[ Started: 2025-03-31 01:10:02 CEST ]
[ decoupleR v2.12.0 for BioC-3.20 from https://git.bioconductor.org/packages/decoupleR@RELEASE_3_20 (bc3245c 2024-10-29 11:00:29) ]
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘decoupleR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘decoupleR.Rmd’ using rmarkdown
Quitting from decoupleR.Rmd:31-46 [vignette_setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `citation()`:
! there is no package called 'AUCell'
---
Backtrace:
▆
1. └─utils::citation("AUCell")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'decoupleR.Rmd' failed with diagnostics:
there is no package called 'AUCell'
--- failed re-building ‘decoupleR.Rmd’
--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2025-03-31 01:10:10] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:10] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-31 01:10:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-31 01:10:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-31 01:10:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-31 01:10:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-31 01:10:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:10] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:10] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:10] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-03-31 01:10:10] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-03-31 01:10:10] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-03-31 01:10:10] [TRACE] [OmnipathR] HTTP 200
[2025-03-31 01:10:10] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:11] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-31 01:10:11] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:11] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-31 01:10:11] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-31 01:10:11] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:11] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-03-31 01:10:11] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Orthology targets:
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-31 01:10:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-03-31 01:10:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-03-31 01:10:11] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-03-31 01:10:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-03-31 01:10:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-03-31 01:10:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-03-31 01:10:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:13] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-03-31 01:10:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-03-31 01:10:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-03-31 01:10:15] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-03-31 01:10:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:15] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-03-31 01:10:15] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
Warning: ggrepel: 445 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘pw_bk.Rmd’
--- re-building ‘pw_sc.Rmd’ using rmarkdown
[2025-03-31 01:10:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-31 01:10:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-03-31 01:10:28] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-31 01:10:28] [TRACE] [OmnipathR] Orthology targets:
[2025-03-31 01:10:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-31 01:10:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-03-31 01:10:29] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-03-31 01:10:29] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-03-31 01:10:29] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
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--- finished re-building ‘pw_sc.Rmd’
--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Orthology targets:
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-03-31 01:10:34] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-03-31 01:10:34] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-03-31 01:10:34] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-03-31 01:10:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:34] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-03-31 01:10:34] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-03-31 01:10:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:34] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-03-31 01:10:36] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Orthology targets:
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-31 01:10:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-03-31 01:10:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-03-31 01:10:36] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-03-31 01:10:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-03-31 01:10:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:36] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-03-31 01:10:36] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-31 01:10:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:36] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-03-31 01:10:36] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-03-31 01:10:37] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
Warning: ggrepel: 754 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘tf_bk.Rmd’
--- re-building ‘tf_sc.Rmd’ using rmarkdown
[2025-03-31 01:10:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-03-31 01:10:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-31 01:10:54] [TRACE] [OmnipathR] Orthology targets:
[2025-03-31 01:10:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-03-31 01:10:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-03-31 01:10:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-03-31 01:10:56] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2025-03-31 01:10:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-03-31 01:10:56] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-31 01:10:56] [TRACE] [OmnipathR] Orthology targets:
[2025-03-31 01:10:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-31 01:10:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-31 01:10:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-03-31 01:10:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-03-31 01:10:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-03-31 01:10:56] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-03-31 01:10:56] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-03-31 01:10:56] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-03-31 01:10:56] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
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--- finished re-building ‘tf_sc.Rmd’
SUMMARY: processing the following file failed:
‘decoupleR.Rmd’
Error: Vignette re-building failed.
Execution halted
[ Finished: 2025-03-31 01:11:03 CEST ]