[ Started: 2023-08-05 23:39:10 CEST ]
[ OmnipathR v3.6.6 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ]

* 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
[2023-08-05 23:39:20] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-08-05 23:39:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-08-05 23:39:20] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-08-05 23:39:20] [TRACE]   [OmnipathR] Contains 1 files.
[2023-08-05 23:39:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-08-05 23:39:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-08-05 23:39:20] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-08-05 23:39:20] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-08-05 23:39:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-08-05 23:39:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-08-05 23:39:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-08-05 23:39:23] [INFO]    [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2023-08-05 23:39:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2023-08-05 23:39:23] [INFO]    [OmnipathR] Download ready [key=f4de1f63d60f35d18bb262dd6de84d1cccd9cc97, version=1]
[2023-08-05 23:39:23] [INFO]    [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:25] [SUCCESS] [OmnipathR] Downloaded 71649 interactions.
[2023-08-05 23:39:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:39:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:39:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:39:27] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-08-05 23:39:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-08-05 23:39:27] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2023-08-05 23:39:27] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:28] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2023-08-05 23:39:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:39:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:39:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:39:29] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-08-05 23:39:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-08-05 23:39:30] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2023-08-05 23:39:30] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:32] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2023-08-05 23:39:32] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2023-08-05 23:39:32] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2023-08-05 23:39:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2023-08-05 23:39:33] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2023-08-05 23:39:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2023-08-05 23:39:33] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2023-08-05 23:39:33] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:33] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2023-08-05 23:39:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-08-05 23:39:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-08-05 23:39:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-08-05 23:39:34] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-08-05 23:39:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-08-05 23:39:34] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2023-08-05 23:39:34] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:34] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2023-08-05 23:39:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-08-05 23:39:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-08-05 23:39:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2023-08-05 23:39:35] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2023-08-05 23:39:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2023-08-05 23:39:35] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2023-08-05 23:39:35] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:35] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2023-08-05 23:39:35] [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.
[2023-08-05 23:39:35] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-08-05 23:39:35] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-08-05 23:39:35] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2023-08-05 23:39:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-08-05 23:39:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-08-05 23:39:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2023-08-05 23:39:36] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2023-08-05 23:39:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2023-08-05 23:39:36] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2023-08-05 23:39:36] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:36] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2023-08-05 23:39:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-08-05 23:39:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-08-05 23:39:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-08-05 23:39:36] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-08-05 23:39:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-08-05 23:39:36] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2023-08-05 23:39:36] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:36] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2023-08-05 23:39:36] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-08-05 23:39:36] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:39:38] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2023-08-05 23:39:39] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-08-05 23:39:39] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-08-05 23:39:39] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2023-08-05 23:39:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2023-08-05 23:39:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2023-08-05 23:39:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2023-08-05 23:39:40] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-08-05 23:39:42] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-08-05 23:39:42] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2023-08-05 23:39:42] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:42] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2023-08-05 23:39:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-08-05 23:39:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-08-05 23:39:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-08-05 23:39:47] [INFO]    [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2023-08-05 23:39:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2023-08-05 23:39:47] [INFO]    [OmnipathR] Download ready [key=498f91238951df23d4d71705063f40254eddbfbf, version=1]
[2023-08-05 23:39:47] [INFO]    [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:50] [SUCCESS] [OmnipathR] Downloaded 84409 interactions.
[2023-08-05 23:39:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-08-05 23:39:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-08-05 23:39:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-08-05 23:39:50] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-08-05 23:39:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-08-05 23:39:51] [INFO]    [OmnipathR] Download ready [key=1ac430724a20c137fc374a8499adabb468a12835, version=1]
[2023-08-05 23:39:51] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:51] [SUCCESS] [OmnipathR] Downloaded 29651 intercellular communication role records.
[2023-08-05 23:39:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:39:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:39:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:39:51] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-08-05 23:39:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-08-05 23:39:51] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2023-08-05 23:39:51] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:52] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2023-08-05 23:39:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-08-05 23:39:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-08-05 23:39:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-08-05 23:39:53] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:39:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-08-05 23:39:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-08-05 23:39:53] [INFO]    [OmnipathR] Download ready [key=552757063f9934c7b745a9c4247c3b5282a66c88, version=1]
[2023-08-05 23:39:53] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `started` to `ready`.
[2023-08-05 23:39:53] [SUCCESS] [OmnipathR] Downloaded 45334 intercellular communication role records.
[2023-08-05 23:40:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-08-05 23:40:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-08-05 23:40:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-08-05 23:40:21] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:40:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-08-05 23:40:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-08-05 23:40:22] [INFO]    [OmnipathR] Download ready [key=3098404926bc0cf155d043ff0c6efe64e3424b74, version=1]
[2023-08-05 23:40:22] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `started` to `ready`.
[2023-08-05 23:40:26] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2023-08-05 23:40:26] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-08-05 23:40:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-08-05 23:40:26] [SUCCESS] [OmnipathR] Loaded 29651 intercellular communication role records from cache.
[2023-08-05 23:40:26] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-08-05 23:40:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-08-05 23:40:26] [SUCCESS] [OmnipathR] Loaded 45334 intercellular communication role records from cache.
[2023-08-05 23:42:45] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-08-05 23:42:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2023-08-05 23:42:46] [SUCCESS] [OmnipathR] Loaded 332447 intercellular communication role records from cache.
[2023-08-05 23:42:46] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-08-05 23:42:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:42:46] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-08-05 23:42:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2023-08-05 23:42:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2023-08-05 23:42:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2023-08-05 23:42:47] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:42:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-08-05 23:42:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-08-05 23:42:47] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2023-08-05 23:42:47] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2023-08-05 23:42:47] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2023-08-05 23:42:47] [INFO]    [OmnipathR] Loading database `Ensembl organism names`.
[2023-08-05 23:42:47] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-08-05 23:42:47] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2023-08-05 23:42:47] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2023-08-05 23:42:47] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2023-08-05 23:42:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2023-08-05 23:42:48] [TRACE]   [OmnipathR] HTTP 200
[2023-08-05 23:42:48] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2023-08-05 23:42:48] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2023-08-05 23:42:48] [INFO]    [OmnipathR] Loaded database `Ensembl organism names`.
[2023-08-05 23:42:48] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2023-08-05 23:42:48] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE)
[2023-08-05 23:42:48] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED)
[2023-08-05 23:42:48] [TRACE]   [OmnipathR] Looking up in cache: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2023-08-05 23:42:48] [INFO]    [OmnipathR] Cache record does not exist: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-08-05 23:42:48] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2023-08-05 23:42:48] [INFO]    [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:42:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`.
[2023-08-05 23:42:48] [INFO]    [OmnipathR] Retrieving URL: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-08-05 23:42:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-08-05 23:42:48] [WARN]    [OmnipathR] Failed to download `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` (attempt 1/3); error: Could not resolve host: legacy.uniprot.org
[2023-08-05 23:42:53] [TRACE]   [OmnipathR] Attempt 2/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-08-05 23:42:53] [WARN]    [OmnipathR] Failed to download `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` (attempt 2/3); error: Could not resolve host: legacy.uniprot.org
[2023-08-05 23:42:58] [TRACE]   [OmnipathR] Attempt 3/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-08-05 23:42:58] [ERROR]   [OmnipathR] Failed to download `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` (attempt 3/3); error: Could not resolve host: legacy.uniprot.org
[2023-08-05 23:42:58] [TRACE]   [OmnipathR] Failed download attempt: `Could not resolve host: legacy.uniprot.org`.

Quitting from lines 461-468 [id-translate-vector] (bioc_workshop.Rmd)
Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
Could not resolve host: legacy.uniprot.org
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
Warning in inherits(x, "factor") :
  closing unused connection 5 (https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no)
Warning in inherits(x, "factor") :
  closing unused connection 4 (https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no)
[2023-08-05 23:42:58] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2023-08-05 23:42:58] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE)
[2023-08-05 23:42:58] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED)
[2023-08-05 23:42:58] [TRACE]   [OmnipathR] Looking up in cache: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2023-08-05 23:42:58] [INFO]    [OmnipathR] No version is available for key `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` (https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no).
[2023-08-05 23:42:58] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2023-08-05 23:42:58] [INFO]    [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 2: status changed from `unknown` to `started`.
[2023-08-05 23:42:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-2.rds`.
[2023-08-05 23:42:58] [INFO]    [OmnipathR] Retrieving URL: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-08-05 23:42:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-08-05 23:42:58] [WARN]    [OmnipathR] Failed to download `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` (attempt 1/3); error: Could not resolve host: legacy.uniprot.org
[2023-08-05 23:43:03] [TRACE]   [OmnipathR] Attempt 2/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-08-05 23:43:03] [WARN]    [OmnipathR] Failed to download `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` (attempt 2/3); error: Could not resolve host: legacy.uniprot.org
[2023-08-05 23:43:08] [TRACE]   [OmnipathR] Attempt 3/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-08-05 23:43:08] [ERROR]   [OmnipathR] Failed to download `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` (attempt 3/3); error: Could not resolve host: legacy.uniprot.org
[2023-08-05 23:43:08] [TRACE]   [OmnipathR] Failed download attempt: `Could not resolve host: legacy.uniprot.org`.

Quitting from lines 67-69 [get] (db_manager.Rmd)
Error: processing vignette 'db_manager.Rmd' failed with diagnostics:
Could not resolve host: legacy.uniprot.org
--- failed re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
Warning in for (n in impnames) if (!is.null(genImp <- impenv[[n]])) { :
  closing unused connection 5 (https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no)
Warning in for (n in impnames) if (!is.null(genImp <- impenv[[n]])) { :
  closing unused connection 4 (https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no)
[2023-08-05 23:43:09] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-08-05 23:43:09] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:43:11] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
Warning in .Internal(paste0(list(...), collapse, recycle0)) :
  closing unused connection 6 (https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no)
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2023-08-05 23:43:15] [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`
[2023-08-05 23:43:15] [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`
[2023-08-05 23:43:15] [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`
[2023-08-05 23:43:21] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:43:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-08-05 23:43:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-08-05 23:43:22] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2023-08-05 23:43:22] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2023-08-05 23:43:30] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
Warning: closing unused connection 7 (https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no)
[2023-08-05 23:47:11] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-08-05 23:47:11] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-08-05 23:47:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-08-05 23:47:11] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2023-08-05 23:47:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2023-08-05 23:47:12] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2023-08-05 23:47:12] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:12] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2023-08-05 23:47:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-08-05 23:47:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-08-05 23:47:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-08-05 23:47:12] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2023-08-05 23:47:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2023-08-05 23:47:12] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2023-08-05 23:47:12] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:12] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships.
--- finished re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2023-08-05 23:47:15] [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`
[2023-08-05 23:47:15] [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`
[2023-08-05 23:47:15] [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`
[2023-08-05 23:47:16] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2023-08-05 23:47:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2023-08-05 23:47:16] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2023-08-05 23:47:16] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:18] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2023-08-05 23:47:21] [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`
[2023-08-05 23:47:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:47:21] [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`
[2023-08-05 23:47:22] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2023-08-05 23:47:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2023-08-05 23:47:22] [INFO]    [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1]
[2023-08-05 23:47:22] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:22] [SUCCESS] [OmnipathR] Downloaded 1532 interactions.
[2023-08-05 23:47:22] [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`
[2023-08-05 23:47:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:47:22] [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`
[2023-08-05 23:47:22] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2023-08-05 23:47:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2023-08-05 23:47:22] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2023-08-05 23:47:22] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:23] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2023-08-05 23:47:23] [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`
[2023-08-05 23:47:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:47:23] [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`
[2023-08-05 23:47:23] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2023-08-05 23:47:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2023-08-05 23:47:23] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2023-08-05 23:47:23] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:23] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2023-08-05 23:47:24] [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`
[2023-08-05 23:47:24] [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`
[2023-08-05 23:47:24] [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`
[2023-08-05 23:47:25] [INFO]    [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2023-08-05 23:47:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2023-08-05 23:47:25] [INFO]    [OmnipathR] Download ready [key=cde98994cdbb4dd0e43d69b43a01b3491332287d, version=1]
[2023-08-05 23:47:25] [INFO]    [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:25] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2023-08-05 23:47:25] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-08-05 23:47:25] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-08-05 23:47:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-08-05 23:47:27] [INFO]    [OmnipathR] Cache item `8281969bb1ab7f3f99e3f1632559158df24b9a40` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8281969bb1ab7f3f99e3f1632559158df24b9a40-1.rds`.
[2023-08-05 23:47:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8281969bb1ab7f3f99e3f1632559158df24b9a40-1.rds`.
[2023-08-05 23:47:28] [INFO]    [OmnipathR] Download ready [key=8281969bb1ab7f3f99e3f1632559158df24b9a40, version=1]
[2023-08-05 23:47:28] [INFO]    [OmnipathR] Cache item `8281969bb1ab7f3f99e3f1632559158df24b9a40` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:28] [SUCCESS] [OmnipathR] Downloaded 25339 interactions.
[2023-08-05 23:47:29] [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`
[2023-08-05 23:47:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:47:29] [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`
[2023-08-05 23:47:29] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2023-08-05 23:47:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2023-08-05 23:47:29] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2023-08-05 23:47:29] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:29] [SUCCESS] [OmnipathR] Downloaded 716 interactions.
[2023-08-05 23:47:29] [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`
[2023-08-05 23:47:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2023-08-05 23:47:29] [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`
[2023-08-05 23:47:29] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2023-08-05 23:47:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2023-08-05 23:47:29] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2023-08-05 23:47:29] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:29] [SUCCESS] [OmnipathR] Downloaded 32 interactions.
[2023-08-05 23:47:30] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2023-08-05 23:47:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:47:31] [SUCCESS] [OmnipathR] Loaded 43269 enzyme-substrate relationships from cache.
[2023-08-05 23:47:31] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-08-05 23:47:31] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:47:33] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2023-08-05 23:47:34] [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`
[2023-08-05 23:47:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:47:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-08-05 23:47:35] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2023-08-05 23:47:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2023-08-05 23:47:35] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2023-08-05 23:47:35] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:36] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships.
[2023-08-05 23:47:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2023-08-05 23:47:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2023-08-05 23:47:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2023-08-05 23:47:37] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2023-08-05 23:47:37] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2023-08-05 23:47:37] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2023-08-05 23:47:37] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:37] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes.
[2023-08-05 23:47:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2023-08-05 23:47:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2023-08-05 23:47:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2023-08-05 23:47:38] [INFO]    [OmnipathR] Cache item `929c2072937af212fa00922d04d210172bd315c8` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/929c2072937af212fa00922d04d210172bd315c8-1.rds`.
[2023-08-05 23:47:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/929c2072937af212fa00922d04d210172bd315c8-1.rds`.
[2023-08-05 23:47:38] [INFO]    [OmnipathR] Download ready [key=929c2072937af212fa00922d04d210172bd315c8, version=1]
[2023-08-05 23:47:38] [INFO]    [OmnipathR] Cache item `929c2072937af212fa00922d04d210172bd315c8` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:38] [SUCCESS] [OmnipathR] Downloaded 95 annotation records.
[2023-08-05 23:47:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-08-05 23:47:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-08-05 23:47:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-08-05 23:47:39] [INFO]    [OmnipathR] Cache item `20cd5eb55475c83ea15e2d2ddb162dcdd528116f` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20cd5eb55475c83ea15e2d2ddb162dcdd528116f-1.rds`.
[2023-08-05 23:47:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20cd5eb55475c83ea15e2d2ddb162dcdd528116f-1.rds`.
[2023-08-05 23:47:39] [INFO]    [OmnipathR] Download ready [key=20cd5eb55475c83ea15e2d2ddb162dcdd528116f, version=1]
[2023-08-05 23:47:39] [INFO]    [OmnipathR] Cache item `20cd5eb55475c83ea15e2d2ddb162dcdd528116f` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:39] [SUCCESS] [OmnipathR] Downloaded 7 annotation records.
[2023-08-05 23:47:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-08-05 23:47:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-08-05 23:47:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2023-08-05 23:47:40] [INFO]    [OmnipathR] Cache item `acaa653138834ed8b6d7d52ce1b3529953f720a2` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/acaa653138834ed8b6d7d52ce1b3529953f720a2-1.rds`.
[2023-08-05 23:47:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/acaa653138834ed8b6d7d52ce1b3529953f720a2-1.rds`.
[2023-08-05 23:47:40] [INFO]    [OmnipathR] Download ready [key=acaa653138834ed8b6d7d52ce1b3529953f720a2, version=1]
[2023-08-05 23:47:40] [INFO]    [OmnipathR] Cache item `acaa653138834ed8b6d7d52ce1b3529953f720a2` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:40] [SUCCESS] [OmnipathR] Downloaded 28 annotation records.
[2023-08-05 23:47:40] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2023-08-05 23:47:40] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2023-08-05 23:47:40] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2023-08-05 23:47:40] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2023-08-05 23:47:40] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary`
[2023-08-05 23:47:40] [SUCCESS] [OmnipathR] Loaded 1098 records from cache.
[2023-08-05 23:47:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2023-08-05 23:47:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2023-08-05 23:47:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2023-08-05 23:47:45] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:47:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2023-08-05 23:47:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2023-08-05 23:47:46] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2023-08-05 23:47:46] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2023-08-05 23:47:46] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records.
[2023-08-05 23:47:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2023-08-05 23:47:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-08-05 23:47:49] [SUCCESS] [OmnipathR] Loaded 84409 interactions from cache.
[2023-08-05 23:47:49] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-08-05 23:47:49] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-08-05 23:47:49] [SUCCESS] [OmnipathR] Loaded 29651 intercellular communication role records from cache.
[2023-08-05 23:47:49] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-08-05 23:47:49] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:47:49] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-08-05 23:47:50] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-08-05 23:47:50] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-08-05 23:47:50] [SUCCESS] [OmnipathR] Loaded 45334 intercellular communication role records from cache.
[2023-08-05 23:48:12] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-08-05 23:48:12] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2023-08-05 23:48:12] [SUCCESS] [OmnipathR] Loaded 332447 intercellular communication role records from cache.
[2023-08-05 23:48:12] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-08-05 23:48:12] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:48:12] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-08-05 23:48:13] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-08-05 23:48:13] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-08-05 23:48:16] [SUCCESS] [OmnipathR] Loaded 134282 interactions from cache.
[2023-08-05 23:48:16] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-08-05 23:48:16] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-08-05 23:48:16] [SUCCESS] [OmnipathR] Loaded 29651 intercellular communication role records from cache.
[2023-08-05 23:48:17] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-08-05 23:48:17] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-08-05 23:48:17] [SUCCESS] [OmnipathR] Loaded 45334 intercellular communication role records from cache.
--- finished re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2023-08-05 23:50:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-08-05 23:50:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-08-05 23:50:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-08-05 23:50:33] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2023-08-05 23:50:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2023-08-05 23:50:33] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2023-08-05 23:50:33] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:33] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2023-08-05 23:50:33] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2023-08-05 23:50:33] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-08-05 23:50:33] [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`.
[2023-08-05 23:50:33] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2023-08-05 23:50:33] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-08-05 23:50:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-08-05 23:50:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2023-08-05 23:50:34] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2023-08-05 23:50:34] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:34] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2023-08-05 23:50:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-08-05 23:50:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-08-05 23:50:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-08-05 23:50:37] [INFO]    [OmnipathR] Cache item `ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2023-08-05 23:50:37] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2023-08-05 23:50:37] [INFO]    [OmnipathR] Download ready [key=ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41, version=1]
[2023-08-05 23:50:38] [INFO]    [OmnipathR] Cache item `ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:40] [SUCCESS] [OmnipathR] Downloaded 87651 interactions.
[2023-08-05 23:50:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2023-08-05 23:50:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2023-08-05 23:50:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2023-08-05 23:50:45] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2023-08-05 23:50:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2023-08-05 23:50:45] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2023-08-05 23:50:45] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:45] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2023-08-05 23:50:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2023-08-05 23:50:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2023-08-05 23:50:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2023-08-05 23:50:46] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2023-08-05 23:50:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2023-08-05 23:50:46] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2023-08-05 23:50:46] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:46] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2023-08-05 23:50:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-08-05 23:50:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:50:47] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-08-05 23:50:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2023-08-05 23:50:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2023-08-05 23:50:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2023-08-05 23:50:47] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2023-08-05 23:50:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2023-08-05 23:50:47] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2023-08-05 23:50:47] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:47] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2023-08-05 23:50:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-08-05 23:50:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:50:47] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-08-05 23:50:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-08-05 23:50:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-08-05 23:50:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2023-08-05 23:50:48] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2023-08-05 23:50:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2023-08-05 23:50:48] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2023-08-05 23:50:48] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:48] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2023-08-05 23:50:48] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-08-05 23:50:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:50:48] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-08-05 23:50:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2023-08-05 23:50:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2023-08-05 23:50:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2023-08-05 23:50:49] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:49] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2023-08-05 23:50:49] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2023-08-05 23:50:49] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2023-08-05 23:50:49] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:49] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2023-08-05 23:50:49] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-08-05 23:50:49] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:50:49] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-08-05 23:50:49] [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`
[2023-08-05 23:50:49] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-08-05 23:50:49] [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`
[2023-08-05 23:50:50] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2023-08-05 23:50:50] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2023-08-05 23:50:50] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2023-08-05 23:50:50] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:51] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2023-08-05 23:50:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2023-08-05 23:50:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2023-08-05 23:50:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2023-08-05 23:50:52] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2023-08-05 23:50:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2023-08-05 23:50:52] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2023-08-05 23:50:52] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:52] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2023-08-05 23:50:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2023-08-05 23:50:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2023-08-05 23:50:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2023-08-05 23:50:52] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2023-08-05 23:50:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2023-08-05 23:50:52] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2023-08-05 23:50:52] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:52] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2023-08-05 23:50:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&entity_types=protein&license=academic`
[2023-08-05 23:50:53] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&entity_types=protein&license=academic`
[2023-08-05 23:50:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&entity_types=protein&license=academic`
[2023-08-05 23:50:55] [INFO]    [OmnipathR] Cache item `fcb9b617e2cd1880fcda07c1509f5e941632e47b` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fcb9b617e2cd1880fcda07c1509f5e941632e47b-1.rds`.
[2023-08-05 23:50:55] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fcb9b617e2cd1880fcda07c1509f5e941632e47b-1.rds`.
[2023-08-05 23:50:55] [INFO]    [OmnipathR] Download ready [key=fcb9b617e2cd1880fcda07c1509f5e941632e47b, version=1]
[2023-08-05 23:50:55] [INFO]    [OmnipathR] Cache item `fcb9b617e2cd1880fcda07c1509f5e941632e47b` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:56] [SUCCESS] [OmnipathR] Downloaded 31345 interactions.
[2023-08-05 23:50:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2023-08-05 23:50:56] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2023-08-05 23:50:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2023-08-05 23:50:57] [INFO]    [OmnipathR] Cache item `b66455a04c1c3908ec8bb3b116a5ad645607e9bd` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b66455a04c1c3908ec8bb3b116a5ad645607e9bd-1.rds`.
[2023-08-05 23:50:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b66455a04c1c3908ec8bb3b116a5ad645607e9bd-1.rds`.
[2023-08-05 23:50:57] [INFO]    [OmnipathR] Download ready [key=b66455a04c1c3908ec8bb3b116a5ad645607e9bd, version=1]
[2023-08-05 23:50:57] [INFO]    [OmnipathR] Cache item `b66455a04c1c3908ec8bb3b116a5ad645607e9bd` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:57] [SUCCESS] [OmnipathR] Downloaded 9030 intercellular communication role records.
[2023-08-05 23:50:57] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-08-05 23:50:57] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-08-05 23:50:57] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2023-08-05 23:50:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2023-08-05 23:50:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2023-08-05 23:50:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2023-08-05 23:50:58] [INFO]    [OmnipathR] Cache item `56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:50:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3-1.rds`.
[2023-08-05 23:50:58] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3-1.rds`.
[2023-08-05 23:50:58] [INFO]    [OmnipathR] Download ready [key=56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3, version=1]
[2023-08-05 23:50:58] [INFO]    [OmnipathR] Cache item `56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3` version 1: status changed from `started` to `ready`.
[2023-08-05 23:50:58] [SUCCESS] [OmnipathR] Downloaded 20478 intercellular communication role records.
[2023-08-05 23:51:01] [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`
[2023-08-05 23:51:01] [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`
[2023-08-05 23:51:01] [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`
[2023-08-05 23:51:01] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:51:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2023-08-05 23:51:01] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2023-08-05 23:51:01] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2023-08-05 23:51:01] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2023-08-05 23:51:02] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2023-08-05 23:51:02] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-08-05 23:51:02] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-08-05 23:51:02] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2023-08-05 23:51:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2023-08-05 23:51:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2023-08-05 23:51:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2023-08-05 23:51:03] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2023-08-05 23:51:03] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2023-08-05 23:51:03] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2023-08-05 23:51:03] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2023-08-05 23:51:03] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2023-08-05 23:51:03] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2023-08-05 23:51:05] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2023-08-05 23:51:05] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2023-08-05 23:51:05] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2023-08-05 23:51:05] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2023-08-05 23:51:05] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2023-08-05 23:51:05] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache.
--- finished re-building ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘bioc_workshop.Rmd’ ‘db_manager.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-08-05 23:51:07 CEST ]