search

saezlab / CollecTRI

Gene regulatory network containing signed transcription factor-target gene interactions
GNU General Public License v3.0
63 stars 6 forks source link

decoupleR::get_collectri error #21

Open cf98 opened 1 month ago

cf98 commented 1 month ago

Hi Saezlab,

Thanks for developing this tool for TF analysis! I am following this vignette, and run into issues with command:

net <- decoupleR::get_collectri(organism='human', split_complexes=FALSE)

The error message also came after a warning, here's the entire message: 

[2024-09-29 12:34:35] [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

My R version is 4.4.1 (arm64, mac) Current package versions:

           decoupleR                dplyr              ggplot2            OmnipathR            patchwork 
   "decoupleR 2.9.7"        "dplyr 1.1.4"      "ggplot2 3.5.1"  "OmnipathR 3.13.26"    "patchwork 1.3.0" 
            pheatmap              remotes               Seurat         SeuratObject                   sp 
   "pheatmap 1.0.12"      "remotes 2.5.0"       "Seurat 5.1.0" "SeuratObject 5.0.2"           "sp 2.1.4" 
              tibble                tidyr 
      "tibble 3.2.1"        "tidyr 1.3.1"

Can you help on this? Thanks!

roxUCL commented 1 month ago

Hello, same here. Same error same R 4.4.1 (arm64, mac) and same installed package versions [1] pheatmap_1.0.12 dplyr_1.1.4 devtools_2.4.5 usethis_3.0.0 decoupleR_2.9.7 OmnipathR_3.13.26. Could you kindly help on this?

gabora commented 1 month ago

Hi @deeenes , this seems to me an Omnipath issue, or what do you think?

deeenes commented 1 month ago

See https://github.com/saezlab/OmnipathR/issues/106

TLDR:

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

library(OmnipathR)
library(decoupleR)

omnipath_cache_wipe()

net = get_collectri(organism='human', split_complexes=FALSE)

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

omnipath_log()
roxUCL commented 1 month ago

Thanks for your supoport in this.

I think the error is still there this is omnipath_log(): [2024-09-30 12:18:53] [INFO] [OmnipathR] Welcome to OmnipathR! [2024-09-30 12:18:53] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 12:18:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 12:18:53] [INFO] [OmnipathR] Initialized cache: /Users/rossellarispoli/Library/Caches/OmnipathR. [2024-09-30 12:18:53] [TRACE] [OmnipathR] Reading JSON from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json (encoding: UTF-8). [2024-09-30 12:18:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 12:18:53] [TRACE] [OmnipathR] Reading JSON from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json (encoding: UTF-8). [2024-09-30 12:18:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 12:18:54] [TRACE] [OmnipathR] Reading JSON from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json (encoding: UTF-8). [2024-09-30 12:18:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 12:18:54] [TRACE] [OmnipathR] Reading JSON from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json (encoding: UTF-8). [2024-09-30 12:18:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 12:19:13] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 12:19:13] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-30 12:19:13] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 12:19:13] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 12:19:13] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 12:19:14] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 12:19:14] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-30 12:19:14] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 12:19:14] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 12:19:14] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 12:19:14] [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. [2024-09-30 12:19:14] [TRACE] [OmnipathR] Looking up in cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 12:19:15] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds. [2024-09-30 12:19:15] [INFO] [OmnipathR] Loaded from cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 12:19:15] [TRACE] [OmnipathR] Converting JSON column evidences to list. [2024-09-30 12:19:17] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-09-30 12:25:29] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 12:25:29] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-30 12:25:29] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 12:25:29] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 12:25:29] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 12:28:27] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 12:28:27] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-30 12:28:27] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 12:28:27] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 12:28:27] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 12:28:28] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 12:28:28] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-30 12:28:28] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 12:28:28] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 12:28:28] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 12:28:29] [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. [2024-09-30 12:28:29] [TRACE] [OmnipathR] Looking up in cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 12:28:29] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds. [2024-09-30 12:28:29] [INFO] [OmnipathR] Loaded from cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 12:28:29] [TRACE] [OmnipathR] Converting JSON column evidences to list. [2024-09-30 12:28:31] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-09-30 12:41:57] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 12:41:57] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-30 12:41:57] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 12:41:57] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 12:41:57] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 12:41:58] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 12:41:58] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-30 12:41:58] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 12:41:58] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 12:41:58] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 12:41:58] [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. [2024-09-30 12:41:58] [TRACE] [OmnipathR] Looking up in cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 12:41:59] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds. [2024-09-30 12:41:59] [INFO] [OmnipathR] Loaded from cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 12:41:59] [TRACE] [OmnipathR] Converting JSON column evidences to list. [2024-09-30 12:42:03] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-09-30 13:28:49] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 13:28:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 13:28:49] [SUCCESS] [OmnipathR] Removing all cache contents from /Users/rossellarispoli/Library/Caches/OmnipathR. [2024-09-30 13:28:53] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 13:28:53] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 13:28:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 13:28:53] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-09-30 13:28:53] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 13:28:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 13:28:53] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-09-30 13:28:53] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 13:28:53] [INFO] [OmnipathR] Retrieving URL: https://www.ensembl.org/info/about/species.html [2024-09-30 13:28:53] [TRACE] [OmnipathR] Attempt 1/3: https://www.ensembl.org/info/about/species.html [2024-09-30 13:28:54] [TRACE] [OmnipathR] HTTP 200 [2024-09-30 13:28:54] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-09-30 13:28:54] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 13:28:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 13:28:54] [INFO] [OmnipathR] Cache item 7332486db7400730697234bad76ca0c8e4d00799 version 1: status changed from unknown to ready. [2024-09-30 13:28:55] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 13:28:55] [INFO] [OmnipathR] Cache record does not exist: https://omabrowser.org/All/oma-species.txt [2024-09-30 13:28:55] [TRACE] [OmnipathR] Could not find in cache, initiating download: https://omabrowser.org/All/oma-species.txt. [2024-09-30 13:28:55] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 13:28:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 13:28:55] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 13:28:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 13:28:55] [INFO] [OmnipathR] Cache item 30e690cbb55dfc63b5903ab337f34ffc2f4be397 version 1: status changed from unknown to started. [2024-09-30 13:28:55] [TRACE] [OmnipathR] Exporting object to RDS: /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 13:28:55] [INFO] [OmnipathR] Retrieving URL: https://omabrowser.org/All/oma-species.txt [2024-09-30 13:28:55] [TRACE] [OmnipathR] Attempt 1/3: https://omabrowser.org/All/oma-species.txt [2024-09-30 13:28:57] [TRACE] [OmnipathR] Exported RDS to /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 13:28:57] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-09-30 13:28:57] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 13:28:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 13:28:57] [INFO] [OmnipathR] Cache item 30e690cbb55dfc63b5903ab337f34ffc2f4be397 version 1: status changed from started to ready. [2024-09-30 13:28:58] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 13:28:58] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-30 13:28:58] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 13:28:58] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 13:28:58] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 13:29:00] [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. [2024-09-30 13:29:00] [TRACE] [OmnipathR] Looking up in cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 13:29:00] [INFO] [OmnipathR] Cache record does not exist: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 13:29:00] [TRACE] [OmnipathR] Attempting http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 13:29:00] [INFO] [OmnipathR] Retrieving URL: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 13:29:00] [TRACE] [OmnipathR] Attempt 1/3: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 13:29:01] [INFO] [OmnipathR] Successfully retrieved: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 13:29:01] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 13:29:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 13:29:01] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 13:29:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 13:29:01] [INFO] [OmnipathR] Cache item a2bbed8b281906d09d7cf983d102402e5de5da8c version 1: status changed from unknown to started. [2024-09-30 13:29:01] [TRACE] [OmnipathR] Exporting object to RDS: /Users/rossellarispoli/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds. [2024-09-30 13:29:01] [TRACE] [OmnipathR] Exported RDS to /Users/rossellarispoli/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds. [2024-09-30 13:29:01] [INFO] [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1] [2024-09-30 13:29:01] [TRACE] [OmnipathR] Reading JSON from /Users/rossellarispoli/Library/Caches/OmnipathR/cache.json (encoding: UTF-8). [2024-09-30 13:29:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-30 13:29:01] [INFO] [OmnipathR] Cache item a2bbed8b281906d09d7cf983d102402e5de5da8c version 1: status changed from started to ready. [2024-09-30 13:29:01] [TRACE] [OmnipathR] Converting JSON column evidences to list. [2024-09-30 13:29:04] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-09-30 13:29:25] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 13:29:25] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-30 13:29:25] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 13:29:26] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 13:29:26] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 13:29:26] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names. [2024-09-30 13:29:26] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-30 13:29:26] [TRACE] [OmnipathR] Cache file path: /Users/rossellarispoli/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-30 13:29:26] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt. [2024-09-30 13:29:26] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds. [2024-09-30 13:29:27] [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. [2024-09-30 13:29:27] [TRACE] [OmnipathR] Looking up in cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 13:29:27] [TRACE] [OmnipathR] Loaded data from RDS /Users/rossellarispoli/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds. [2024-09-30 13:29:27] [INFO] [OmnipathR] Loaded from cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz [2024-09-30 13:29:27] [TRACE] [OmnipathR] Converting JSON column evidences to list. [2024-09-30 13:29:30] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any

deeenes commented 1 month ago

Hi @roxUCL,

Have you done both of these?

If so, can you please share the version of the loaded package, and the output of the oma_organisms function?

library(OmnipathR)

packageVersion('OmnipathR')

oma_organisms()
roxUCL commented 1 month ago

Hello, thanks for your support yes I have installed from the github page and this is the version ‘3.13.26’.

For the oma_ornaism() it return a tibble of2,927 × 5 do you want me to save it into a file and share with you or just check the human organism?

deeenes commented 1 month ago

No need for the whole tibble, just copy-paste the header and first row, like this:

 oma_organisms()
# A tibble: 2,927 × 6
   oma_code ncbi_tax_id latin_name                                                                                          genome_source  oma_version                                                    gtdb_tax_id
   <chr>          <dbl> <chr>                                                                                               <chr>          <chr>                                                                <dbl>
 1 ABSGL           4829 Absidia glauca                                                                                      EnsemblGenomes Ensembl Fungi 48; AG_v1                                                 NA

The column layout of this dataset has been changed by its provider, this caused the error for 3-4 other users, hence we first have to make sure it's correctly processed in your system. If it is, then you have a different error, and we'll look for it further.

roxUCL commented 1 month ago 

# A tibble: 2,927 × 5
   oma_code  oma_tax_id ncbi_tax_id                                                                                         gtdb_genome    latin_name                                                
   <chr>          <dbl> <chr>                                                                                               <chr>          <chr>                                                     
 1 ABSGL           4829 Absidia glauca                                                                                      EnsemblGenomes Ensembl Fungi 48; AG_v1                                   
 2 ACACA        1257118 Acanthamoeba castellanii str. Neff                                                                  Genbank        Genbank; Acastellanii.strNEFF v1; GCF_000313135.1; 07-OCT…
 3 ACAM1     -644103924 Acaryochloris marina (strain MBIC 11017)   ```
deeenes commented 1 month ago

@roxUCL This is the new content, but old header: you need to get rid of the old cache file, easiest way is to wipe the cache completely, still before calling oma_organisms. Then check if you get the same column layout as in my comment above.

library(OmnipathR)

omnipath_cache_wipe()

oma_organisms()
roxUCL commented 1 month ago

I think I have tried this before with no success.

I have done it now again and again it does not seams to me that there is a change

> library(OmnipathR)
> 
> omnipath_cache_wipe()
[2024-09-30 14:47:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/rossellarispoli/Library/Caches/OmnipathR`.
> 
 oma_organisms()
# A tibble: 2,927 × 5
   oma_code  oma_tax_id ncbi_tax_id                                                                                         gtdb_genome    latin_name                                                
   <chr>          <dbl> <chr>                                                                                               <chr>          <chr>                                                     
 1 ABSGL           4829 Absidia glauca                                                                                      EnsemblGenomes Ensembl Fungi 48; AG_v1                                   
 2 ACACA        1257118 Acanthamoeba castellanii str. Neff                                                                  Genbank        Genbank; Acastellanii.strNEFF v1; GCF_000313135.1; 07-OCT…
 3 ACAM1     -644103924 Acaryochloris marina (strain MBIC 11017)

should I amnually change the header?

deeenes commented 1 month ago

I can explain the 5 columns layout we see in your environment only if I assume the new file has been saved in the cache by the old code, and then read from there also by the old code. This definitely happened before you updated OmnipathR. But the absence of gtdb_tax_id column suggests that still the old code is active in your current session. However, packageVersion('OmnipathR') == '3.13.26' should guarantee that the code is up-to-date. I assume, since the reinstallation and cache wipe you've started a new R session?

First, let's check the loaded code is indeed up-to-date:

print(oma_organisms)

Then let's see all the details about the cache item:

omnipathr.env$cache[['30e690cbb55dfc63b5903ab337f34ffc2f4be397']]

Though the wipe above should've removed this file, so it should be a very fresh copy, maybe you can try manually removing and loading it again in a fresh session:

rm /Users/rossellarispoli/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397*
library(OmnipathR)
omnipath_set_console_loglevel('trace')
omnipath_cache_clean_db()
oma_organisms()
cf98 commented 1 month ago

I think I have tried this before with no success.

I have done it now again and again it does not seams to me that there is a change

> library(OmnipathR)
> 
> omnipath_cache_wipe()
[2024-09-30 14:47:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/rossellarispoli/Library/Caches/OmnipathR`.
> 
 oma_organisms()
# A tibble: 2,927 × 5
   oma_code  oma_tax_id ncbi_tax_id                                                                                         gtdb_genome    latin_name                                                
   <chr>          <dbl> <chr>                                                                                               <chr>          <chr>                                                     
 1 ABSGL           4829 Absidia glauca                                                                                      EnsemblGenomes Ensembl Fungi 48; AG_v1                                   
 2 ACACA        1257118 Acanthamoeba castellanii str. Neff                                                                  Genbank        Genbank; Acastellanii.strNEFF v1; GCF_000313135.1; 07-OCT…
 3 ACAM1     -644103924 Acaryochloris marina (strain MBIC 11017)

should I amnually change the header?

Same here! I have also tried wipe out old cache files again and again, it didn't work unfortunately. Thanks for sharing the issues you run into!

deeenes commented 1 month ago

@cf98 I can tell you the same as 2 comments above: the question is why and how the old code operates here when the package is supposed to be updated. We should check what is the loaded code:

library(OmnipathR)

print(oma_organisms)

And a sessionInfo would be helpful too:

library(OmnipathR)

sessionInfo()
roxUCL commented 1 month ago

thanks @deeenes removing the file OmnipathR cache file and loading it again in a fresh session worked for me

deeenes commented 1 month ago

@roxUCL I'm glad to hear! It means omnipath_cache_wipe didn't work, that's really weird.

@cf98 - Then maybe it will work for you too -- see 4 comments above, how an individual cache file can be removed.