[ Started: 2024-10-07 15:50:03 CEST ] [ decoupleR v2.9.7 for BioC-3.20 from https://github.com/saezlab/decoupleR@master (8716d1a 2024-04-11 16:27:42) ] * 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 [2024-10-07 15:50:12] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Contains 1 files. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [TRACE] [OmnipathR] Cache locked: FALSE [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-10-07 15:50:12] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-10-07 15:50:12] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-10-07 15:50:12] [TRACE] [OmnipathR] HTTP 200 [2024-10-07 15:50:12] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-10-07 15:50:12] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-10-07 15:50:12] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:13] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-10-07 15:50:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-10-07 15:50:13] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-10-07 15:50:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-10-07 15:50:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-10-07 15:50:13] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-10-07 15:50:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:13] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-10-07 15:50:13] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-10-07 15:50:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2024-10-07 15:50:13] [TRACE] [OmnipathR] Organism(s): 9606 [2024-10-07 15:50:13] [TRACE] [OmnipathR] Orthology targets: [2024-10-07 15:50:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-10-07 15:50:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:13] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: HTTP error 500. [2024-10-07 15:50:18] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:18] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 2/3); error: HTTP error 500. [2024-10-07 15:50:23] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:23] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 3/3); error: HTTP error 500. [2024-10-07 15:50:23] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`; error: HTTP error 500. [2024-10-07 15:50:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:23] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2024-10-07 15:50:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-10-07 15:50:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-10-07 15:50:23] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2024-10-07 15:50:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:23] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2024-10-07 15:50:23] [SUCCESS] [OmnipathR] Downloaded 2 annotation records. [2024-10-07 15:50:23] [WARN] [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2024-10-07 15:50:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-10-07 15:50:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-10-07 15:50:23] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-10-07 15:50:23] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-10-07 15:50:23] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-10-07 15:50:25] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-10-07 15:50:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:25] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`. [2024-10-07 15:50:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-10-07 15:50:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-10-07 15:50:27] [INFO] [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1] [2024-10-07 15:50:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:27] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`. [2024-10-07 15:50:27] [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 [2024-10-07 15:50:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-10-07 15:50:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2024-10-07 15:50:40] [TRACE] [OmnipathR] Organism(s): 9606 [2024-10-07 15:50:40] [TRACE] [OmnipathR] Orthology targets: [2024-10-07 15:50:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-10-07 15:50:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-10-07 15:50:40] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-10-07 15:50:40] [SUCCESS] [OmnipathR] Loaded 2 annotation records from cache. [2024-10-07 15:50:40] [WARN] [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2024-10-07 15:50:40] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-10-07 15:50:41] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-10-07 15:50:41] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-10-07 15:50:41] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2024-10-07 15:50:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,extra_attrs=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2024-10-07 15:50:45] [TRACE] [OmnipathR] Organism(s): 9606 [2024-10-07 15:50:45] [TRACE] [OmnipathR] Orthology targets: [2024-10-07 15:50:45] [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` [2024-10-07 15:50:45] [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` [2024-10-07 15:50:45] [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` [2024-10-07 15:50:45] [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` [2024-10-07 15:50:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2024-10-07 15:50:45] [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` [2024-10-07 15:50:45] [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` [2024-10-07 15:50:46] [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` [2024-10-07 15:50:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:46] [INFO] [OmnipathR] Cache item `76e3673f92890910194d45678b3125a5674920d6` version 1: status changed from `unknown` to `started`. [2024-10-07 15:50:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76e3673f92890910194d45678b3125a5674920d6-1.rds`. [2024-10-07 15:50:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76e3673f92890910194d45678b3125a5674920d6-1.rds`. [2024-10-07 15:50:46] [INFO] [OmnipathR] Download ready [key=76e3673f92890910194d45678b3125a5674920d6, version=1] [2024-10-07 15:50:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:50:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:46] [INFO] [OmnipathR] Cache item `76e3673f92890910194d45678b3125a5674920d6` version 1: status changed from `started` to `ready`. [2024-10-07 15:50:46] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2024-10-07 15:50:49] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2024-10-07 15:50:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,extra_attrs=TRUE,query_type=interactions,datasets=tf_mirna] [2024-10-07 15:50:49] [TRACE] [OmnipathR] Organism(s): 9606 [2024-10-07 15:50:49] [TRACE] [OmnipathR] Orthology targets: [2024-10-07 15:50:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-10-07 15:50:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:50:49] [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` [2024-10-07 15:50:49] [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` [2024-10-07 15:50:49] [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` [2024-10-07 15:50:49] [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` [2024-10-07 15:50:49] [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` [2024-10-07 15:50:49] [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` [2024-10-07 15:50:49] [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` [2024-10-07 15:50:49] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` (attempt 1/3); error: HTTP error 500. [2024-10-07 15:50:54] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-10-07 15:50:54] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` (attempt 2/3); error: HTTP error 500. [2024-10-07 15:50:59] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2024-10-07 15:51:00] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` (attempt 3/3); error: HTTP error 500. [2024-10-07 15:51:00] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic`; error: HTTP error 500. [2024-10-07 15:51:00] [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` [2024-10-07 15:51:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:51:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:51:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:51:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:51:00] [INFO] [OmnipathR] Cache item `911416570c2aaa914be32ebf7b85e1eb3d1ff162` version 1: status changed from `unknown` to `started`. [2024-10-07 15:51:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/911416570c2aaa914be32ebf7b85e1eb3d1ff162-1.rds`. [2024-10-07 15:51:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/911416570c2aaa914be32ebf7b85e1eb3d1ff162-1.rds`. [2024-10-07 15:51:00] [INFO] [OmnipathR] Download ready [key=911416570c2aaa914be32ebf7b85e1eb3d1ff162, version=1] [2024-10-07 15:51:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-07 15:51:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:51:00] [INFO] [OmnipathR] Cache item `911416570c2aaa914be32ebf7b85e1eb3d1ff162` version 1: status changed from `started` to `ready`. [2024-10-07 15:51:00] [ERROR] [OmnipathR] `only_from` can be called only on data frames with `evidences` column. [2024-10-07 15:51:00] [ERROR] [OmnipathR] [decoupleR] Failed to download TF-miRNA interactions from OmniPath. For more information, see the OmnipathR log. 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 [2024-10-07 15:51:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,extra_attrs=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2024-10-07 15:51:17] [TRACE] [OmnipathR] Organism(s): 9606 [2024-10-07 15:51:17] [TRACE] [OmnipathR] Orthology targets: [2024-10-07 15:51:17] [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` [2024-10-07 15:51:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/76e3673f92890910194d45678b3125a5674920d6-1.rds`. [2024-10-07 15:51:17] [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` [2024-10-07 15:51:17] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2024-10-07 15:51:20] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache. [2024-10-07 15:51:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,extra_attrs=TRUE,query_type=interactions,datasets=tf_mirna] [2024-10-07 15:51:20] [TRACE] [OmnipathR] Organism(s): 9606 [2024-10-07 15:51:20] [TRACE] [OmnipathR] Orthology targets: [2024-10-07 15:51:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-10-07 15:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-07 15:51:20] [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` [2024-10-07 15:51:20] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/911416570c2aaa914be32ebf7b85e1eb3d1ff162-1.rds`. [2024-10-07 15:51:20] [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` [2024-10-07 15:51:20] [ERROR] [OmnipathR] `only_from` can be called only on data frames with `evidences` column. [2024-10-07 15:51:20] [ERROR] [OmnipathR] [decoupleR] Failed to download TF-miRNA interactions from OmniPath. For more information, see the OmnipathR log. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘tf_sc.Rmd’ SUMMARY: processing the following file failed: ‘decoupleR.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2024-10-07 15:51:26 CEST ]