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saezlab / OmnipathR

R client for the OmniPath web service
https://r.omnipathdb.org/
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`kegg_pathway_annotations` fails with uninformative error #113

Open danhalligan-la opened 3 weeks ago

danhalligan-la commented 3 weeks ago

Note sure exactly what is going wrong here, so have struggled to debug.

> library("OmnipathR")
> kegg_pathway_annotations()
[2024-11-03 10:14:46] [SUCCESS] [OmnipathR] KEGG (www.genome.jp): loaded 555 records from cache
[2024-11-03 10:14:47] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 2 records
Error in `pmap()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'rename' applied to an object of class "list"
Run `rlang::last_trace()` to see where the error occurred.

Here's the last_trace

> rlang::last_trace()
<error/purrr_error_indexed>
Error in `pmap()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'rename' applied to an object of class "list"
---
Backtrace:
     ▆
  1. ├─OmnipathR::kegg_pathway_annotations()
  2. │ └─pathways %<>% ...
  3. ├─. %||% kegg_pathways_download()
  4. ├─OmnipathR::kegg_pathways_download()
  5. │ └─... %>% kegg_simplify(simplify = simplify)
  6. ├─OmnipathR:::kegg_simplify(., simplify = simplify)
  7. ├─dplyr::bind_rows(.)
  8. │ └─rlang::list2(...)
  9. ├─purrr::pmap(...)
 10. │ └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
 11. │   ├─purrr:::with_indexed_errors(...)
 12. │   │ └─base::withCallingHandlers(...)
 13. │   ├─purrr:::call_with_cleanup(...)
 14. │   └─OmnipathR (local) .f(id = .l[[1L]][[i]], name = .l[[2L]][[i]], ...)
 15. │     ├─... %>% ...
 16. │     └─OmnipathR::kegg_pathway_download(...)
 17. │       └─OmnipathR::kegg_process(entries, relations, max_expansion, simplify)
 18. │         └─OmnipathR::get_db("up_gs", organism = 9606)
 19. │           └─OmnipathR::load_db(key, param = param)
 20. │             ├─rlang::exec(loader, !!!param)
 21. │             └─OmnipathR (local) `<fn>`(organism = 9606, to = "genesymbol")
 22. │               └─... %>% trim_and_distinct
 23. ├─OmnipathR:::null_or_call(., mutate, pathway = name, pathway_id = id)
 24. │ └─value %>% is.null %>% if (NULL) fun(value, ...)
 25. ├─OmnipathR:::trim_and_distinct(.)
 26. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 27. ├─dplyr::distinct(.)
 28. ├─dplyr::mutate(., across(everything(), str_trim))
 29. ├─dplyr::filter(., !is.na(From) & !is.na(To))
 30. ├─tidyr::separate_rows(., To, sep = "[; ]")
 31. ├─tidyr::separate_rows(., From, sep = "[; ]")
 32. ├─dplyr::mutate(., From = strip_semicol(From), To = strip_semicol(To))
 33. └─dplyr::rename(., From = 1, To = 2)
Run rlang::last_trace(drop = FALSE) to see 4 hidden frames.

This is with the latest (GitHub) version: 3.13.28. Here's the session info.

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] OmnipathR_3.13.28

loaded via a namespace (and not attached):
 [1] xfun_0.49           tzdb_0.4.0          vctrs_0.6.5        
 [4] tools_4.4.2         generics_0.1.3      curl_5.2.3         
 [7] tibble_3.2.1        fansi_1.0.6         RSQLite_2.3.7      
[10] blob_1.2.4          pkgconfig_2.0.3     R.oo_1.27.0        
[13] checkmate_2.3.2     readxl_1.4.3        lifecycle_1.0.4    
[16] compiler_4.4.2      stringr_1.5.1       progress_1.2.3     
[19] htmltools_0.5.8.1   yaml_2.3.10         later_1.3.2        
[22] pillar_1.9.0        crayon_1.5.3        tidyr_1.3.1        
[25] R.utils_2.12.3      cachem_1.1.0        tidyselect_1.2.1   
[28] rvest_1.0.4         zip_2.3.1           digest_0.6.37      
[31] stringi_1.8.4       dplyr_1.1.4         purrr_1.0.2        
[34] fastmap_1.2.0       cli_3.6.3           logger_0.4.0       
[37] magrittr_2.0.3      XML_3.99-0.17       utf8_1.2.4         
[40] readr_2.1.5         withr_3.0.2         prettyunits_1.2.0  
[43] backports_1.5.0     rappdirs_0.3.3      bit64_4.5.2        
[46] lubridate_1.9.3     timechange_0.3.0    rmarkdown_2.28     
[49] httr_1.4.7          igraph_2.1.1        bit_4.5.0          
[52] cellranger_1.1.0    R.methodsS3_1.8.2   hms_1.1.3          
[55] memoise_2.0.1       evaluate_1.0.1      knitr_1.48         
[58] rlang_1.1.4         Rcpp_1.0.13         glue_1.8.0         
[61] DBI_1.2.3           selectr_0.4-2       BiocManager_1.30.25
[64] xml2_1.3.6          renv_1.0.11         vroom_1.6.5        
[67] jsonlite_1.8.9      R6_2.5.1