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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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get_progeny fails when using `organsim = "mouse"` #128

Closed Christian-Heyer closed 1 month ago

Christian-Heyer commented 1 month ago

The following error occurs when attempting to get the progeny network data with the newest versions of decoupleR (and OmnipathR) from github.

Please include a minimal reproducible example (AKA a reprex).

prog_net <- decoupleR::get_progeny(organism = "mouse", top = 250) 
[2024-05-29 12:03:24] [SUCCESS] [OmnipathR] Loaded 700257 annotation records from cache.
Error in !sym(organism_b) : invalid argument type

I installed the newest versions of decoupleR and OminpathR from github

Brief description of the problem Works without issue if I use organism = "human"

Traceback()

38: vctrs_vec_compat(.x, .purrr_user_env)
37: map_("integer", .x, .f, ..., .progress = .progress)
36: map_int(., taxon_name, "ncbi")
35: name %>% map_int(taxon_name, "ncbi") %>% as.integer
34: ncbi_taxid(.)
33: organism %<>% ncbi_taxid
32: translate_ids(., `:=`(id_organism_b, !!sym(oma_id_type)), `:=`(id_organism_b, 
        !!sym(id_type)), organism = !!sym(organism_b))
31: filter(., !is.na(id_organism_a) & !is.na(id_organism_b))
30: environment() %>% as.list %>% extract(!startsWith(names(.), "id_organism_")) %>% 
        inset2("id_type", oma_id_type) %>% extract(names(.) != "oma_id_type") %>% 
        exec(oma_pairwise, !!!.) %>% translate_ids(`:=`(id_organism_a, 
        !!sym(oma_id_type)), `:=`(id_organism_a, !!sym(id_type)), 
        organism = !!sym(organism_a)) %>% translate_ids(`:=`(id_organism_b, 
        !!sym(oma_id_type)), `:=`(id_organism_b, !!sym(id_type)), 
        organism = !!sym(organism_b)) %>% filter(!is.na(id_organism_a) & 
        !is.na(id_organism_b))
29: (function (organism_a = "human", organism_b = "mouse", id_type = "uniprot", 
        oma_id_type = "uniprot_entry", mappings = c("1:1", "1:m", 
            "n:1", "n:m"), only_ids = TRUE) 
    {
        .slow_doctest()
        id_organism_a <- id_organism_b <- NULL
        organism_a <- .nse_ensure_str(!!enquo(organism_a))
        organism_b <- .nse_ensure_str(!!enquo(organism_b))
        environment() %>% as.list %>% extract(!startsWith(names(.), 
            "id_organism_")) %>% inset2("id_type", oma_id_type) %>% 
            extract(names(.) != "oma_id_type") %>% exec(oma_pairwise, 
            !!!.) %>% translate_ids(`:=`(id_organism_a, !!sym(oma_id_type)), 
            `:=`(id_organism_a, !!sym(id_type)), organism = !!sym(organism_a)) %>% 
            translate_ids(`:=`(id_organism_b, !!sym(oma_id_type)), 
                `:=`(id_organism_b, !!sym(id_type)), organism = !!sym(organism_b)) %>% 
            filter(!is.na(id_organism_a) & !is.na(id_organism_b))
    })(organism_a = 9606L, organism_b = 10090L, id_type = "uniprot", 
        mappings = c("1:1", "1:m", "n:1", "n:m"), only_ids = TRUE)
28: exec(oma_pairwise_translated, !!!.)
27: environment() %>% as.list %>% exec(oma_pairwise_translated, !!!.)
26: (function (organism_a = "human", organism_b = "mouse", id_type = "uniprot", 
        mappings = c("1:1", "1:m", "n:1", "n:m"), only_ids = TRUE) 
    {
        .slow_doctest()
        if (!id_type %in% names(omnipath.env$id_types$oma)) {
            return(environment() %>% as.list %>% exec(oma_pairwise_translated, 
                !!!.))
        }
        id_organism_a <- id_organism_b <- mapping <- NULL
        organism_a %<>% organism_for("oma")
        organism_b %<>% organism_for("oma")
        id_type %<>% oma_id_type
        args <- match.call() %>% as.list %>% tail(-1L)
        for (arg in names(args)) {
            if (is.null(get(arg)) || any(is.na(get(arg)))) {
                msg <- sprintf("Could not recognize %s: `%s`.", if (arg == 
                    "id_type") 
                    "ID type"
                else "organism", args[[arg]])
                log_error(msg)
     ...
25: exec(loader, !!!param)
24: load_db(key, param = param)
23: get_db(db_name, param = orthology_param)
22: select(., -any_of("hgroup"))
21: set_names(., c(ORTHO_SOURCE_COL, ORTHO_TARGET_COL))
20: get_db(db_name, param = orthology_param) %>% select(-any_of("hgroup")) %>% 
        set_names(c(ORTHO_SOURCE_COL, ORTHO_TARGET_COL)) %>% {
        if (translate_complexes) 
            bind_rows(., complex_orthology(orthology = ., identifiers = data %>% 
                pull(!!sym(column)), one_to_many = translate_complexes))
        else .
    }
19: OmnipathR::orthology_translate_column(., "uniprot", target_organism = organism, 
        replace = TRUE)
18: OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism)
17: OmnipathR::orthology_translate_column(., "uniprot", target_organism = organism, 
        replace = TRUE) %>% OmnipathR::translate_ids(., uniprot, 
        genesymbol, organism = organism)
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 = 250)

SessionInfo 

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/heyer/mambaforge/lib/libopenblasp-r0.3.21.so

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

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

other attached packages:
[1] reprex_2.1.0

loaded via a namespace (and not attached):
  [1] colorspace_2.1-0            selectr_0.4-2               ellipsis_0.3.2             
  [4] XVector_0.38.0              GenomicRanges_1.50.2        fs_1.6.4                   
  [7] rstudioapi_0.16.0           remotes_2.5.0               bit64_4.0.5                
 [10] AnnotationDbi_1.60.2        fansi_1.0.6                 lubridate_1.9.3            
 [13] decoupleR_2.9.7             xml2_1.3.6                  R.methodsS3_1.8.2          
 [16] codetools_0.2-20            cachem_1.0.8                geneplotter_1.76.0         
 [19] knitr_1.46                  pkgload_1.3.4               jsonlite_1.8.8             
 [22] annotate_1.76.0             R.oo_1.26.0                 png_0.1-8                  
 [25] shiny_1.8.1.1               readr_2.1.5                 compiler_4.2.0             
 [28] httr_1.4.7                  backports_1.4.1             Matrix_1.6-5               
 [31] fastmap_1.2.0               cli_3.6.2                   later_1.3.2                
 [34] htmltools_0.5.8.1           prettyunits_1.2.0           tools_4.2.0                
 [37] igraph_2.0.3                gtable_0.3.4                glue_1.7.0                 
 [40] GenomeInfoDbData_1.2.9      dplyr_1.1.4                 rappdirs_0.3.3             
 [43] Rcpp_1.0.12                 Biobase_2.58.0              styler_1.10.3              
 [46] cellranger_1.1.0            vctrs_0.6.5                 Biostrings_2.66.0          
 [49] OmnipathR_3.11.16           xfun_0.44                   stringr_1.5.1              
 [52] ps_1.7.6                    rvest_1.0.4                 timechange_0.3.0           
 [55] mime_0.12                   miniUI_0.1.1.1              lifecycle_1.0.4            
 [58] devtools_2.4.5              XML_3.99-0.16.1             zlibbioc_1.44.0            
 [61] scales_1.3.0                vroom_1.6.5                 hms_1.1.3                  
 [64] promises_1.3.0              MatrixGenerics_1.10.0       parallel_4.2.0             
 [67] SummarizedExperiment_1.28.0 RColorBrewer_1.1-3          yaml_2.3.8                 
 [70] curl_5.2.1                  memoise_2.0.1               ggplot2_3.5.0              
 [73] stringi_1.8.4               RSQLite_2.3.6               S4Vectors_0.36.2           
 [76] checkmate_2.3.1             BiocGenerics_0.44.0         pkgbuild_1.4.4             
 [79] BiocParallel_1.32.6         GenomeInfoDb_1.34.9         rlang_1.1.3                
 [82] pkgconfig_2.0.3             matrixStats_1.1.0           bitops_1.0-7               
 [85] evaluate_0.23               lattice_0.22-6              purrr_1.0.2                
 [88] htmlwidgets_1.6.4           processx_3.8.4              bit_4.0.5                  
 [91] tidyselect_1.2.1            parallelly_1.37.1           logger_0.3.0               
 [94] magrittr_2.0.3              DESeq2_1.38.3               R6_2.5.1                   
 [97] IRanges_2.32.0              generics_0.1.3              profvis_0.3.8              
[100] DelayedArray_0.24.0         DBI_1.2.2                   pillar_1.9.0               
[103] withr_3.0.0                 KEGGREST_1.38.0             RCurl_1.98-1.14            
[106] tibble_3.2.1                crayon_1.5.2                utf8_1.2.4                 
[109] tzdb_0.4.0                  rmarkdown_2.26              urlchecker_1.0.1           
[112] progress_1.2.3              usethis_2.2.3               locfit_1.5-9.9             
[115] grid_4.2.0                  readxl_1.4.3                callr_3.7.6                
[118] blob_1.2.4                  digest_0.6.35               R.cache_0.16.0             
[121] xtable_1.8-4                tidyr_1.3.1                 httpuv_1.6.15              
[124] R.utils_2.12.3              stats4_4.2.0                munsell_0.5.1              
[127] sessioninfo_1.2.2
deeenes commented 1 month ago

Wow, I'm surprised no one reported yet this one! Thanks for reporting, should be working now.

Christian-Heyer commented 1 month ago

Is Fixed. Thanks for the quick turn around.

atzatsos commented 1 month ago

Hello! I also experience problem with the "mouse". Below is the error message. thank you! alex

progeny <- decoupleR::get_progeny(organism='mouse', top=500) [2024-06-07 21:14:07] [WARN] [OmnipathR] HTTP 403 [2024-06-07 21:14:07] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 1/3); error: HTTP 403 [2024-06-07 21:14:12] [WARN] [OmnipathR] HTTP 403 [2024-06-07 21:14:12] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 2/3); error: HTTP 403 [2024-06-07 21:14:18] [WARN] [OmnipathR] HTTP 403 [2024-06-07 21:14:18] [ERROR] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 3/3); error: HTTP 403 [2024-06-07 21:14:18] [WARN] [OmnipathR] HTTP 403 [2024-06-07 21:14:18] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 1/3); error: HTTP 403 [2024-06-07 21:14:23] [WARN] [OmnipathR] HTTP 403 [2024-06-07 21:14:23] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 2/3); error: HTTP 403 [2024-06-07 21:14:28] [WARN] [OmnipathR] HTTP 403 [2024-06-07 21:14:28] [ERROR] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 3/3); error: HTTP 403 [2024-06-07 21:14:29] [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. [2024-06-07 21:14:29] [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.

deeenes commented 1 month ago

Hello @atzatsos, Here we see a HTTP 403 code from www.ensembl.org. I've never seen the actual Ensembl site returning HTTP 403, which raises the suspicion that this response originates from an intermediary, such as proxy server, firewall or other network security device. I recommend you to 1) try from another network; 2) when you get the HTTP 403 in R, try to access www.ensembl.org from the same computer from the web browser, and see if it also returns HTTP 403 there.

The alternative explanation would be that Ensembl had a temporary issue that made it return wrong HTTP error codes. In this case it should be working again. Though I find this very unlikely, I assume you've already tried it more than once.

Hayao-jp commented 1 month ago

Hello!

I also get an error with organism = "mouse". By traceback, generic_downloader function of OmnipathR::orthology_translate_column() in get_resource() seems to generate the error.

OmnipathR::omnipath_cache_clean_db() net <- decoupleR::get_progeny(organism = "mouse", top = 500) [2024-06-12 12:09:09] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. [2024-06-12 12:09:10] [WARN] [OmnipathR] Failed to download https://omabrowser.org/cgi-bin/gateway.pl?f=PairwiseOrthologs&p1=HUMAN&p2=MOUSE&p3=UniProt (attempt 1/3); error: HTTP error 503. [2024-06-12 12:09:16] [WARN] [OmnipathR] Failed to download https://omabrowser.org/cgi-bin/gateway.pl?f=PairwiseOrthologs&p1=HUMAN&p2=MOUSE&p3=UniProt (attempt 2/3); error: HTTP error 503. [2024-06-12 12:09:22] [ERROR] [OmnipathR] Failed to download https://omabrowser.org/cgi-bin/gateway.pl?f=PairwiseOrthologs&p1=HUMAN&p2=MOUSE&p3=UniProt (attempt 3/3); error: HTTP error 503. Error in open.connection(3L, "rb"): HTTP error 503.

thank you

sessionInfo() R version 4.4.0 (2024-04-24 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale: [1] LC_COLLATE=Japanese_Japan.utf8 LC_CTYPE=Japanese_Japan.utf8
[3] LC_MONETARY=Japanese_Japan.utf8 LC_NUMERIC=C
[5] LC_TIME=Japanese_Japan.utf8

time zone: Asia/Tokyo tzcode source: internal

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

other attached packages: [1] decoupleR_2.9.7 devtools_2.4.5 usethis_2.2.3 openxlsx_4.2.5.2
[5] magrittr_2.0.3 dplyr_1.1.4 Seurat_5.1.0 SeuratObject_5.0.2 [9] sp_2.1-4

loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.4.0 later_1.3.2
[4] tibble_3.2.1 cellranger_1.1.0 polyclip_1.10-6
[7] fastDummies_1.7.3 lifecycle_1.0.4 globals_0.16.3
[10] processx_3.8.4 lattice_0.22-6 vroom_1.6.5
[13] MASS_7.3-60.2 backports_1.5.0 plotly_4.10.4
[16] rmarkdown_2.27 yaml_2.3.8 remotes_2.5.0
[19] httpuv_1.6.15 sctransform_0.4.1 spam_2.10-0
[22] zip_2.3.1 sessioninfo_1.2.2 pkgbuild_1.4.4
[25] spatstat.sparse_3.0-3 reticulate_1.37.0 cowplot_1.1.3
[28] pbapply_1.7-2 RColorBrewer_1.1-3 lubridate_1.9.3
[31] abind_1.4-5 pkgload_1.3.4 rvest_1.0.4
[34] Rtsne_0.17 purrr_1.0.2 rappdirs_0.3.3
[37] ggrepel_0.9.5 irlba_2.3.5.1 listenv_0.9.1
[40] spatstat.utils_3.0-4 goftest_1.2-3 RSpectra_0.16-1
[43] spatstat.random_3.2-3 fitdistrplus_1.1-11 parallelly_1.37.1
[46] leiden_0.4.3.1 codetools_0.2-20 xml2_1.3.6
[49] tidyselect_1.2.1 matrixStats_1.3.0 spatstat.explore_3.2-7 [52] jsonlite_1.8.8 ellipsis_0.3.2 progressr_0.14.0
[55] ggridges_0.5.6 survival_3.7-0 tools_4.4.0
[58] progress_1.2.3 ica_1.0-3 Rcpp_1.0.12
[61] glue_1.7.0 gridExtra_2.3 xfun_0.44
[64] withr_3.0.0 fastmap_1.2.0 fansi_1.0.6
[67] callr_3.7.6 digest_0.6.35 timechange_0.3.0
[70] R6_2.5.1 mime_0.12 colorspace_2.1-0
[73] scattermore_1.2 tensor_1.5 spatstat.data_3.0-4
[76] utf8_1.2.4 tidyr_1.3.1 generics_0.1.3
[79] data.table_1.15.4 prettyunits_1.2.0 httr_1.4.7
[82] htmlwidgets_1.6.4 uwot_0.2.2 pkgconfig_2.0.3
[85] gtable_0.3.5 lmtest_0.9-40 selectr_0.4-2
[88] OmnipathR_3.13.4 htmltools_0.5.8.1 profvis_0.3.8
[91] dotCall64_1.1-1 scales_1.3.0 png_0.1-8
[94] knitr_1.47 rstudioapi_0.16.0 tzdb_0.4.0
[97] reshape2_1.4.4 checkmate_2.3.1 nlme_3.1-165
[100] curl_5.2.1 zoo_1.8-12 cachem_1.1.0
[103] stringr_1.5.1 KernSmooth_2.23-24 parallel_4.4.0
[106] miniUI_0.1.1.1 desc_1.4.3 pillar_1.9.0
[109] grid_4.4.0 logger_0.3.0 vctrs_0.6.5
[112] RANN_2.6.1 urlchecker_1.0.1 promises_1.3.0
[115] xtable_1.8-4 cluster_2.1.6 evaluate_0.24.0
[118] readr_2.1.5 cli_3.6.2 compiler_4.4.0
[121] rlang_1.1.4 crayon_1.5.2 future.apply_1.11.2
[124] ps_1.7.6 plyr_1.8.9 fs_1.6.4
[127] stringi_1.8.4 viridisLite_0.4.2 deldir_2.0-4
[130] BiocParallel_1.38.0 munsell_0.5.1 lazyeval_0.2.2
[133] spatstat.geom_3.2-9 Matrix_1.7-0 RcppHNSW_0.6.0
[136] hms_1.1.3 patchwork_1.2.0 bit64_4.0.5
[139] future_1.33.2 ggplot2_3.5.1 shiny_1.8.1.1
[142] ROCR_1.0-11 igraph_2.0.3 memoise_2.0.1
[145] bit_4.0.5 readxl_1.4.3

fedenichetti commented 1 month ago

Hi there, I also get an error: 

net <- get_progeny(organism = 'mouse', top = 100)
[2024-06-12 12:00:03] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
Error in UseMethod("mutate") : 
  no applicable method for 'mutate' applied to an object of class "list"
In addition: Warning message:
In .ensure_safe_path(.) :
  OmnipathR: Falling back to path `/var/folders/d7/7k20s5nx4l58y2qh9395cn0m0000gn/T//RtmpRi99Zn/omnipathr-20240612-1200.log` instead of `//omnipathr-log/omnipathr-20240612-1200.log`.

R version 4.4.0 (2024-04-24) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.5

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

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

time zone: Europe/Rome tzcode source: internal

attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] DESeq2_1.44.0 circlize_0.4.16 ComplexHeatmap_2.20.0 rstatix_0.7.2 dlookr_0.6.3 limma_3.60.2
[7] ggfortify_0.4.17 ggpubr_0.6.0 ggridges_0.5.6 readxl_1.4.3 org.Mm.eg.db_3.19.1 AnnotationDbi_1.66.0
[13] clusterProfiler_4.12.0 decoupleR_2.10.0 SummarizedExperiment_1.34.0 GenomicRanges_1.56.0 GenomeInfoDb_1.40.1 IRanges_2.38.0
[19] S4Vectors_0.42.0 MatrixGenerics_1.16.0 matrixStats_1.3.0 janitor_2.2.0 lubridate_1.9.3 forcats_1.0.0
[25] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[31] ggplot2_3.5.1 tidyverse_2.0.0 viper_1.38.0 Biobase_2.64.0 BiocGenerics_0.50.0 dorothea_1.16.0

loaded via a namespace (and not attached): [1] segmented_2.1-0 fs_1.6.4 reactable_0.4.4 enrichplot_1.24.0 HDO.db_0.99.1 httr_1.4.7 RColorBrewer_1.1-3 doParallel_1.0.17
[9] tools_4.4.0 backports_1.5.0 utf8_1.2.4 R6_2.5.1 mgcv_1.9-1 lazyeval_0.2.2 GetoptLong_1.0.5 withr_3.0.0
[17] prettyunits_1.2.0 gridExtra_2.3 cli_3.6.2 gt_0.10.1 pacman_0.5.1 scatterpie_0.2.3 labeling_0.4.3 proxy_0.4-27
[25] systemfonts_1.1.0 yulab.utils_0.1.4 gson_0.1.0 svglite_2.1.3 gfonts_0.2.0 DOSE_3.30.1 showtext_0.9-7 parallelly_1.37.1
[33] bcellViper_1.40.0 sysfonts_0.8.9 rstudioapi_0.16.0 RSQLite_2.3.7 httpcode_0.3.0 generics_0.1.3 gridGraphics_0.5-1 shape_1.4.6.1
[41] vroom_1.6.5 car_3.1-2 GO.db_3.19.1 Matrix_1.7-0 fansi_1.0.6 logger_0.3.0 abind_1.4-5 lifecycle_1.0.4
[49] yaml_2.3.8 snakecase_0.11.1 carData_3.0-5 gtsummary_1.7.2 qvalue_2.36.0 SparseArray_1.4.8 Rtsne_0.17 blob_1.2.4
[57] promises_1.3.0 crayon_1.5.2 lattice_0.22-6 cowplot_1.1.3 KEGGREST_1.44.0 pillar_1.9.0 knitr_1.47 fgsea_1.30.0
[65] rjson_0.2.21 codetools_0.2-20 fastmatch_1.1-4 glue_1.7.0 beepr_1.3 pagedown_0.20 ggfun_0.1.5 fontLiberation_0.1.0
[73] data.table_1.15.4 broom.helpers_1.15.0 vctrs_0.6.5 png_0.1-8 treeio_1.28.0 EnhancedVolcano_1.22.0 cellranger_1.1.0 gtable_0.3.5
[81] kernlab_0.9-32 cachem_1.1.0 OmnipathR_3.11.10 xfun_0.44 S4Arrays_1.4.1 mime_0.12 tidygraph_1.3.1 survival_3.7-0
[89] audio_0.1-11 iterators_1.0.14 showtextdb_3.0 statmod_1.5.0 nlme_3.1-165 ggtree_3.12.0 bit64_4.0.5 fontquiver_0.2.1
[97] progress_1.2.3 KernSmooth_2.23-24 colorspace_2.1-0 DBI_1.2.3 tidyselect_1.2.1 bit_4.0.5 compiler_4.4.0 extrafontdb_1.0
[105] curl_5.2.1 rvest_1.0.4 xml2_1.3.6 fontBitstreamVera_0.1.1 DelayedArray_0.30.1 plotly_4.10.4 shadowtext_0.1.3 checkmate_2.3.1
[113] scales_1.3.0 rappdirs_0.3.3 digest_0.6.35 mixtools_2.0.0 rmarkdown_2.27 XVector_0.44.0 htmltools_0.5.8.1 pkgconfig_2.0.3
[121] extrafont_0.19 fastmap_1.2.0 rlang_1.1.4 GlobalOptions_0.1.2 htmlwidgets_1.6.4 UCSC.utils_1.0.0 shiny_1.8.1.1 farver_2.1.2
[129] jsonlite_1.8.8 BiocParallel_1.38.0 GOSemSim_2.30.0 magrittr_2.0.3 kableExtra_1.4.0 GenomeInfoDbData_1.2.12 ggplotify_0.1.2 patchwork_1.2.0
[137] munsell_0.5.1 Rcpp_1.0.12 ape_5.8 viridis_0.6.5 gdtools_0.3.7 stringi_1.8.4 ggraph_2.2.1 zlibbioc_1.50.0
[145] MASS_7.3-60.2 plyr_1.8.9 hrbrthemes_0.8.7 parallel_4.4.0 ggrepel_0.9.5 Biostrings_2.72.1 graphlayouts_1.1.1 splines_4.4.0
[153] hms_1.1.3 locfit_1.5-9.9 igraph_2.0.3 ggsignif_0.6.4 reshape2_1.4.4 crul_1.4.2 evaluate_0.24.0 selectr_0.4-2
[161] tzdb_0.4.0 foreach_1.5.2 tweenr_2.0.3 httpuv_1.6.15 Rttf2pt1_1.3.12 polyclip_1.10-6 clue_0.3-65 ggforce_0.4.2
[169] broom_1.0.6 xtable_1.8-4 e1071_1.7-14 tidytree_0.4.6 later_1.3.2 viridisLite_0.4.2 class_7.3-22 aplot_0.2.2
[177] memoise_2.0.1 cluster_2.1.6 timechange_0.3.0

deeenes commented 1 month ago

Hi @Hayao-jp, Your session info shows version 3.13.4 for OmnipathR, however, we replaced the old OMA URL (the one visible in your log, omabrowser.org/cgi-bin/gateway.pl...) already end of April. To see more clear, could you please freshly install OmnipathR and test it with an empty cache? If you experience the error, a traceback and OmnipathR log would provide more information:

remotes::install_github('OmnipathR')
library(OmnipathR)
omnipath_set_console_log_level('trace')
omnipath_set_cachedir(tempdir())

human_mouse <- oma_pairwise()

# if you see the error:
traceback()
deeenes commented 1 month ago

Hi @atzatsos, I've just fixed your issue with the Ensembl HTTP 403 error, see here. After updating OmnipathR from git, this error should go away.

remotes::install_github('OmnipathR')
atzatsos commented 1 month ago

Thanks @deeenes - it works!

Hayao-jp commented 1 month ago

Thank you so much @deeenes. I tried the code and get [SUCCESS].