76. ├─purrr:::call_with_cleanup(...)
77. └─dplyr (local) .f(.x[[i]], ...)
78. └─rlang::check_dots_unnamed()
79. └─rlang:::action_dots(...)
80. ├─base (local) try_dots(...)
81. └─rlang (local) action(...)

[PauBadiaM]

Hi @roskcl

It looks like there is an issue coming from OmniPath, could you install its latest version from GitHub and try again?

remotes::install_github("saezlab/OmnipathR")

[roskcl]

Yes! That solved the issue, thanks! :)