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get_progeny Error: no applicable method for 'rename' applied to an object of class "list" #143

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bbowles1 opened this issue Oct 20, 2024 · 5 comments
Open

get_progeny Error: no applicable method for 'rename' applied to an object of class "list" #143

bbowles1 opened this issue Oct 20, 2024 · 5 comments
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@deeenes
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database/omnipath Database (OmniPath) related issues

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@bbowles1
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I am attempting to run a simple get_progeny command as shown:

net <- decoupleR::get_progeny(organism = 'mouse', top = 500)

The output below is shown:

[2024-10-19 21:25:49] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-10-19 21:25:50] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 2 records
Error in UseMethod("rename") : 
  no applicable method for 'rename' applied to an object of class "list"

I am using decoupleR_2.10.0 and R v4.4.1.
@deeenes deeenes self-assigned this Oct 20, 2024
@deeenes
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deeenes commented Oct 20, 2024

The "UniProt (rest.uniprot.org): downloaded 2 records" suggests that the response from UniProt contained an error message despite looking like a normal response. Maybe the easiest solution is to wipe the cache of OmnipathR and try the download again:

library(OmnipathR)
library(decoupleR)

omnipath_cache_wipe()
omnipath_set_console_loglevel('trace')

net <- get_progeny(organism = 'mouse', top = 500L)

If it keeps failing, please share the OmnipathR log.

@bbowles1
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Hello, thanks for the quick response! I wiped the cache as directed, but it appears I'm still having trouble downloading the uniprot data. With the expanded logging, I can see that the specific error is: Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, : embedded nul in string... but I've provided the full stack trace below.

This appears to be causing the original no applicable method for 'rename' error, but after clearing the cache and retrying the download successive times (4 at current count) I am unfortunately unable to download the data in the recommended manner.

> net <- get_progeny(organism = 'mouse', top = 500L)

[2024-10-20 15:32:41] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-20 15:32:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:41] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-20 15:32:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:41] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-10-20 15:32:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:41] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-10-20 15:32:41] [TRACE]   [OmnipathR] Cache file path: /Users/bbowles/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-10-20 15:32:41] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-10-20 15:32:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] HTTP 200
[2024-10-20 15:32:43] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:43] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-20 15:32:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:43] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/bbowles/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-20 15:32:43] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-10-20 15:32:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-10-20 15:32:44] [TRACE]   [OmnipathR] Exported RDS to `/Users/bbowles/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-20 15:32:44] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-10-20 15:32:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:44] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-10-20 15:32:44] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-10-20 15:32:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-20 15:32:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-20 15:32:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-20 15:32:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-20 15:32:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-20 15:32:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-20 15:32:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-20 15:32:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-20 15:32:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-20 15:32:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:47] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-10-20 15:32:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/bbowles/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-10-20 15:32:49] [TRACE]   [OmnipathR] Exported RDS to `/Users/bbowles/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-10-20 15:32:49] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-10-20 15:32:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:49] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-10-20 15:32:49] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-10-20 15:32:50] [INFO]    [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/bbowles/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/bbowles/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-10-20 15:32:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:32:50] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/bbowles/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-10-20 15:32:50] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-10-20 15:32:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/bbowles/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-10-20 15:33:17] [INFO]    [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:33:17] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2024-10-20 15:33:17] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/bbowles/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:33:17] [INFO]    [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/bbowles/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2024-10-20 15:33:17] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-10-20 15:33:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-10-20 15:33:36] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` (attempt 1/3); error: embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'
[2024-10-20 15:33:41] [TRACE]   [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-10-20 15:33:57] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` (attempt 2/3); error: embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'
[2024-10-20 15:34:02] [TRACE]   [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-10-20 15:34:20] [ERROR]   [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` (attempt 3/3); error: embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'
Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names,  : 
  embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'

Here's the log trace for rerunning the net <- get_progeny(organism = 'mouse', top = 500L) command and reproducing the original error.

> net <- get_progeny(organism = 'mouse', top = 500L)

[2024-10-20 15:46:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-20 15:46:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:46:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-20 15:46:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-20 15:46:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-20 15:46:51] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/bbowles/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-10-20 15:46:51] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-20 15:46:51] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-10-20 15:46:52] [INFO]    [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2024-10-20 15:46:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-20 15:46:52] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/bbowles/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-20 15:46:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-20 15:46:52] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/bbowles/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-20 15:46:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-10-20 15:46:52] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/bbowles/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-10-20 15:46:52] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2024-10-20 15:46:52] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2024-10-20 15:46:52] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2024-10-20 15:46:52] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2024-10-20 15:46:52] [INFO]    [OmnipathR] No version is available for key `6558a1824894a625b8e3f80538cd3aa6e8a44379` (https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true).
[2024-10-20 15:46:52] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 2 records
Error in UseMethod("rename") : 
  no applicable method for 'rename' applied to an object of class "list"
In addition: Warning message:
In for (i in seq_len(n)) { :
  closing unused connection 3 (https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true)

@koenprange
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koenprange commented Nov 7, 2024 •
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Hi,

I'm having the exact same issue!
It seems to be that uniprot is returning a space somewhere in the middle of a string, and that's breaking the download.

Here's the tail end of the trace log:

> net <- get_progeny(organism = 'mouse', top = 500)

[2024-11-07 12:21:33] [TRACE]   [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-07 12:21:50] [ERROR]   [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` (attempt 3/3); error: embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'
Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names,  : 
  embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'
In addition: Warning messages:
1: In OmnipathR::get_annotation_resources() :
  'OmnipathR::get_annotation_resources' is deprecated.
Use 'annotation_resources' instead.
See help("Deprecated")
2: In OmnipathR::import_omnipath_annotations(resources = name, ...,  :
  'OmnipathR::import_omnipath_annotations' is deprecated.
Use 'annotations' instead.
See help("Deprecated")

@TS83
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TS83 commented Dec 7, 2024

I am getting the same error.
It works with organism=human, but not with mouse or rat.
net <- decoupleR::get_progeny(organism = 'rat', top = 500)
[2024-12-07 07:17:31] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-12-07 07:17:34] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 2 records
Error in UseMethod("rename") :
no applicable method for 'rename' applied to an object of class "list"

packageVersion('decoupleR')
[1] ‘2.9.7’

version
_
platform x86_64-apple-darwin20
arch x86_64
os darwin20
system x86_64, darwin20
status
major 4
minor 4.2
year 2024
month 10
day 31
svn rev 87279
language R
version.string R version 4.4.2 (2024-10-31)
nickname Pile of Leaves

@PauBadiaM
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Any update on this @deeenes ?

@PauBadiaM PauBadiaM added the database/omnipath Database (OmniPath) related issues label Jan 10, 2025
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