decoupleR::get_progeny fails

[ZZQ-1117]

When I use decoupleR to obtain the progeny network data, the following error occurs：

net <- decoupleR::get_progeny(organism = 'mouse', top = 500)
[2025-08-22 18:46:14] [WARN] [OmnipathR] [decoupleR] Failed to check the list of available resources in OmniPath. Proceeding anyways.
[2025-08-22 18:46:14] [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.
[2025-08-22 18:46:15] [ERROR] [OmnipathR] [decoupleR] Failed to download annotation resource PROGENy from OmniPath. For more information, see the OmnipathR log.
Error in value[3L] :
[decoupleR] Failed to download annotation resource PROGENy from OmniPath. For more information, see the OmnipathR log.

> packageVersion("OmnipathR")
[1] ‘3.17.4’
> packageVersion("decoupleR")
[1] ‘2.9.7’

Traceback

> traceback()
25: stop(msg)
24: value[[3L]](cond)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(OmnipathR::static_table(query = "annotations", resource = name, 
        organism = organism), error = function(e) {
        msg <- sprintf(paste0("[decoupleR] Failed to download annotation resource `%s` ", 
            "from OmniPath. For more information, see the OmnipathR log."), 
            name)
        OmnipathR::omnipath_msg("error", msg)
        stop(msg)
    })
20: value[[3L]](cond)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(OmnipathR::import_omnipath_annotations(resources = name, 
        ..., wide = TRUE), error = function(e) {
        tryCatch(OmnipathR::static_table(query = "annotations", resource = name, 
            organism = organism), error = function(e) {
            msg <- sprintf(paste0("[decoupleR] Failed to download annotation resource `%s` ", 
                "from OmniPath. For more information, see the OmnipathR log."), 
                name)
            OmnipathR::omnipath_msg("error", msg)
            stop(msg)
        })
    })
16: tryCatch(OmnipathR::import_omnipath_annotations(resources = name, 
        ..., wide = TRUE), error = function(e) {
        tryCatch(OmnipathR::static_table(query = "annotations", resource = name, 
            organism = organism), error = function(e) {
            msg <- sprintf(paste0("[decoupleR] Failed to download annotation resource `%s` ", 
                "from OmniPath. For more information, see the OmnipathR log."), 
                name)
            OmnipathR::omnipath_msg("error", msg)
            stop(msg)
        })
    }) %>% {
        if (organism != 9606L) 
            OmnipathR::orthology_translate_column(., "uniprot", target_organism = organism, 
                replace = TRUE) %>% OmnipathR::translate_ids(., uniprot, 
                genesymbol, organism = organism)
        else .
    }
15: get_resource("PROGENy", organism = organism)
14: dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
13: dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
12: dplyr::select(., genesymbol, p_value, pathway, weight)
11: dplyr::group_by(., pathway)
10: dplyr::group_split(.)
9: vctrs_vec_compat(.x, .purrr_user_env)
8: map_("list", .x, .f, ..., .progress = .progress)
7: purrr::map(., function(df) {
       df %>% dplyr::arrange(p_value) %>% head(top)
   })
6: list2(...)
5: dplyr::bind_rows(.)
4: dplyr::select(., pathway, genesymbol, weight, p_value)
3: rlang::set_names(., c("source", "target", "weight", "p_value"))
2: get_resource("PROGENy", organism = organism) %>% dplyr::distinct(pathway, 
       genesymbol, .keep_all = TRUE) %>% dplyr::mutate(weight = as.double(weight), 
       p_value = as.double(p_value)) %>% dplyr::select(genesymbol, 
       p_value, pathway, weight) %>% dplyr::group_by(pathway) %>% 
       dplyr::group_split() %>% purrr::map(function(df) {
       df %>% dplyr::arrange(p_value) %>% head(top)
   }) %>% dplyr::bind_rows() %>% dplyr::select(pathway, genesymbol, 
       weight, p_value) %>% rlang::set_names(c("source", "target", 
       "weight", "p_value"))
1: decoupleR::get_progeny(organism = "mouse", top = 500)

SessionInfo

> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22        splines_4.3.1           later_1.4.3             cellranger_1.1.0        tibble_3.3.0           
  [6] R.oo_1.27.1             polyclip_1.10-7         XML_3.99-0.19           fastDummies_1.7.5       lifecycle_1.0.4        
 [11] httr2_1.2.1             tcltk_4.3.1             vroom_1.6.5             globals_0.18.0          lattice_0.22-7         
 [16] MASS_7.3-60.0.1         backports_1.5.0         magrittr_2.0.3          openxlsx_4.2.8          plotly_4.11.0          
 [21] rmarkdown_2.29          yaml_2.3.10             httpuv_1.6.16           Seurat_5.3.0            sctransform_0.4.2      
 [26] spam_2.11-1             zip_2.3.2               askpass_1.2.1           sessioninfo_1.2.3       sp_2.2-0               
 [31] spatstat.sparse_3.1-0   reticulate_1.43.0       cowplot_1.2.0           pbapply_1.7-4           DBI_1.2.3              
 [36] RColorBrewer_1.1-3      lubridate_1.9.4         abind_1.4-8             rvest_1.0.4             Rtsne_0.17             
 [41] purrr_1.1.0             R.utils_2.13.0          rappdirs_0.3.3          gdtools_0.4.2           ggrepel_0.9.6          
 [46] irlba_2.3.5.1           listenv_0.9.1           spatstat.utils_3.1-5    pheatmap_1.0.13         goftest_1.2-3          
 [51] RSpectra_0.16-2         spatstat.random_3.4-1   fitdistrplus_1.2-4      parallelly_1.45.1       codetools_0.2-20       
 [56] xml2_1.4.0              tidyselect_1.2.1        farver_2.1.2            matrixStats_1.5.0       spatstat.explore_3.5-2 
 [61] jsonlite_2.0.0          progressr_0.15.1        ggridges_0.5.6          survival_3.8-3          systemfonts_1.2.3      
 [66] progress_1.2.3          tools_4.3.1             ragg_1.4.0              ica_1.0-3               Rcpp_1.1.0             
 [71] glue_1.8.0              gridExtra_2.3           xfun_0.53               decoupleR_2.9.7         dplyr_1.1.4            
 [76] withr_3.0.2             fastmap_1.2.0           openssl_2.3.3           digest_0.6.37           timechange_0.3.0       
 [81] R6_2.6.1                mime_0.13               textshaping_1.0.1       scattermore_1.2         tensor_1.5.1           
 [86] spatstat.data_3.1-8     RSQLite_2.4.3           R.methodsS3_1.8.2       tidyr_1.3.1             generics_0.1.4         
 [91] fontLiberation_0.1.0    data.table_1.17.8       prettyunits_1.2.0       httr_1.4.7              htmlwidgets_1.6.4      
 [96] uwot_0.2.3              pkgconfig_2.0.3         gtable_0.3.6            blob_1.2.4              lmtest_0.9-40          
[101] selectr_0.4-2           OmnipathR_3.17.4        htmltools_0.5.8.1       fontBitstreamVera_0.1.1 dotCall64_1.2          
[106] rvg_0.3.5               SeuratObject_5.1.0      scales_1.4.0            png_0.1-8               spatstat.univar_3.1-4  
[111] knitr_1.50              rstudioapi_0.17.1       tzdb_0.5.0              reshape2_1.4.4          uuid_1.2-1             
[116] checkmate_2.3.3         nlme_3.1-168            curl_7.0.0              zoo_1.8-14              cachem_1.1.0           
[121] flextable_0.9.9         stringr_1.5.1           KernSmooth_2.23-26      parallel_4.3.1          miniUI_0.1.2           
[126] pillar_1.11.0           grid_4.3.1              logger_0.4.0            vctrs_0.6.5             RANN_2.6.2             
[131] promises_1.3.3          xtable_1.8-4            cluster_2.1.8.1         evaluate_1.0.4          readr_2.1.5            
[136] cli_3.6.5               compiler_4.3.1          rlang_1.1.6             crayon_1.5.3            future.apply_1.20.0    
[141] plyr_1.8.9              fs_1.6.6                stringi_1.8.7           viridisLite_0.4.2       deldir_2.0-4           
[146] BiocParallel_1.36.0     lazyeval_0.2.2          spatstat.geom_3.5-0     fontquiver_0.2.1        Matrix_1.6-5           
[151] RcppHNSW_0.6.0          hms_1.1.3               patchwork_1.3.1         bit64_4.6.0-1           future_1.67.0          
[156] ggplot2_3.5.2           jjAnno_0.0.3            devEMF_4.5-1            stargazer_5.2.3         shiny_1.11.1           
[161] ROCR_1.0-11             igraph_2.1.4            broom_1.0.9             memoise_2.0.1           bit_4.6.0              
[166] export_0.3.2            readxl_1.4.5            officer_0.6.10  

[vukojicic-nevena]

I had the exact same issue and used the same versions, did you solve it?

[zhangj1115]

I had the exact same issue,too