issue with get_progeny

[costibonf]

Hi! I had some issue with get_progeny() function.
This is the warning:

[2024-10-31 16:40:37] [WARN]    [OmnipathR] [decoupleR] Failed to check the list of available resources in OmniPath. Proceeding anyways.
[2024-10-31 16:40:39] [WARN]    [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2024-10-31 16:40:39] [ERROR]   [OmnipathR] [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log.
Errore in value[[3L]](cond) : 
  [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log.
In aggiunta: Messaggi di avvertimento:
1: In OmnipathR::get_annotation_resources() :
  'OmnipathR::get_annotation_resources' è deprecato.
Usare 'annotation_resources' al suo posto.
Si veda help("Deprecated")
2: In value[[3L]](cond) :
  [decoupleR] Failed to check the list of available resources in OmniPath. Proceeding anyways.
3: In OmnipathR::import_omnipath_annotations(resources = name, ...,  :
  'OmnipathR::import_omnipath_annotations' è deprecato.
Usare 'annotations' al suo posto.
Si veda help("Deprecated")

How can I proceed?

There my sessionInfo():

R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=Italian_Italy.utf8  LC_CTYPE=Italian_Italy.utf8    LC_MONETARY=Italian_Italy.utf8
[4] LC_NUMERIC=C                   LC_TIME=Italian_Italy.utf8    

time zone: Europe/Rome
tzcode source: internal

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

other attached packages:
[1] remotes_2.5.0     decoupleR_2.10.0  OmnipathR_3.13.28

loaded via a namespace (and not attached):
 [1] xfun_0.48           lattice_0.22-6      tzdb_0.4.0          vctrs_0.6.5         tools_4.4.1        
 [6] generics_0.1.3      parallel_4.4.1      curl_5.2.3          tibble_3.2.1        fansi_1.0.6        
[11] RSQLite_2.3.7       blob_1.2.4          pkgconfig_2.0.3     R.oo_1.26.0         Matrix_1.7-0       
[16] checkmate_2.3.2     readxl_1.4.3        lifecycle_1.0.4     compiler_4.4.1      stringr_1.5.1      
[21] progress_1.2.3      codetools_0.2-20    htmltools_0.5.8.1   yaml_2.3.10         later_1.3.2        
[26] pillar_1.9.0        crayon_1.5.3        tidyr_1.3.1         R.utils_2.12.3      BiocParallel_1.38.0
[31] cachem_1.1.0        parallelly_1.38.0   tidyselect_1.2.1    rvest_1.0.4         zip_2.3.1          
[36] digest_0.6.37       stringi_1.8.4       dplyr_1.1.4         purrr_1.0.2         grid_4.4.1         
[41] fastmap_1.2.0       cli_3.6.3           logger_0.4.0        magrittr_2.0.3      XML_3.99-0.17      
[46] utf8_1.2.4          broom_1.0.7         readr_2.1.5         withr_3.0.2         prettyunits_1.2.0  
[51] backports_1.5.0     rappdirs_0.3.3      bit64_4.5.2         lubridate_1.9.3     timechange_0.3.0   
[56] rmarkdown_2.28      httr_1.4.7          igraph_2.1.1        bit_4.5.0           cellranger_1.1.0   
[61] R.methodsS3_1.8.2   hms_1.1.3           memoise_2.0.1       evaluate_1.0.1      knitr_1.48         
[66] rlang_1.1.4         Rcpp_1.0.13         glue_1.7.0          DBI_1.2.3           selectr_0.4-2      
[71] xml2_1.3.6          vroom_1.6.5         rstudioapi_0.17.1   jsonlite_1.8.9      R6_2.5.1  

[deeenes]

Hi, The warnings are not related to the error, we'll fix those in decoupleR. The error itself is hidden by the exception handling in decoupleR. To find out what is the real error, you can call the annotations function from OmnipathR directly, see the real error message, and check the traceback and the log:

library(OmnipathR)

progeny <- annotations(resources = 'PROGENy', wide = TRUE)

# the error might happen here

# please show us the traceback:
traceback()

# and the contents of the OmnipathR log:
omnipath_logfile()