[ Started: 2024-11-14 12:22:46 CET ] [ OmnipathR v3.15.1 for BioC-3.20 from https://github.com/saezlab/OmnipathR@master (4ffd9ec 2024-11-07 16:20:19) ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Contains 1 files. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpEsgPFJ/Rinst18f00017a21459/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpEsgPFJ/Rinst18f00017a21459/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpEsgPFJ/Rinst18f00017a21459/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpEsgPFJ/Rinst18f00017a21459/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [TRACE] [OmnipathR] Cache locked: FALSE [2024-11-14 12:22:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2024-11-14 12:22:59] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-11-14 12:22:59] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-14 12:22:59] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-14 12:22:59] [TRACE] [OmnipathR] HTTP 200 [2024-11-14 12:22:59] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-11-14 12:22:59] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-11-14 12:22:59] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-11-14 12:22:59] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-11-14 12:22:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-11-14 12:22:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-11-14 12:22:59] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-11-14 12:22:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:22:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:22:59] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-11-14 12:22:59] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-11-14 12:22:59] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:22:59] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:22:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-11-14 12:22:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-11-14 12:22:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-11-14 12:22:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-11-14 12:22:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-11-14 12:22:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-11-14 12:22:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-11-14 12:23:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-11-14 12:23:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:00] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2024-11-14 12:23:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2024-11-14 12:23:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2024-11-14 12:23:00] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2024-11-14 12:23:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:00] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2024-11-14 12:23:04] [SUCCESS] [OmnipathR] Downloaded 128218 interactions. [2024-11-14 12:23:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2024-11-14 12:23:07] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:23:07] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:23:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:07] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2024-11-14 12:23:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2024-11-14 12:23:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2024-11-14 12:23:07] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2024-11-14 12:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:07] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2024-11-14 12:23:08] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships. [2024-11-14 12:23:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2024-11-14 12:23:09] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:23:09] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:23:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:09] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2024-11-14 12:23:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-11-14 12:23:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-11-14 12:23:10] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2024-11-14 12:23:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:10] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2024-11-14 12:23:12] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. [2024-11-14 12:23:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2024-11-14 12:23:12] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:23:12] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:23:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2024-11-14 12:23:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2024-11-14 12:23:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2024-11-14 12:23:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2024-11-14 12:23:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2024-11-14 12:23:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2024-11-14 12:23:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2024-11-14 12:23:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2024-11-14 12:23:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:12] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2024-11-14 12:23:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2024-11-14 12:23:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2024-11-14 12:23:13] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2024-11-14 12:23:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:13] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2024-11-14 12:23:13] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes. [2024-11-14 12:23:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2024-11-14 12:23:13] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:23:13] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:23:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-11-14 12:23:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-11-14 12:23:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-11-14 12:23:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-11-14 12:23:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-11-14 12:23:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-11-14 12:23:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-11-14 12:23:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-11-14 12:23:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-11-14 12:23:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:13] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2024-11-14 12:23:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-11-14 12:23:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-11-14 12:23:14] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2024-11-14 12:23:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:14] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2024-11-14 12:23:14] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records. [2024-11-14 12:23:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2024-11-14 12:23:14] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:23:14] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:23:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-11-14 12:23:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-11-14 12:23:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-11-14 12:23:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-11-14 12:23:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-11-14 12:23:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-11-14 12:23:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-11-14 12:23:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-11-14 12:23:14] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` (attempt 1/3); error: cannot open the connection [2024-11-14 12:23:19] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-11-14 12:23:19] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` (attempt 2/3); error: cannot open the connection [2024-11-14 12:23:24] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-11-14 12:23:24] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` (attempt 3/3); error: cannot open the connection [2024-11-14 12:23:24] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`; error: cannot open the connection [2024-11-14 12:23:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-11-14 12:23:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:24] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2024-11-14 12:23:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2024-11-14 12:23:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2024-11-14 12:23:24] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2024-11-14 12:23:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:24] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2024-11-14 12:23:24] [SUCCESS] [OmnipathR] Downloaded 2 annotation records. Quitting from lines 313-317 [uniprot-loc-1] (bioc_workshop.Rmd) Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics: no applicable method for 'pull' applied to an object of class "list" --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2024-11-14 12:23:24] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2024-11-14 12:23:24] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-11-14 12:23:25] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2024-11-14 12:23:25] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-11-14 12:23:25] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2024-11-14 12:23:25] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-11-14 12:23:25] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2024-11-14 12:23:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2024-11-14 12:23:25] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:23:25] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:23:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:25] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-11-14 12:23:25] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:23:27] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2024-11-14 12:23:27] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2024-11-14 12:23:27] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2024-11-14 12:23:27] [TRACE] [OmnipathR] BioMart query: [2024-11-14 12:23:27] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2024-11-14 12:23:27] [INFO] [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2024-11-14 12:23:27] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2024-11-14 12:23:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:27] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2024-11-14 12:23:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2024-11-14 12:23:27] [INFO] [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2024-11-14 12:23:27] [TRACE] [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2024-11-14 12:23:38] [TRACE] [OmnipathR] HTTP 200 [2024-11-14 12:23:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2024-11-14 12:23:38] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2024-11-14 12:23:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:38] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2024-11-14 12:23:38] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 122413 records [2024-11-14 12:23:38] [TRACE] [OmnipathR] Translating complexes: 592 complexes in data. [2024-11-14 12:23:38] [TRACE] [OmnipathR] 433 complexes after removing the ones mapping to more than 1 items in target identifier space. [2024-11-14 12:23:39] [TRACE] [OmnipathR] Translated 433 complexes to 433. [2024-11-14 12:23:39] [TRACE] [OmnipathR] 67526 rows before translation, 4551 uniprot IDs in column `source`. [2024-11-14 12:23:39] [TRACE] [OmnipathR] 67599 rows after translation; translated 4551 `uniprot` IDs in column `source` to 4392 `genesymbol` IDs in column `genesymbol_source`. [2024-11-14 12:23:39] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2024-11-14 12:23:39] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2024-11-14 12:23:39] [TRACE] [OmnipathR] BioMart query: [2024-11-14 12:23:39] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2024-11-14 12:23:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2024-11-14 12:23:40] [SUCCESS] [OmnipathR] www.ensembl.org: loaded 122413 records from cache [2024-11-14 12:23:40] [TRACE] [OmnipathR] Translating complexes: 311 complexes in data. [2024-11-14 12:23:40] [TRACE] [OmnipathR] 220 complexes after removing the ones mapping to more than 1 items in target identifier space. [2024-11-14 12:23:40] [TRACE] [OmnipathR] Translated 220 complexes to 220. [2024-11-14 12:23:40] [TRACE] [OmnipathR] 67599 rows before translation, 4638 uniprot IDs in column `target`. [2024-11-14 12:23:40] [TRACE] [OmnipathR] 69184 rows after translation; translated 4638 `uniprot` IDs in column `target` to 4555 `genesymbol` IDs in column `genesymbol_target`. [2024-11-14 12:23:40] [INFO] [OmnipathR] OmniPath PPI for COSMOS PKN ready: 138490 interactions. --- finished re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2024-11-14 12:23:41] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2024-11-14 12:23:41] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2024-11-14 12:23:41] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2024-11-14 12:23:41] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2024-11-14 12:23:41] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2024-11-14 12:23:41] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2024-11-14 12:23:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:41] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2024-11-14 12:23:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2024-11-14 12:23:41] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2024-11-14 12:23:41] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2024-11-14 12:23:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2024-11-14 12:23:58] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2024-11-14 12:23:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:23:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:23:58] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2024-11-14 12:23:58] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20428 records [2024-11-14 12:23:58] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2024-11-14 12:24:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2024-11-14 12:24:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2024-11-14 12:24:09] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:24:09] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:24:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:09] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-11-14 12:24:09] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:12] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2024-11-14 12:24:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2024-11-14 12:24:13] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:24:13] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:24:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-11-14 12:24:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-11-14 12:24:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-11-14 12:24:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-11-14 12:24:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-11-14 12:24:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-11-14 12:24:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-11-14 12:24:13] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 1/3); error: cannot open the connection [2024-11-14 12:24:18] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-11-14 12:24:18] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 2/3); error: cannot open the connection [2024-11-14 12:24:23] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-11-14 12:24:24] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 3/3); error: cannot open the connection [2024-11-14 12:24:24] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`; error: cannot open the connection [2024-11-14 12:24:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-11-14 12:24:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:24:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:24:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:24] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2024-11-14 12:24:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2024-11-14 12:24:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2024-11-14 12:24:24] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2024-11-14 12:24:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:24:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:24] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. Quitting from lines 56-58 [load-interactions] (extra_attrs.Rmd) Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics: no applicable method for 'mutate' applied to an object of class "list" --- failed re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2024-11-14 12:24:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-11-14 12:24:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2024-11-14 12:24:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2024-11-14 12:24:25] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:24:25] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:24:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-11-14 12:24:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:25] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:25] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:25] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 1/3); error: cannot open the connection [2024-11-14 12:24:30] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:30] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 2/3); error: cannot open the connection [2024-11-14 12:24:35] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:35] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 3/3); error: cannot open the connection [2024-11-14 12:24:35] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`; error: cannot open the connection [2024-11-14 12:24:35] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-11-14 12:24:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:24:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:24:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:35] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2024-11-14 12:24:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2024-11-14 12:24:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2024-11-14 12:24:35] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2024-11-14 12:24:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:24:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:35] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. Quitting from lines 167-175 [interactions] (omnipath_intro.Rmd) Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics: no applicable method for 'mutate' applied to an object of class "list" --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2024-11-14 12:24:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2024-11-14 12:24:36] [TRACE] [OmnipathR] Organism(s): 9606 [2024-11-14 12:24:36] [TRACE] [OmnipathR] Orthology targets: [2024-11-14 12:24:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-11-14 12:24:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-11-14 12:24:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-11-14 12:24:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-11-14 12:24:36] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-11-14 12:24:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-11-14 12:24:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-11-14 12:24:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-11-14 12:24:36] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` (attempt 1/3); error: cannot open the connection [2024-11-14 12:24:41] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-11-14 12:24:41] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` (attempt 2/3); error: cannot open the connection [2024-11-14 12:24:46] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-11-14 12:24:46] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` (attempt 3/3); error: cannot open the connection [2024-11-14 12:24:46] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`; error: cannot open the connection [2024-11-14 12:24:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-11-14 12:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:46] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2024-11-14 12:24:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2024-11-14 12:24:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2024-11-14 12:24:46] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2024-11-14 12:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-14 12:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-14 12:24:46] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2024-11-14 12:24:46] [SUCCESS] [OmnipathR] Downloaded 2 annotation records. Quitting from lines 56-67 [tfcensus-op] (paths.Rmd) Error: processing vignette 'paths.Rmd' failed with diagnostics: no applicable method for 'pull' applied to an object of class "list" --- failed re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘bioc_workshop.Rmd’ ‘extra_attrs.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2024-11-14 12:24:46 CET ]