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saezlab / OmnipathR

R client for the OmniPath web service
https://r.omnipathdb.org/
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get_dorothea and get_progeny error #106

Closed MutluHamanakaLab closed 1 month ago

MutluHamanakaLab commented 2 months ago

Hello, I'm currently having problem getting dorothea and progeny.

Here is example code and error message for get_progeny()

> net <- get_progeny(organism = 'human', top = 500) 
Warning in OmnipathR::get_annotation_resources() :
  'OmnipathR::get_annotation_resources' is deprecated.
Use 'get_annotation_resources' instead.
See help("Deprecated")
Warning in OmnipathR::import_omnipath_annotations(resources = name, ...,  :
  'OmnipathR::import_omnipath_annotations' is deprecated.
Use 'import_omnipath_annotations' instead.
See help("Deprecated")
[2024-09-26 10:47:58] [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.
[2024-09-26 10:47:58] [SUCCESS] [OmnipathR] Loaded 2 annotation records from cache.
[2024-09-26 10:47:58] [ERROR]   [OmnipathR] [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log.
Error in value[[3L]](cond) : 
  [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log.

this is error message for get_dorothea()

> net <- get_dorothea(levels=c('A', 'B', 'C'))
[2024-09-26 10:43:49] [WARN]    [OmnipathR] Accessing `dorothea` 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.
[2024-09-26 10:43:49] [ERROR]   [OmnipathR] `only_from` can be called only on data frames with `evidences` column.
Error in do.call(stop, list(m), envir = env) : 
  `only_from` can be called only on data frames with `evidences` column.

This is my current session info

> sessionInfo()
R version 4.4.1 (2024-06-14)
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: America/Chicago
tzcode source: internal

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

other attached packages:
[1] OmnipathR_3.13.25 dplyr_1.1.4       ggplot2_3.5.1     decoupleR_2.10.0  dorothea_1.16.0  

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22       splines_4.4.1          later_1.3.2            tibble_3.2.1           R.oo_1.26.0           
  [6] cellranger_1.1.0       polyclip_1.10-7        XML_3.99-0.17          fastDummies_1.7.4      lifecycle_1.0.4       
 [11] vroom_1.6.5            globals_0.16.3         lattice_0.22-6         MASS_7.3-61            backports_1.5.0       
 [16] magrittr_2.0.3         plotly_4.10.4          rmarkdown_2.28         yaml_2.3.10            remotes_2.5.0         
 [21] httpuv_1.6.15          Seurat_5.1.0           sctransform_0.4.1      zip_2.3.1              spam_2.10-0           
 [26] sp_2.1-4               spatstat.sparse_3.1-0  reticulate_1.39.0      cowplot_1.1.3          pbapply_1.7-2         
 [31] DBI_1.2.3              RColorBrewer_1.1-3     lubridate_1.9.3        abind_1.4-8            rvest_1.0.4           
 [36] Rtsne_0.17             purrr_1.0.2            R.utils_2.12.3         rappdirs_0.3.3         ggrepel_0.9.6         
 [41] irlba_2.3.5.1          listenv_0.9.1          spatstat.utils_3.1-0   goftest_1.2-3          RSpectra_0.16-2       
 [46] spatstat.random_3.3-2  fitdistrplus_1.2-1     parallelly_1.38.0      leiden_0.4.3.1         codetools_0.2-20      
 [51] xml2_1.3.6             tidyselect_1.2.1       farver_2.1.2           matrixStats_1.4.1      spatstat.explore_3.3-2
 [56] jsonlite_1.8.9         progressr_0.14.0       ggridges_0.5.6         survival_3.7-0         tools_4.4.1           
 [61] progress_1.2.3         ica_1.0-3              Rcpp_1.0.13            glue_1.7.0             gridExtra_2.3         
 [66] xfun_0.47              withr_3.0.1            fastmap_1.2.0          fansi_1.0.6            digest_0.6.37         
 [71] timechange_0.3.0       R6_2.5.1               mime_0.12              colorspace_2.1-1       scattermore_1.2       
 [76] tensor_1.5             spatstat.data_3.1-2    RSQLite_2.3.7          R.methodsS3_1.8.2      utf8_1.2.4            
 [81] tidyr_1.3.1            generics_0.1.3         data.table_1.16.0      prettyunits_1.2.0      httr_1.4.7            
 [86] htmlwidgets_1.6.4      uwot_0.2.2             pkgconfig_2.0.3        gtable_0.3.5           blob_1.2.4            
 [91] lmtest_0.9-40          selectr_0.4-2          htmltools_0.5.8.1      dotCall64_1.1-1        SeuratObject_5.0.2    
 [96] scales_1.3.0           png_0.1-8              spatstat.univar_3.0-1  knitr_1.48             rstudioapi_0.16.0     
[101] tzdb_0.4.0             reshape2_1.4.4         checkmate_2.3.2        nlme_3.1-166           curl_5.2.3            
[106] zoo_1.8-12             cachem_1.1.0           stringr_1.5.1          KernSmooth_2.23-24     parallel_4.4.1        
[111] miniUI_0.1.1.1         pillar_1.9.0           grid_4.4.1             logger_0.3.0           vctrs_0.6.5           
[116] RANN_2.6.2             promises_1.3.0         xtable_1.8-4           cluster_2.1.6          evaluate_1.0.0        
[121] readr_2.1.5            cli_3.6.3              compiler_4.4.1         rlang_1.1.4            crayon_1.5.3          
[126] future.apply_1.11.2    bcellViper_1.40.0      plyr_1.8.9             stringi_1.8.4          viridisLite_0.4.2     
[131] deldir_2.0-4           BiocParallel_1.38.0    munsell_0.5.1          lazyeval_0.2.2         spatstat.geom_3.3-3   
[136] Matrix_1.7-0           RcppHNSW_0.6.0         hms_1.1.3              patchwork_1.3.0        bit64_4.5.2           
[141] future_1.34.0          shiny_1.9.1            ROCR_1.0-11            igraph_2.0.3           memoise_2.0.1         
[146] bit_4.5.0              readxl_1.4.3

Thanks in advance

deeenes commented 2 months ago

Hello,

First, please ignore the deprecation warning, that's something we should silence. About the actual error, it is a network communication error, however, it is hidden by the error handling. It would be indeed useful to see the logs. But even easier, just try to download anything by curl and see what kind of error happens:

library(curl)

req <- curl_fetch_memory("https://omnipathdb.org/annotations?resources=PROGENy")
MutluHamanakaLab commented 2 months ago

Hello,

First, please ignore the deprecation warning, that's something we should silence. About the actual error, it is a network communication error, however, it is hidden by the error handling. It would be indeed useful to see the logs. But even easier, just try to download anything by curl and see what kind of error happens:

library(curl)

req <- curl_fetch_memory("https://omnipathdb.org/annotations?resources=PROGENy")

Thank you for quick comment. Before trying what is suggested, I removed all the files in

"/path/to/Library/Caches/OmnipathR" and performed omnipath_cache_clean_db()

After this, I was successful fetching the progeny model with warning. Do you think I can ignore this warning?

> net <- get_progeny(organism = 'human', top = 500) 
[2024-09-26 14:22:07] [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.
[2024-09-26 14:22:09] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.

I had no problem running this as well.

> library(curl)
Using libcurl 8.6.0 with LibreSSL/3.3.6

Attaching package: ‘curl’

The following object is masked from ‘package:readr’:

    parse_date

> req <- curl_fetch_memory("https://omnipathdb.org/annotations?resources=PROGENy")
> head(req)
$url
[1] "https://omnipathdb.org/annotations?resources=PROGENy"

$status_code
[1] 200

$type
[1] "text/plain; charset=utf-8"

$headers
  [1] 48 54 54 50 2f 31 2e 31 20 32 30 30 20 4f 4b 0d 0a 53 65 72 76 65 72 3a 20 6e 67 69 6e 78 0d 0a 44 61 74 65 3a 20 54 68
 [41] 75 2c 20 32 36 20 53 65 70 20 32 30 32 34 20 31 39 3a 31 36 3a 30 33 20 47 4d 54 0d 0a 43 6f 6e 74 65 6e 74 2d 54 79 70
 [81] 65 3a 20 74 65 78 74 2f 70 6c 61 69 6e 3b 20 63 68 61 72 73 65 74 3d 75 74 66 2d 38 0d 0a 54 72 61 6e 73 66 65 72 2d 45
[121] 6e 63 6f 64 69 6e 67 3a 20 63 68 75 6e 6b 65 64 0d 0a 43 6f 6e 6e 65 63 74 69 6f 6e 3a 20 6b 65 65 70 2d 61 6c 69 76 65
[161] 0d 0a 43 61 63 68 65 2d 43 6f 6e 74 72 6f 6c 3a 20 6d 61 78 2d 61 67 65 3d 33 36 30 30 0d 0a 41 63 63 65 73 73 2d 43 6f
[201] 6e 74 72 6f 6c 2d 41 6c 6c 6f 77 2d 4f 72 69 67 69 6e 3a 20 2a 0d 0a 45 78 70 69 72 65 73 3a 20 54 68 75 2c 20 32 36 20
[241] 53 65 70 20 32 30 32 34 20 32 30 3a 31 36 3a 30 33 20 47 4d 54 0d 0a 43 61 63 68 65 2d 43 6f 6e 74 72 6f 6c 3a 20 70 75
[281] 62 6c 69 63 0d 0a 58 2d 46 72 61 6d 65 2d 4f 70 74 69 6f 6e 73 3a 20 44 45 4e 59 0d 0a 43 6f 6e 74 65 6e 74 2d 45 6e 63
[321] 6f 64 69 6e 67 3a 20 67 7a 69 70 0d 0a 0d 0a

$modified
[1] NA

$times
     redirect    namelookup       connect   pretransfer starttransfer         total 
     0.000000      0.056416      0.152701      0.256321      0.447839      2.368893
MutluHamanakaLab commented 2 months ago

It seems I can't really ignore the warning, it seems my computer have hard time connecting.

> net <- get_collectri(organism='human', split_complexes=FALSE)
[2024-09-26 16:44:25] [WARN]    [OmnipathR] Accessing `collectri` 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.
Error in if (.keep) . else select(., -!!evs_col) : 
  argument is of length zero
> net_dor <- get_dorothea(levels=c('A', 'B', 'C'))
[2024-09-26 16:46:13] [WARN]    [OmnipathR] Accessing `dorothea` 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.
Error in if (.keep) . else select(., -!!evs_col) : 
  argument is of length zero
cnk113 commented 2 months ago

I'm having a similar issue as above

> net <- get_collectri(organism='human', split_complexes=FALSE)
[2024-09-27 01:18:58] [WARN]    [OmnipathR] Accessing `collectri` 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.
Error in if (.keep) . else select(., -!!evs_col) : 
  argument is of length zero
Lemenyeux commented 1 month ago

I'm having a similar issue as above net = get_dorothea(organism = "human", levels = c("A", "B", "C"), weight_dict = list(A = 1, B = 2, C = 3, D = 4)) [2024-09-28 21:18:44] [WARN] [OmnipathR] Accessingdorotheaas 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. Error in if (.keep) . else select(., -!!evs_col) : argument is of length zero

deeenes commented 1 month ago

Here the reason is an error that happens still before the warning, something that causes the original download fail. It might be related to a recent update in the Orthologous Matrix, I've just adjusted OmnipathR to work with the new format, you can try if this fixes your issue:

library(remotes)
remotes::install_github('saezlab/OmnipathR')

library(OmnipathR)
library(decoupleR)

omnipath_cache_wipe()

net = get_dorothea(organism = "human",  levels = c("A", "B", "C"),   weight_dict = list(A = 1, B = 2, C = 3, D = 4))

# if it still fails, please share the OmnipathR log:

omnipath_log()

@MutluHamanakaLab By trying the basic curl example, you confirmed that there is no basic networking issue, such as a TLS issue. And this makes sense if indeed the above mentioned OMA update is the reason.

cnk113 commented 1 month ago

Works for me!

Lemenyeux commented 1 month ago

Works for me! Thanks!

hwoihann commented 1 month ago

This still not works. Log here:

[2024-09-29 02:55:52] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2024-09-29 02:55:52] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 02:55:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 02:55:52] [INFO]    [OmnipathR] Initialized cache: `/home/rstudio/.cache/OmnipathR`.
[2024-09-29 02:55:52] [TRACE]   [OmnipathR] Reading JSON from `/usr/local/lib/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-09-29 02:55:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 02:55:52] [TRACE]   [OmnipathR] Reading JSON from `/usr/local/lib/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-09-29 02:55:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 02:55:52] [TRACE]   [OmnipathR] Reading JSON from `/usr/local/lib/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-09-29 02:55:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 02:55:52] [TRACE]   [OmnipathR] Reading JSON from `/usr/local/lib/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-09-29 02:55:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 02:55:56] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 02:55:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 02:55:56] [TRACE]   [OmnipathR] Removing cache entry 7283c694af48aa30b1b705ccc7613190b1fb3ec5 (omnipath_search_index): no files available.
[2024-09-29 02:56:00] [INFO]    [OmnipathR] Loading database `OmniPath search index`.
[2024-09-29 02:56:00] [INFO]    [OmnipathR] Cache record does not exist: `omnipath_search_index`
[2024-09-29 02:56:00] [SUCCESS] [OmnipathR] Building search index, this may take a few minutes.
[2024-09-29 02:56:00] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 02:56:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 02:56:00] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 02:56:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 02:56:00] [INFO]    [OmnipathR] Cache item `7283c694af48aa30b1b705ccc7613190b1fb3ec5` version 1: status changed from `unknown` to `started`.
[2024-09-29 02:56:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/rstudio/.cache/OmnipathR/7283c694af48aa30b1b705ccc7613190b1fb3ec5-1.rds`.
[2024-09-29 02:56:00] [INFO]    [OmnipathR] Building search index for the interactions database.
[2024-09-29 02:56:00] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 02:56:00] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 02:56:00] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 02:56:00] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 02:56:00] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 02:57:56] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 02:57:56] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 02:57:56] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 02:57:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 02:57:56] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:11:26] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:11:26] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 03:11:26] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:11:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:11:26] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:11:26] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:11:26] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 03:11:26] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:11:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:11:26] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:11:27] [WARN]    [OmnipathR] Accessing `dorothea` 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.
[2024-09-29 03:11:28] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:11:28] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:11:28] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:11:28] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:11:28] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:12:00] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:12:00] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:12:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:12:01] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:12:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:12:01] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `unknown` to `started`.
[2024-09-29 03:12:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/rstudio/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2024-09-29 03:12:03] [TRACE]   [OmnipathR] Exported RDS to `/home/rstudio/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2024-09-29 03:12:03] [INFO]    [OmnipathR] Download ready [key=fd6905e4319c257381102863e2b4443ca0969f15, version=1]
[2024-09-29 03:12:03] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:12:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:12:03] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `started` to `ready`.
[2024-09-29 03:12:03] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-09-29 03:12:21] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-09-29 03:12:58] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:12:58] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 03:12:58] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:12:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:12:59] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:13:31] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:13:31] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 03:13:31] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:13:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:13:31] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:24:01] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:24:01] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 03:24:01] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:24:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:24:01] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:24:40] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:24:40] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 03:24:40] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:24:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:24:40] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:30:28] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:30:28] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 03:30:28] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:30:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:30:28] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:37:13] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:37:13] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 03:37:13] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:37:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:37:13] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:37:14] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:37:14] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 03:37:14] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:37:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:37:14] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:37:14] [WARN]    [OmnipathR] Accessing `dorothea` 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.
[2024-09-29 03:37:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:37:16] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2024-09-29 03:37:17] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:37:17] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-09-29 03:37:35] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-09-29 03:38:22] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:38:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:38:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/rstudio/.cache/OmnipathR`.
[2024-09-29 03:38:23] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:38:23] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:38:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:38:23] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-09-29 03:38:23] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:38:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:38:23] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-09-29 03:38:23] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:38:23] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-09-29 03:38:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] HTTP 200
[2024-09-29 03:38:28] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:38:28] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:38:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:38:28] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:38:28] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-09-29 03:38:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-09-29 03:38:29] [TRACE]   [OmnipathR] Exported RDS to `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:38:29] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-09-29 03:38:29] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:38:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:38:29] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-09-29 03:38:30] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 03:38:30] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 03:38:30] [TRACE]   [OmnipathR] Cache file path: /home/rstudio/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 03:38:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 03:38:30] [TRACE]   [OmnipathR] Loaded data from RDS `/home/rstudio/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 03:38:30] [WARN]    [OmnipathR] Accessing `dorothea` 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.
[2024-09-29 03:38:32] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:38:32] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:38:32] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:38:32] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:38:32] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:38:53] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-09-29 03:38:53] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:38:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:38:53] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:38:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:38:53] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `unknown` to `started`.
[2024-09-29 03:38:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/rstudio/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2024-09-29 03:38:55] [TRACE]   [OmnipathR] Exported RDS to `/home/rstudio/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2024-09-29 03:38:55] [INFO]    [OmnipathR] Download ready [key=fd6905e4319c257381102863e2b4443ca0969f15, version=1]
[2024-09-29 03:38:55] [TRACE]   [OmnipathR] Reading JSON from `/home/rstudio/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 03:38:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 03:38:55] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `started` to `ready`.
[2024-09-29 03:38:55] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-09-29 03:39:11] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
MutluHamanakaLab commented 1 month ago

It worked for me as well! Thanks for the support!!

@hwoihann Have you tried detaching the OmnipathR and updated the package and re-attach the package after the update?

detach("package:OmnipathR", unload = TRUE) # or restart the R session
library(remotes)
remotes::install_github('saezlab/OmnipathR', force = T)

library(OmnipathR)
library(decoupleR)

omnipath_cache_wipe()

net_test = get_dorothea(organism = "human",  levels = c("A", "B", "C"),   weight_dict = list(A = 1, B = 2, C = 3, D = 4))
deeenes commented 1 month ago

@hwoihann I'm assisting someone with the same problem here. Also @MutluHamanakaLab is right, after updating the package and wiping the cache, you should restart the R session (or at least wait 5 min and re-attach the package).