[ Started: 2023-04-05 00:16:56 CEST ]
[ OmnipathR v3.7.11 for BioC-3.17 from https://github.com/saezlab/OmnipathR@master ]
* 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
Warning in png(..., res = dpi, units = "in") :
unable to open connection to X11 display ''
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:04] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Contains 1 files.
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpdQ3KXv/Rinst367c1541b50f3e/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-05 00:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpdQ3KXv/Rinst367c1541b50f3e/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-05 00:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpdQ3KXv/Rinst367c1541b50f3e/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-05 00:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpdQ3KXv/Rinst367c1541b50f3e/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-05 00:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:04] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-04-05 00:17:04] [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`
[2023-04-05 00:17:04] [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`
[2023-04-05 00:17:04] [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`
[2023-04-05 00:17:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:05] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2023-04-05 00:17:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2023-04-05 00:17:05] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2023-04-05 00:17:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:05] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:08] [SUCCESS] [OmnipathR] Downloaded 125303 interactions.
[2023-04-05 00:17:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:17:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:17:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:17:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:11] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-04-05 00:17:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-04-05 00:17:11] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2023-04-05 00:17:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:11] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:12] [SUCCESS] [OmnipathR] Downloaded 42248 enzyme-substrate relationships.
[2023-04-05 00:17:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:17:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:17:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:17:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:13] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-04-05 00:17:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-04-05 00:17:14] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2023-04-05 00:17:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:14] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:16] [SUCCESS] [OmnipathR] Downloaded 92262 interactions.
[2023-04-05 00:17:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2023-04-05 00:17:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2023-04-05 00:17:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2023-04-05 00:17:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:17] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2023-04-05 00:17:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2023-04-05 00:17:17] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2023-04-05 00:17:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:17] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:17] [SUCCESS] [OmnipathR] Downloaded 32761 protein complexes.
[2023-04-05 00:17:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-04-05 00:17:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-04-05 00:17:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-04-05 00:17:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:18] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-04-05 00:17:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-04-05 00:17:18] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2023-04-05 00:17:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:18] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:18] [SUCCESS] [OmnipathR] Downloaded 73481 annotation records.
[2023-04-05 00:17:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-04-05 00:17:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-04-05 00:17:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-04-05 00:17:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:19] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2023-04-05 00:17:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2023-04-05 00:17:19] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2023-04-05 00:17:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:19] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:19] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2023-04-05 00:17:19] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest.
[2023-04-05 00:17:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:19] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-04-05 00:17:19] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-04-05 00:17:19] [SUCCESS] [OmnipathR] Loaded 73481 annotation records from cache.
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-04-05 00:17:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:20] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2023-04-05 00:17:20] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:20] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:20] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-04-05 00:17:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:20] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-04-05 00:17:20] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2023-04-05 00:17:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:20] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:20] [SUCCESS] [OmnipathR] Downloaded 2451 annotation records.
[2023-04-05 00:17:21] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-04-05 00:17:21] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:17:23] [SUCCESS] [OmnipathR] Loaded 92262 interactions from cache.
[2023-04-05 00:17:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:24] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-04-05 00:17:24] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-04-05 00:17:24] [SUCCESS] [OmnipathR] Loaded 2451 annotation records from cache.
[2023-04-05 00:17:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2023-04-05 00:17:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2023-04-05 00:17:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2023-04-05 00:17:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:25] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-04-05 00:17:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-04-05 00:17:26] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2023-04-05 00:17:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:26] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:27] [SUCCESS] [OmnipathR] Downloaded 323572 intercellular communication role records.
[2023-04-05 00:17:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-05 00:17:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-05 00:17:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-05 00:17:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:28] [INFO] [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2023-04-05 00:17:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2023-04-05 00:17:28] [INFO] [OmnipathR] Download ready [key=498f91238951df23d4d71705063f40254eddbfbf, version=1]
[2023-04-05 00:17:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:28] [INFO] [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:30] [SUCCESS] [OmnipathR] Downloaded 92855 interactions.
[2023-04-05 00:17:30] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-04-05 00:17:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-04-05 00:17:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:31] [INFO] [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-04-05 00:17:31] [INFO] [OmnipathR] Download ready [key=1ac430724a20c137fc374a8499adabb468a12835, version=1]
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:31] [INFO] [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:31] [SUCCESS] [OmnipathR] Downloaded 27928 intercellular communication role records.
[2023-04-05 00:17:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-05 00:17:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:31] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-04-05 00:17:31] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:31] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:31] [SUCCESS] [OmnipathR] Downloaded 21325 intercellular communication role records.
[2023-04-05 00:17:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-04-05 00:17:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-04-05 00:17:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-04-05 00:17:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:32] [INFO] [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-04-05 00:17:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-04-05 00:17:32] [INFO] [OmnipathR] Download ready [key=552757063f9934c7b745a9c4247c3b5282a66c88, version=1]
[2023-04-05 00:17:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:32] [INFO] [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:32] [SUCCESS] [OmnipathR] Downloaded 43967 intercellular communication role records.
[2023-04-05 00:17:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-05 00:17:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-05 00:17:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-05 00:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:55] [INFO] [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:17:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-04-05 00:17:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-04-05 00:17:55] [INFO] [OmnipathR] Download ready [key=3098404926bc0cf155d043ff0c6efe64e3424b74, version=1]
[2023-04-05 00:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:17:55] [INFO] [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `started` to `ready`.
[2023-04-05 00:17:59] [SUCCESS] [OmnipathR] Downloaded 134592 interactions.
[2023-04-05 00:17:59] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-04-05 00:17:59] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-04-05 00:17:59] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache.
[2023-04-05 00:17:59] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-04-05 00:17:59] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-04-05 00:17:59] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache.
[2023-04-05 00:20:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-04-05 00:20:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2023-04-05 00:20:01] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache.
[2023-04-05 00:20:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-04-05 00:20:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-05 00:20:01] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:20:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:20:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2023-04-05 00:20:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:20:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:20:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:20:02] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-04-05 00:20:02] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:20:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:20:02] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2023-04-05 00:20:02] [SUCCESS] [OmnipathR] Downloaded 1097 records.
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Bypassing call: `translate_ids(d, uniprot_id = uniprot, genesymbol)`.
[2023-04-05 00:20:02] [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.
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`.
[2023-04-05 00:20:02] [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.
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2023-04-05 00:20:02] [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.
[2023-04-05 00:20:02] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2023-04-05 00:20:02] [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.
--- finished re-building ‘bioc_workshop.Rmd’
--- re-building ‘db_manager.Rmd’ using rmarkdown
[2023-04-05 00:20:03] [TRACE] [OmnipathR] Bypassing call: `get_db("up_gs")`.
[2023-04-05 00:20:03] [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.
[2023-04-05 00:20:13] [TRACE] [OmnipathR] Bypassing call: `get_db("up_gs")`.
[2023-04-05 00:20:13] [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.
--- finished re-building ‘db_manager.Rmd’
--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2023-04-05 00:20:14] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-04-05 00:20:14] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:20:16] [SUCCESS] [OmnipathR] Loaded 92262 interactions from cache.
The magick package is required to crop "/tmp/RtmpdQ3KXv/Rbuild367c15224cb517/OmnipathR/vignettes/drug_targets_files/figure-html/unnamed-chunk-12-1.svg" but not available.
--- finished re-building ‘drug_targets.Rmd’
--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2023-04-05 00:20:19] [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`
[2023-04-05 00:20:19] [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`
[2023-04-05 00:20:19] [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`
[2023-04-05 00:20:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:20:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:20:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:20:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:20:20] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:20:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-04-05 00:20:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-04-05 00:20:21] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2023-04-05 00:20:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:20:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:20:21] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2023-04-05 00:20:29] [SUCCESS] [OmnipathR] Downloaded 134592 interactions.
[2023-04-05 00:23:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:23:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-04-05 00:23:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-04-05 00:23:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-04-05 00:23:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:23:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:23:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:52] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:23:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2023-04-05 00:23:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2023-04-05 00:23:53] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2023-04-05 00:23:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:23:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:53] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2023-04-05 00:23:53] [SUCCESS] [OmnipathR] Downloaded 204222 annotation records.
[2023-04-05 00:23:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-04-05 00:23:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-04-05 00:23:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-04-05 00:23:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:23:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:23:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:53] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:23:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2023-04-05 00:23:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2023-04-05 00:23:53] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2023-04-05 00:23:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:23:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:53] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2023-04-05 00:23:53] [SUCCESS] [OmnipathR] Downloaded 52 enzyme-substrate relationships.
--- finished re-building ‘extra_attrs.Rmd’
--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’
--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2023-04-05 00:23:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:23:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:23:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:56] [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`
[2023-04-05 00:23:56] [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`
[2023-04-05 00:23:56] [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`
[2023-04-05 00:23:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:23:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:23:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:57] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:23:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2023-04-05 00:23:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2023-04-05 00:23:57] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2023-04-05 00:23:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:23:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:23:57] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2023-04-05 00:23:58] [SUCCESS] [OmnipathR] Downloaded 64574 interactions.
[2023-04-05 00:24:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:03] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2023-04-05 00:24:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2023-04-05 00:24:03] [INFO] [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1]
[2023-04-05 00:24:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:03] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:03] [SUCCESS] [OmnipathR] Downloaded 1526 interactions.
[2023-04-05 00:24:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:04] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2023-04-05 00:24:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2023-04-05 00:24:04] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2023-04-05 00:24:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:04] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:04] [SUCCESS] [OmnipathR] Downloaded 6880 interactions.
[2023-04-05 00:24:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:05] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2023-04-05 00:24:05] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:05] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:05] [SUCCESS] [OmnipathR] Downloaded 3008 interactions.
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-05 00:24:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:05] [INFO] [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2023-04-05 00:24:05] [INFO] [OmnipathR] Download ready [key=cde98994cdbb4dd0e43d69b43a01b3491332287d, version=1]
[2023-04-05 00:24:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:05] [INFO] [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:06] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2023-04-05 00:24:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-05 00:24:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-05 00:24:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-04-05 00:24:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:06] [INFO] [OmnipathR] Cache item `c379f6c4e64c654ffb321b3134d065934007cc0e` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c379f6c4e64c654ffb321b3134d065934007cc0e-1.rds`.
[2023-04-05 00:24:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c379f6c4e64c654ffb321b3134d065934007cc0e-1.rds`.
[2023-04-05 00:24:06] [INFO] [OmnipathR] Download ready [key=c379f6c4e64c654ffb321b3134d065934007cc0e, version=1]
[2023-04-05 00:24:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:06] [INFO] [OmnipathR] Cache item `c379f6c4e64c654ffb321b3134d065934007cc0e` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:07] [SUCCESS] [OmnipathR] Downloaded 25339 interactions.
[2023-04-05 00:24:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:07] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2023-04-05 00:24:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2023-04-05 00:24:07] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2023-04-05 00:24:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:08] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:08] [SUCCESS] [OmnipathR] Downloaded 728 interactions.
[2023-04-05 00:24:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2023-04-05 00:24:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2023-04-05 00:24:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2023-04-05 00:24:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:08] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2023-04-05 00:24:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2023-04-05 00:24:08] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2023-04-05 00:24:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:08] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:08] [SUCCESS] [OmnipathR] Downloaded 32 interactions.
[2023-04-05 00:24:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:08] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-04-05 00:24:08] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:09] [SUCCESS] [OmnipathR] Loaded 42248 enzyme-substrate relationships from cache.
[2023-04-05 00:24:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-04-05 00:24:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:12] [SUCCESS] [OmnipathR] Loaded 92262 interactions from cache.
[2023-04-05 00:24:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-04-05 00:24:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:13] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2023-04-05 00:24:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2023-04-05 00:24:13] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2023-04-05 00:24:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:13] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:14] [SUCCESS] [OmnipathR] Downloaded 17530 enzyme-substrate relationships.
[2023-04-05 00:24:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2023-04-05 00:24:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2023-04-05 00:24:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2023-04-05 00:24:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:15] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2023-04-05 00:24:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2023-04-05 00:24:15] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2023-04-05 00:24:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:15] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:15] [SUCCESS] [OmnipathR] Downloaded 7183 protein complexes.
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2023-04-05 00:24:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:16] [INFO] [OmnipathR] Cache item `929c2072937af212fa00922d04d210172bd315c8` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/929c2072937af212fa00922d04d210172bd315c8-1.rds`.
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/929c2072937af212fa00922d04d210172bd315c8-1.rds`.
[2023-04-05 00:24:16] [INFO] [OmnipathR] Download ready [key=929c2072937af212fa00922d04d210172bd315c8, version=1]
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:16] [INFO] [OmnipathR] Cache item `929c2072937af212fa00922d04d210172bd315c8` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:16] [SUCCESS] [OmnipathR] Downloaded 41 annotation records.
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-04-05 00:24:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:16] [INFO] [OmnipathR] Cache item `20cd5eb55475c83ea15e2d2ddb162dcdd528116f` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20cd5eb55475c83ea15e2d2ddb162dcdd528116f-1.rds`.
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20cd5eb55475c83ea15e2d2ddb162dcdd528116f-1.rds`.
[2023-04-05 00:24:16] [INFO] [OmnipathR] Download ready [key=20cd5eb55475c83ea15e2d2ddb162dcdd528116f, version=1]
[2023-04-05 00:24:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:16] [INFO] [OmnipathR] Cache item `20cd5eb55475c83ea15e2d2ddb162dcdd528116f` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:16] [SUCCESS] [OmnipathR] Downloaded 7 annotation records.
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-04-05 00:24:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:17] [INFO] [OmnipathR] Cache item `acaa653138834ed8b6d7d52ce1b3529953f720a2` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/acaa653138834ed8b6d7d52ce1b3529953f720a2-1.rds`.
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/acaa653138834ed8b6d7d52ce1b3529953f720a2-1.rds`.
[2023-04-05 00:24:17] [INFO] [OmnipathR] Download ready [key=acaa653138834ed8b6d7d52ce1b3529953f720a2, version=1]
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:17] [INFO] [OmnipathR] Cache item `acaa653138834ed8b6d7d52ce1b3529953f720a2` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:17] [SUCCESS] [OmnipathR] Downloaded 28 annotation records.
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:24:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-04-05 00:24:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-04-05 00:24:17] [SUCCESS] [OmnipathR] Loaded 2451 annotation records from cache.
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-04-05 00:24:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary`
[2023-04-05 00:24:17] [SUCCESS] [OmnipathR] Loaded 1097 records from cache.
[2023-04-05 00:24:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2023-04-05 00:24:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2023-04-05 00:24:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2023-04-05 00:24:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:18] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:24:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2023-04-05 00:24:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2023-04-05 00:24:20] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2023-04-05 00:24:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:24:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:24:20] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2023-04-05 00:24:20] [SUCCESS] [OmnipathR] Downloaded 231187 intercellular communication role records.
[2023-04-05 00:24:20] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2023-04-05 00:24:20] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-05 00:24:23] [SUCCESS] [OmnipathR] Loaded 92855 interactions from cache.
[2023-04-05 00:24:23] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-04-05 00:24:23] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-04-05 00:24:23] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache.
[2023-04-05 00:24:23] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-04-05 00:24:23] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-05 00:24:23] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2023-04-05 00:24:23] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-04-05 00:24:23] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-04-05 00:24:23] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache.
[2023-04-05 00:24:47] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-04-05 00:24:47] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2023-04-05 00:24:47] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache.
[2023-04-05 00:24:47] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-04-05 00:24:47] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-04-05 00:24:47] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2023-04-05 00:24:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-04-05 00:24:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-04-05 00:24:51] [SUCCESS] [OmnipathR] Loaded 134592 interactions from cache.
[2023-04-05 00:24:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-04-05 00:24:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-04-05 00:24:51] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache.
[2023-04-05 00:24:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-04-05 00:24:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-04-05 00:24:51] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache.
--- finished re-building ‘omnipath_intro.Rmd’
--- re-building ‘paths.Rmd’ using rmarkdown
[2023-04-05 00:26:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-04-05 00:26:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:26:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-04-05 00:26:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-04-05 00:26:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-04-05 00:26:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:26:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:26:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:26:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:26:53] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2023-04-05 00:26:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2023-04-05 00:26:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2023-04-05 00:26:53] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2023-04-05 00:26:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-05 00:26:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-05 00:26:53] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2023-04-05 00:26:53] [SUCCESS] [OmnipathR] Downloaded 3516 annotation records.
[2023-04-05 00:26:53] [TRACE] [OmnipathR] Bypassing call: `tfcensus_download()`.
[2023-04-05 00:26:53] [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.
Quitting from lines 73-80 (paths.Rmd)
Error: processing vignette 'paths.Rmd' failed with diagnostics:
no applicable method for 'pull' applied to an object of class "NULL"
--- failed re-building ‘paths.Rmd’
SUMMARY: processing the following file failed:
‘paths.Rmd’
Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-04-05 00:26:54 CEST ]