[ Started: 2024-12-06 13:05:19 CET ] [ decoupleR v2.9.7 for BioC-3.20 from https://github.com/saezlab/decoupleR@master (3a41229 2024-10-19 14:06:09) ] * 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 lines 32-46 [vignette_setup] (decoupleR.Rmd) 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 [2024-12-06 13:05:28] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:28] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Contains 1 files. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-06 13:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-06 13:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-06 13:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-06 13:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:28] [TRACE] [OmnipathR] Cache locked: FALSE [2024-12-06 13:05:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-06 13:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:28] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:28] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:28] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-12-06 13:05:28] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-12-06 13:05:28] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-12-06 13:05:28] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-12-06 13:05:28] [TRACE] [OmnipathR] HTTP 200 [2024-12-06 13:05:28] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-12-06 13:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:28] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-12-06 13:05:29] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-12-06 13:05:29] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-12-06 13:05:29] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-12-06 13:05:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:29] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-12-06 13:05:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-12-06 13:05:29] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-12-06 13:05:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-12-06 13:05:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-12-06 13:05:29] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-12-06 13:05:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:29] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-12-06 13:05:29] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-12-06 13:05:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2024-12-06 13:05:29] [TRACE] [OmnipathR] Organism(s): 9606 [2024-12-06 13:05:29] [TRACE] [OmnipathR] Orthology targets: [2024-12-06 13:05:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-06 13:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-06 13:05:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-06 13:05:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-06 13:05:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-06 13:05:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-06 13:05:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-06 13:05:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-06 13:05:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-06 13:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:31] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2024-12-06 13:05:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-12-06 13:05:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-12-06 13:05:33] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2024-12-06 13:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:33] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2024-12-06 13:05:33] [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 [2024-12-06 13:05:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-06 13:05:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2024-12-06 13:05:45] [TRACE] [OmnipathR] Organism(s): 9606 [2024-12-06 13:05:45] [TRACE] [OmnipathR] Orthology targets: [2024-12-06 13:05:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-06 13:05:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-06 13:05:46] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-12-06 13:05:46] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-06 13:05:46] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2024-12-06 13:05:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,extra_attrs=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2024-12-06 13:05:51] [TRACE] [OmnipathR] Organism(s): 9606 [2024-12-06 13:05:51] [TRACE] [OmnipathR] Orthology targets: [2024-12-06 13:05:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-12-06 13:05:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-12-06 13:05:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-12-06 13:05:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-12-06 13:05:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-12-06 13:05:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-12-06 13:05:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-12-06 13:05:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-12-06 13:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:54] [INFO] [OmnipathR] Cache item `76e3673f92890910194d45678b3125a5674920d6` version 1: status changed from `unknown` to `started`. [2024-12-06 13:05:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76e3673f92890910194d45678b3125a5674920d6-1.rds`. [2024-12-06 13:05:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76e3673f92890910194d45678b3125a5674920d6-1.rds`. [2024-12-06 13:05:54] [INFO] [OmnipathR] Download ready [key=76e3673f92890910194d45678b3125a5674920d6, version=1] [2024-12-06 13:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:54] [INFO] [OmnipathR] Cache item `76e3673f92890910194d45678b3125a5674920d6` version 1: status changed from `started` to `ready`. [2024-12-06 13:05:54] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2024-12-06 13:05:57] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2024-12-06 13:05:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,extra_attrs=TRUE,query_type=interactions,datasets=tf_mirna] [2024-12-06 13:05:57] [TRACE] [OmnipathR] Organism(s): 9606 [2024-12-06 13:05:57] [TRACE] [OmnipathR] Orthology targets: [2024-12-06 13:05:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-06 13:05:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-12-06 13:05:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-12-06 13:05:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-12-06 13:05:57] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-12-06 13:05:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-12-06 13:05:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-12-06 13:05:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-12-06 13:05:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-12-06 13:05:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:58] [INFO] [OmnipathR] Cache item `911416570c2aaa914be32ebf7b85e1eb3d1ff162` version 1: status changed from `unknown` to `started`. [2024-12-06 13:05:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/911416570c2aaa914be32ebf7b85e1eb3d1ff162-1.rds`. [2024-12-06 13:05:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/911416570c2aaa914be32ebf7b85e1eb3d1ff162-1.rds`. [2024-12-06 13:05:58] [INFO] [OmnipathR] Download ready [key=911416570c2aaa914be32ebf7b85e1eb3d1ff162, version=1] [2024-12-06 13:05:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-06 13:05:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:05:58] [INFO] [OmnipathR] Cache item `911416570c2aaa914be32ebf7b85e1eb3d1ff162` version 1: status changed from `started` to `ready`. [2024-12-06 13:05:58] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2024-12-06 13:05:58] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-12-06 13:05:58] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2024-12-06 13:05:58] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2024-12-06 13:05:58] [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 [2024-12-06 13:06:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,extra_attrs=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2024-12-06 13:06:16] [TRACE] [OmnipathR] Organism(s): 9606 [2024-12-06 13:06:16] [TRACE] [OmnipathR] Orthology targets: [2024-12-06 13:06:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-12-06 13:06:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/76e3673f92890910194d45678b3125a5674920d6-1.rds`. [2024-12-06 13:06:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-12-06 13:06:17] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2024-12-06 13:06:19] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache. [2024-12-06 13:06:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,extra_attrs=TRUE,query_type=interactions,datasets=tf_mirna] [2024-12-06 13:06:19] [TRACE] [OmnipathR] Organism(s): 9606 [2024-12-06 13:06:19] [TRACE] [OmnipathR] Orthology targets: [2024-12-06 13:06:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-06 13:06:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-06 13:06:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-12-06 13:06:20] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/911416570c2aaa914be32ebf7b85e1eb3d1ff162-1.rds`. [2024-12-06 13:06:20] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-12-06 13:06:20] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2024-12-06 13:06:20] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-12-06 13:06:20] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2024-12-06 13:06:20] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2024-12-06 13:06:20] [SUCCESS] [OmnipathR] Downloaded 232 interactions. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘tf_sc.Rmd’ SUMMARY: processing the following file failed: ‘decoupleR.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2024-12-06 13:06:28 CET ]