[ Started: 2023-05-19 01:04:23 CEST ]
[ OmnipathR v3.9.2 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 ''
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:32] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Contains 1 files.
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpu26QiY/Rinst3475797a834f40/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-19 01:04:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpu26QiY/Rinst3475797a834f40/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-19 01:04:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpu26QiY/Rinst3475797a834f40/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-19 01:04:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpu26QiY/Rinst3475797a834f40/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-19 01:04:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:32] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-05-19 01:04:32] [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`
[2023-05-19 01:04:32] [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`
[2023-05-19 01:04:32] [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`
[2023-05-19 01:04:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:33] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:04:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2023-05-19 01:04:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2023-05-19 01:04:34] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2023-05-19 01:04:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:34] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2023-05-19 01:04:37] [SUCCESS] [OmnipathR] Downloaded 125025 interactions.
[2023-05-19 01:04:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:04:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:04:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:04:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:40] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:04:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-05-19 01:04:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-05-19 01:04:40] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2023-05-19 01:04:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:40] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2023-05-19 01:04:41] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2023-05-19 01:04:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:04:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:04:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:04:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:42] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:04:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-05-19 01:04:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-05-19 01:04:42] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2023-05-19 01:04:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:42] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2023-05-19 01:04:45] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2023-05-19 01:04:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2023-05-19 01:04:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2023-05-19 01:04:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2023-05-19 01:04:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:45] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:04:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2023-05-19 01:04:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2023-05-19 01:04:46] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2023-05-19 01:04:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:46] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2023-05-19 01:04:46] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2023-05-19 01:04:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:04:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-05-19 01:04:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-05-19 01:04:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-05-19 01:04:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:46] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:04:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-05-19 01:04:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-05-19 01:04:47] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2023-05-19 01:04:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:47] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2023-05-19 01:04:47] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2023-05-19 01:04:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:04:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-05-19 01:04:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-05-19 01:04:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-05-19 01:04:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:47] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:04:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2023-05-19 01:04:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2023-05-19 01:04:47] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2023-05-19 01:04:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:47] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2023-05-19 01:04:47] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2023-05-19 01:04:47] [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.
[2023-05-19 01:04:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:04:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-05-19 01:04:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-05-19 01:04:48] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2023-05-19 01:04:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:04:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-05-19 01:04:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-05-19 01:04:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-05-19 01:04:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:48] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:04:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2023-05-19 01:04:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2023-05-19 01:04:48] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2023-05-19 01:04:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:48] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2023-05-19 01:04:48] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2023-05-19 01:04:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:04:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-05-19 01:04:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-05-19 01:04:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-05-19 01:04:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:49] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:04:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-05-19 01:04:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-05-19 01:04:49] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2023-05-19 01:04:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:49] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2023-05-19 01:04:49] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2023-05-19 01:04:49] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-05-19 01:04:49] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:04:51] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2023-05-19 01:04:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:04:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:52] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-05-19 01:04:52] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-05-19 01:04:52] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2023-05-19 01:04:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2023-05-19 01:04:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2023-05-19 01:04:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2023-05-19 01:04:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:53] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:04:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-05-19 01:04:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-05-19 01:04:55] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2023-05-19 01:04:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:55] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2023-05-19 01:04:55] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Bypassing call: `import_intercell_network(high_confidence = TRUE)`.
[2023-05-19 01:04:56] [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.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Bypassing call: `import_intercell_network()`.
[2023-05-19 01:04:56] [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.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`.
[2023-05-19 01:04:56] [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.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:04:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2023-05-19 01:04:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:56] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-05-19 01:04:56] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:04:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:04:56] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2023-05-19 01:04:56] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Bypassing call: `translate_ids(d, uniprot_id = uniprot, genesymbol)`.
[2023-05-19 01:04:56] [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.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`.
[2023-05-19 01:04:56] [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.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2023-05-19 01:04:56] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘bioc_workshop.Rmd’
--- re-building ‘db_manager.Rmd’ using rmarkdown
[2023-05-19 01:04:57] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: `(function (to, from = "id", reviewed = TRUE, organism = 9606) `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: `{`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` .slow_doctest()`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` From <- To <- NULL`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` strip_semicol <- function(v) {`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` sub(";$", "", v)`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` }`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` reviewed <- if ("trembl" %in% ids) `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` FALSE`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` else if ("swissprot" %in% ids) `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` TRUE`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` else reviewed`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` reens <- "ENS[A-Z]+\\d+"`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` to_ens <- to == "database(Ensembl)"`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` from_ens <- from == "database(Ensembl)"`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` "for organism %d (only reviewed: %s)"), from, to, organism, `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` reviewed)`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` To = strip_semicol(To)) %>% separate_rows(From, sep = ";") %>% `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` separate_rows(To, sep = ";") %>% filter(!is.na(From) & `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` !is.na(To)) %>% {`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` if (from_ens) `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` mutate(., From = str_extract(From, reens))`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` else .`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` } %>% {`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` if (to_ens) `.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` mutate(., To = str_extract(To, reens))`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` else .`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: ` } %>% trim_and_distinct`.
[2023-05-19 01:04:57] [TRACE] [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`.
[2023-05-19 01:04:57] [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.
[2023-05-19 01:04:57] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’
--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2023-05-19 01:05:08] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-05-19 01:05:08] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:05:11] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
The magick package is required to crop "/tmp/Rtmpu26QiY/Rbuild347579129e2408/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
[2023-05-19 01:05:14] [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`
[2023-05-19 01:05:14] [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`
[2023-05-19 01:05:14] [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`
[2023-05-19 01:05:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:15] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-05-19 01:05:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-05-19 01:05:16] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2023-05-19 01:05:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:16] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:19] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
Quitting from lines 56-58 (extra_attrs.Rmd)
Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics:
Can't subset columns that don't exist.
✖ Column `extra_attrs` doesn't exist.
--- failed re-building ‘extra_attrs.Rmd’
--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’
--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2023-05-19 01:05:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:22] [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`
[2023-05-19 01:05:22] [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`
[2023-05-19 01:05:22] [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`
[2023-05-19 01:05:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:23] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2023-05-19 01:05:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2023-05-19 01:05:23] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2023-05-19 01:05:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:23] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:24] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2023-05-19 01:05:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:29] [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`
[2023-05-19 01:05:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:05:29] [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`
[2023-05-19 01:05:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:29] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2023-05-19 01:05:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2023-05-19 01:05:29] [INFO] [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1]
[2023-05-19 01:05:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:29] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:29] [SUCCESS] [OmnipathR] Downloaded 1532 interactions.
[2023-05-19 01:05:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:29] [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`
[2023-05-19 01:05:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:05:29] [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`
[2023-05-19 01:05:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:29] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2023-05-19 01:05:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2023-05-19 01:05:30] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2023-05-19 01:05:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:30] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:30] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2023-05-19 01:05:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:30] [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`
[2023-05-19 01:05:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:05:30] [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`
[2023-05-19 01:05:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:30] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2023-05-19 01:05:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2023-05-19 01:05:30] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2023-05-19 01:05:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:30] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:30] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2023-05-19 01:05:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:31] [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`
[2023-05-19 01:05:31] [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`
[2023-05-19 01:05:31] [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`
[2023-05-19 01:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:31] [INFO] [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2023-05-19 01:05:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2023-05-19 01:05:31] [INFO] [OmnipathR] Download ready [key=cde98994cdbb4dd0e43d69b43a01b3491332287d, version=1]
[2023-05-19 01:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:31] [INFO] [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:31] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2023-05-19 01:05:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:31] [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`
[2023-05-19 01:05:31] [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`
[2023-05-19 01:05:31] [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`
[2023-05-19 01:05:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:32] [INFO] [OmnipathR] Cache item `c379f6c4e64c654ffb321b3134d065934007cc0e` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c379f6c4e64c654ffb321b3134d065934007cc0e-1.rds`.
[2023-05-19 01:05:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c379f6c4e64c654ffb321b3134d065934007cc0e-1.rds`.
[2023-05-19 01:05:32] [INFO] [OmnipathR] Download ready [key=c379f6c4e64c654ffb321b3134d065934007cc0e, version=1]
[2023-05-19 01:05:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:32] [INFO] [OmnipathR] Cache item `c379f6c4e64c654ffb321b3134d065934007cc0e` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:33] [SUCCESS] [OmnipathR] Downloaded 25339 interactions.
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:33] [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`
[2023-05-19 01:05:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:05:33] [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`
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:33] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2023-05-19 01:05:33] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:33] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:33] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2023-05-19 01:05:33] [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`
[2023-05-19 01:05:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2023-05-19 01:05:33] [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`
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:33] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2023-05-19 01:05:33] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2023-05-19 01:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:33] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:33] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2023-05-19 01:05:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:34] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-05-19 01:05:34] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:05:35] [SUCCESS] [OmnipathR] Loaded 43269 enzyme-substrate relationships from cache.
[2023-05-19 01:05:35] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-05-19 01:05:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:05:37] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2023-05-19 01:05:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:38] [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`
[2023-05-19 01:05:38] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:05:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-05-19 01:05:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:38] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2023-05-19 01:05:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2023-05-19 01:05:38] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2023-05-19 01:05:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:38] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:39] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships.
[2023-05-19 01:05:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2023-05-19 01:05:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2023-05-19 01:05:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2023-05-19 01:05:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:39] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2023-05-19 01:05:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2023-05-19 01:05:40] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2023-05-19 01:05:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:40] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:40] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes.
[2023-05-19 01:05:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:40] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2023-05-19 01:05:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2023-05-19 01:05:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:41] [INFO] [OmnipathR] Cache item `929c2072937af212fa00922d04d210172bd315c8` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/929c2072937af212fa00922d04d210172bd315c8-1.rds`.
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/929c2072937af212fa00922d04d210172bd315c8-1.rds`.
[2023-05-19 01:05:41] [INFO] [OmnipathR] Download ready [key=929c2072937af212fa00922d04d210172bd315c8, version=1]
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:41] [INFO] [OmnipathR] Cache item `929c2072937af212fa00922d04d210172bd315c8` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:41] [SUCCESS] [OmnipathR] Downloaded 95 annotation records.
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-05-19 01:05:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:41] [INFO] [OmnipathR] Cache item `20cd5eb55475c83ea15e2d2ddb162dcdd528116f` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20cd5eb55475c83ea15e2d2ddb162dcdd528116f-1.rds`.
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20cd5eb55475c83ea15e2d2ddb162dcdd528116f-1.rds`.
[2023-05-19 01:05:41] [INFO] [OmnipathR] Download ready [key=20cd5eb55475c83ea15e2d2ddb162dcdd528116f, version=1]
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:41] [INFO] [OmnipathR] Cache item `20cd5eb55475c83ea15e2d2ddb162dcdd528116f` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:41] [SUCCESS] [OmnipathR] Downloaded 7 annotation records.
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-05-19 01:05:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-05-19 01:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:42] [INFO] [OmnipathR] Cache item `acaa653138834ed8b6d7d52ce1b3529953f720a2` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/acaa653138834ed8b6d7d52ce1b3529953f720a2-1.rds`.
[2023-05-19 01:05:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/acaa653138834ed8b6d7d52ce1b3529953f720a2-1.rds`.
[2023-05-19 01:05:42] [INFO] [OmnipathR] Download ready [key=acaa653138834ed8b6d7d52ce1b3529953f720a2, version=1]
[2023-05-19 01:05:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:42] [INFO] [OmnipathR] Cache item `acaa653138834ed8b6d7d52ce1b3529953f720a2` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:42] [SUCCESS] [OmnipathR] Downloaded 28 annotation records.
[2023-05-19 01:05:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:42] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-05-19 01:05:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-05-19 01:05:42] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2023-05-19 01:05:42] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-05-19 01:05:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary`
[2023-05-19 01:05:42] [SUCCESS] [OmnipathR] Loaded 1098 records from cache.
[2023-05-19 01:05:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2023-05-19 01:05:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2023-05-19 01:05:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2023-05-19 01:05:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:43] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2023-05-19 01:05:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2023-05-19 01:05:44] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2023-05-19 01:05:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:44] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:45] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records.
[2023-05-19 01:05:45] [TRACE] [OmnipathR] Bypassing call: `import_intercell_network(high_confidence = TRUE)`.
[2023-05-19 01:05:45] [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.
[2023-05-19 01:05:45] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2023-05-19 01:05:45] [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 ‘omnipath_intro.Rmd’
--- re-building ‘paths.Rmd’ using rmarkdown
[2023-05-19 01:05:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-05-19 01:05:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-05-19 01:05:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:47] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2023-05-19 01:05:47] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:47] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:47] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2023-05-19 01:05:47] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:47] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2023-05-19 01:05:47] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2023-05-19 01:05:47] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:47] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:47] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2023-05-19 01:05:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-05-19 01:05:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-05-19 01:05:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-05-19 01:05:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:48] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2023-05-19 01:05:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2023-05-19 01:05:48] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2023-05-19 01:05:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:48] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:51] [SUCCESS] [OmnipathR] Downloaded 117662 interactions.
[2023-05-19 01:05:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2023-05-19 01:05:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2023-05-19 01:05:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2023-05-19 01:05:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:52] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2023-05-19 01:05:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2023-05-19 01:05:53] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2023-05-19 01:05:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:53] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:53] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2023-05-19 01:05:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2023-05-19 01:05:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2023-05-19 01:05:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:54] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2023-05-19 01:05:54] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:54] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:54] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2023-05-19 01:05:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-05-19 01:05:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:54] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-05-19 01:05:54] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2023-05-19 01:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:54] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:54] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2023-05-19 01:05:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2023-05-19 01:05:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2023-05-19 01:05:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2023-05-19 01:05:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:55] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2023-05-19 01:05:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2023-05-19 01:05:55] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2023-05-19 01:05:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:55] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:55] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2023-05-19 01:05:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-05-19 01:05:55] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-05-19 01:05:55] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-05-19 01:05:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-05-19 01:05:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-05-19 01:05:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:56] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2023-05-19 01:05:56] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:56] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:56] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-05-19 01:05:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-05-19 01:05:56] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-05-19 01:05:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2023-05-19 01:05:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:56] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2023-05-19 01:05:56] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:56] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:56] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2023-05-19 01:05:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-05-19 01:05:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-05-19 01:05:56] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-05-19 01:05:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-05-19 01:05:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-05-19 01:05:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-05-19 01:05:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:57] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2023-05-19 01:05:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2023-05-19 01:05:57] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2023-05-19 01:05:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:57] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:58] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2023-05-19 01:05:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2023-05-19 01:05:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2023-05-19 01:05:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2023-05-19 01:05:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:59] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2023-05-19 01:05:59] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:59] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:59] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2023-05-19 01:05:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:59] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2023-05-19 01:05:59] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2023-05-19 01:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:05:59] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2023-05-19 01:05:59] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2023-05-19 01:06:00] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2023-05-19 01:06:00] [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.
[2023-05-19 01:06:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-05-19 01:06:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-05-19 01:06:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-05-19 01:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:00] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:06:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2023-05-19 01:06:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2023-05-19 01:06:00] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2023-05-19 01:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:00] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2023-05-19 01:06:00] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2023-05-19 01:06:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-05-19 01:06:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-05-19 01:06:01] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2023-05-19 01:06:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:06:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2023-05-19 01:06:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2023-05-19 01:06:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2023-05-19 01:06:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:06:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:06:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:01] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2023-05-19 01:06:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2023-05-19 01:06:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2023-05-19 01:06:01] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2023-05-19 01:06:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-19 01:06:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:01] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2023-05-19 01:06:01] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2023-05-19 01:06:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:06:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:04] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-05-19 01:06:04] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-05-19 01:06:04] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2023-05-19 01:06:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-19 01:06:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-19 01:06:04] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2023-05-19 01:06:04] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2023-05-19 01:06:04] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache.
--- finished re-building ‘paths.Rmd’
SUMMARY: processing the following file failed:
‘extra_attrs.Rmd’
Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-05-19 01:06:05 CEST ]