Can't fetch Dorothea regulons

[SophieGaiani]

Hello!

I try to fetch Dorothea regulons, but I encounter this error message.

library(decoupleR)

get_dorothea(organism = "human", levels = "A")
#> 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
#> Backtrace:
#>      ▆
#>   1. ├─decoupleR::get_dorothea(organism = "human", levels = "A")
#>   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(...)

xfun::session_info()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 18.04.6 LTS
#> 
#> Locale:
#>   LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>   LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>   LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>   LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>   LC_ADDRESS=C               LC_TELEPHONE=C            
#>   LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> Package version:
#>   askpass_1.1        backports_1.4.1    base64enc_0.1.3   
#>   bit_4.0.5          bit64_4.0.5        broom_1.0.1       
#>   bslib_0.4.1        cachem_1.0.6       callr_3.7.3       
#>   cellranger_1.1.0   checkmate_2.1.0    cli_3.4.1         
#>   clipr_0.8.0        colorspace_2.0.3   compiler_4.2.1    
#>   cpp11_0.4.3        crayon_1.5.2       curl_4.3.3        
#>   decoupleR_2.4.0    digest_0.6.30      dplyr_1.1.1       
#>   ellipsis_0.3.2     evaluate_0.18      fansi_1.0.3       
#>   farver_2.1.1       fastmap_1.1.0      fs_1.5.2          
#>   generics_0.1.3     ggplot2_3.4.0      glue_1.6.2        
#>   graphics_4.2.1     grDevices_4.2.1    grid_4.2.1        
#>   gtable_0.3.1       highr_0.9          hms_1.1.2         
#>   htmltools_0.5.3    httr_1.4.4         igraph_1.3.5      
#>   isoband_0.2.6      jquerylib_0.1.4    jsonlite_1.8.3    
#>   knitr_1.41         labeling_0.4.2     later_1.3.0       
#>   lattice_0.20-45    lifecycle_1.0.3    logger_0.2.2      
#>   magrittr_2.0.3     MASS_7.3.58.1      Matrix_1.5-3      
#>   memoise_2.0.1      methods_4.2.1      mgcv_1.8.40       
#>   mime_0.12          munsell_0.5.0      nlme_3.1.159      
#>   OmnipathR_3.7.0    openssl_2.0.4      pillar_1.8.1      
#>   pkgconfig_2.0.3    prettyunits_1.1.1  processx_3.8.0    
#>   progress_1.2.2     ps_1.7.2           purrr_1.0.1       
#>   R6_2.5.1           rappdirs_0.3.3     RColorBrewer_1.1.3
#>   Rcpp_1.0.9         readr_2.1.3        readxl_1.4.1      
#>   rematch_1.0.1      reprex_2.0.2       rlang_1.1.0       
#>   rmarkdown_2.19     rstudioapi_0.14    rvest_1.0.3       
#>   sass_0.4.4         scales_1.2.1       selectr_0.4.2     
#>   splines_4.2.1      stats_4.2.1        stringi_1.7.8     
#>   stringr_1.4.1      sys_3.4.1          tibble_3.2.1      
#>   tidyr_1.2.1        tidyselect_1.2.0   tinytex_0.43      
#>   tools_4.2.1        tzdb_0.3.0         utf8_1.2.2        
#>   utils_4.2.1        vctrs_0.6.1        viridisLite_0.4.1 
#>   vroom_1.6.0        withr_2.5.0        xfun_0.35         
#>   xml2_1.3.3         yaml_2.3.6

^{Created on 2023-07-19 with reprex v2.0.2}

Thanks for your package I use it a lot! Could you help me please to solve this issue? Best Sophie

[PauBadiaM]

Hi @SophieGaiani

You need to update both decoupleR and OmnipathR:

remotes::install_github('saezlab/omnipathr')
remotes::install_github('saezlab/decoupleR')

Let me know if this works

[SophieGaiani]

Hi Pau, It works ! Thank you very much ! Best

De : Pau Badia i Mompel @.> Envoyé : jeudi 20 juillet 2023 16:02 À : saezlab/decoupleR @.> Cc : COURTADE-GAIANI Sophie IDRS @.>; Mention @.> Objet : Re: [saezlab/decoupleR] Can't fetch Dorothea regulons (Issue #90)

CAUTION: This email originated from outside the company.

Hi @SophieGaianihttps://github.com/SophieGaiani

You need to update both decoupleR and OmnipathR:

remotes::install_github('saezlab/omnipathr')

remotes::install_github('saezlab/decoupleR')

Let me know if this works

- Reply to this email directly, view it on GitHubhttps://github.com/saezlab/decoupleR/issues/90#issuecomment-1643984838, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUHLB7HYUWD27HSGBJT4RBLXRE25FANCNFSM6AAAAAA2PP3MMM. You are receiving this because you were mentioned.Message ID: @.**@.>>