agalhoz / wppi Goto Github PK

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.7

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] wppi_1.6.0          BiocManager_1.30.19

loaded via a namespace (and not attached):
 [1] progress_1.2.2    tidyselect_1.2.0  xfun_0.37         purrr_1.0.1       lattice_0.20-45   vctrs_0.5.2       generics_0.1.3   
 [8] htmltools_0.5.4   yaml_2.3.7        utf8_1.2.3        rlang_1.0.6       later_1.3.0       pillar_1.8.1      glue_1.6.2       
[15] withr_2.5.0       rappdirs_0.3.3    bit64_4.0.5       readxl_1.4.2      lifecycle_1.0.3   stringr_1.5.0     cellranger_1.1.0 
[22] rvest_1.0.3       evaluate_0.20     knitr_1.42        tzdb_0.3.0        fastmap_1.1.0     curl_5.0.0        fansi_1.0.4      
[29] Rcpp_1.0.10       readr_2.1.3       backports_1.4.1   checkmate_2.1.0   vroom_1.6.1       jsonlite_1.8.4    bit_4.0.5        
[36] hms_1.1.2         digest_0.6.31     stringi_1.7.12    dplyr_1.1.0       grid_4.2.0        OmnipathR_3.6.0   cli_3.6.0        
[43] tools_4.2.0       bitops_1.0-7      magrittr_2.0.3    logger_0.2.2      RCurl_1.98-1.10   tibble_3.1.8      crayon_1.5.2     
[50] tidyr_1.3.0       pkgconfig_2.0.3   ellipsis_0.3.2    Matrix_1.5-3      xml2_1.3.3        prettyunits_1.1.1 rmarkdown_2.20   
[57] httr_1.4.4        rstudioapi_0.14   R6_2.5.1          igraph_1.3.5      compiler_4.2.0   

trace(score_candidate_genes_from_PPI(genes_interest))
[2023-02-10 11:03:38] [INFO]    [wppi] Executing WPPI workflow.
[2023-02-10 11:03:38] [INFO]    [wppi] Collecting database knowledge.
Error in `mutate()`:
ℹ In argument: `across(everything(), na_if, "-")`.
Caused by error in `across()`:
! Can't compute column `entrez_gene_id`.
Caused by error in `fn()`:
! Can't convert `y` <character> to match type of `x` <double>.

rlang::last_error()
<error/dplyr:::mutate_error>
Error in `mutate()`:
ℹ In argument: `across(everything(), na_if, "-")`.
Caused by error in `across()`:
! Can't compute column `entrez_gene_id`.
---
Backtrace:
  1. base::trace(score_candidate_genes_from_PPI(genes_interest))
 41. dplyr (local) `<fn>`(`<vctrs_r_>`)
Caused by error in `fn()`:
! Can't convert `y` <character> to match type of `x` <double>.
---
Backtrace:
  1. base::trace(score_candidate_genes_from_PPI(genes_interest))
 25. dplyr::across(everything(), na_if, "-")
 27. dplyr (local) fn(col, ...)

<error/dplyr:::mutate_error>
Error in `**mutate()**`:
ℹ In argument: `across(everything(), na_if, "-")`.
Caused by error in `**across()**`:
! Can't compute column `entrez_gene_id`.
---
Backtrace:
     ▆
  1. ├─base::trace(score_candidate_genes_from_PPI(genes_interest))
  2. ├─wppi::score_candidate_genes_from_PPI(genes_interest)
  3. │ ├─databases %||% ...
  4. │ └─wppi::wppi_data(...)
  5. │   └─wppi::wppi_hpo_data()
  6. │     ├─... %>% distinct()
  7. │     └─OmnipathR::hpo_download()
  8. │       └─... %T>% load_success()
  9. ├─dplyr::distinct(.)
 10. ├─dplyr::select(...)
 11. ├─OmnipathR:::load_success(.)
 12. │ └─from_cache %<>% if_null(data %>% is_from_cache)
 13. ├─OmnipathR:::if_null(., data %>% is_from_cache)
 14. │ └─value1 %>% is.null %>% if (value2) value1
 15. ├─data %>% is_from_cache
 16. ├─OmnipathR:::is_from_cache(.)
 17. │ └─obj %>% attr("origin") %>% ...
 18. ├─dplyr::mutate(., across(everything(), na_if, "-"))
 19. ├─dplyr:::mutate.data.frame(., across(everything(), na_if, "-"))
 20. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
 21. │   ├─base::withCallingHandlers(...)
 22. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 23. │     └─mask$eval_all_mutate(quo)
 24. │       └─dplyr (local) eval()
 25. ├─dplyr::across(everything(), na_if, "-")
 26. │ ├─base::withCallingHandlers(...)
 27. │ └─dplyr (local) fn(col, ...)
 28. │   └─vctrs::vec_cast(x = y, to = x, x_arg = "y", to_arg = "x")
 29. ├─vctrs (local) `<fn>`()
 30. │ └─vctrs::vec_default_cast(...)
 31. │   ├─base::withRestarts(...)
 32. │   │ └─base (local) withOneRestart(expr, restarts[[1L]])
 33. │   │   └─base (local) doWithOneRestart(return(expr), restart)
 34. │   └─vctrs::stop_incompatible_cast(...)
 35. │     └─vctrs::stop_incompatible_type(...)
 36. │       └─vctrs:::stop_incompatible(...)
 37. │         └─vctrs:::stop_vctrs(...)
 38. │           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
 39. │             └─rlang:::signal_abort(cnd, .file)
 40. │               └─base::signalCondition(cnd)
 41. ├─dplyr (local) `<fn>`(`<vctrs_r_>`)
 42. │ └─rlang::abort(bullets, call = error_call, parent = cnd)
 43. │   └─rlang:::signal_abort(cnd, .file)
 44. │     └─base::signalCondition(cnd)
 45. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
 46.   └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Caused by error in `fn()`:
! Can't convert `y` <character> to match type of `x` <double>.
---
Backtrace:
     ▆
  1. ├─base::trace(score_candidate_genes_from_PPI(genes_interest))
  2. ├─wppi::score_candidate_genes_from_PPI(genes_interest)
  3. │ ├─databases %||% ...
  4. │ └─wppi::wppi_data(...)
  5. │   └─wppi::wppi_hpo_data()
  6. │     ├─... %>% distinct()
  7. │     └─OmnipathR::hpo_download()
  8. │       └─... %T>% load_success()
  9. ├─dplyr::distinct(.)
 10. ├─dplyr::select(...)
 11. ├─OmnipathR:::load_success(.)
 12. │ └─from_cache %<>% if_null(data %>% is_from_cache)
 13. ├─OmnipathR:::if_null(., data %>% is_from_cache)
 14. │ └─value1 %>% is.null %>% if (value2) value1
 15. ├─data %>% is_from_cache
 16. ├─OmnipathR:::is_from_cache(.)
 17. │ └─obj %>% attr("origin") %>% ...
 18. ├─dplyr::mutate(., across(everything(), na_if, "-"))
 19. ├─dplyr:::mutate.data.frame(., across(everything(), na_if, "-"))
 20. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
 21. │   ├─base::withCallingHandlers(...)
 22. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 23. │     └─mask$eval_all_mutate(quo)
 24. │       └─dplyr (local) eval()
 25. ├─dplyr::across(everything(), na_if, "-")
 26. │ ├─base::withCallingHandlers(...)
 27. │ └─dplyr (local) fn(col, ...)
 28. │   └─vctrs::vec_cast(x = y, to = x, x_arg = "y", to_arg = "x")
 29. └─vctrs (local) `<fn>`()
 30.   └─vctrs::vec_default_cast(...)
 31.     ├─base::withRestarts(...)
 32.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
 33.     │   └─base (local) doWithOneRestart(return(expr), restart)
 34.     └─vctrs::stop_incompatible_cast(...)
 35.       └─vctrs::stop_incompatible_type(...)
 36.         └─vctrs:::stop_incompatible(...)
 37.           └─vctrs:::stop_vctrs(...)
 38.             └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))