* 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
[2021-11-28 12:00:11] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2021-11-28 12:00:11] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2021-11-28 12:00:12] [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`
[2021-11-28 12:00:12] [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`
[2021-11-28 12:00:12] [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`
[2021-11-28 12:00:12] [INFO]    [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:00:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2021-11-28 12:00:13] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2021-11-28 12:00:13] [INFO]    [OmnipathR] Download ready [key=f4de1f63d60f35d18bb262dd6de84d1cccd9cc97, version=1]
[2021-11-28 12:00:13] [INFO]    [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `started` to `ready`.
[2021-11-28 12:00:13] [SUCCESS] [OmnipathR] Downloaded 62752 interactions.
[2021-11-28 12:00:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:00:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:00:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:00:19] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:00:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2021-11-28 12:00:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2021-11-28 12:00:19] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2021-11-28 12:00:19] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2021-11-28 12:00:19] [SUCCESS] [OmnipathR] Downloaded 42162 enzyme-substrate relationships.
[2021-11-28 12:00:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:00:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:00:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:00:23] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:00:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2021-11-28 12:00:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2021-11-28 12:00:23] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2021-11-28 12:00:23] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2021-11-28 12:00:24] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2021-11-28 12:00:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2021-11-28 12:00:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2021-11-28 12:00:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2021-11-28 12:00:25] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:00:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2021-11-28 12:00:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2021-11-28 12:00:25] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2021-11-28 12:00:25] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2021-11-28 12:00:25] [SUCCESS] [OmnipathR] Downloaded 32535 protein complexes.
[2021-11-28 12:00:25] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-11-28 12:00:25] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-11-28 12:00:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-11-28 12:00:26] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:00:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2021-11-28 12:00:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2021-11-28 12:00:27] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2021-11-28 12:00:27] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2021-11-28 12:00:27] [SUCCESS] [OmnipathR] Downloaded 72383 annotation records.
[2021-11-28 12:00:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2021-11-28 12:00:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2021-11-28 12:00:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2021-11-28 12:00:27] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:00:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2021-11-28 12:00:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2021-11-28 12:00:27] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2021-11-28 12:00:27] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2021-11-28 12:00:27] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2021-11-28 12:00:27] [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.
[2021-11-28 12:00:28] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2021-11-28 12:00:28] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-11-28 12:00:28] [SUCCESS] [OmnipathR] Loaded 72383 annotation records from cache.
[2021-11-28 12:00:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&license=academic`
[2021-11-28 12:00:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&license=academic`
[2021-11-28 12:00:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&license=academic`
[2021-11-28 12:04:21] [INFO]    [OmnipathR] Cache item `dd59d7a35c8b884377b2f0136efd720aa32b9d72` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:04:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/dd59d7a35c8b884377b2f0136efd720aa32b9d72-1.rds`.
[2021-11-28 12:04:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/dd59d7a35c8b884377b2f0136efd720aa32b9d72-1.rds`.
[2021-11-28 12:04:57] [INFO]    [OmnipathR] Download ready [key=dd59d7a35c8b884377b2f0136efd720aa32b9d72, version=1]
[2021-11-28 12:04:57] [INFO]    [OmnipathR] Cache item `dd59d7a35c8b884377b2f0136efd720aa32b9d72` version 1: status changed from `started` to `ready`.
[2021-11-28 12:04:57] [SUCCESS] [OmnipathR] Downloaded 13408585 annotation records.
[2021-11-28 12:05:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2021-11-28 12:05:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2021-11-28 12:05:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2021-11-28 12:05:17] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:05:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2021-11-28 12:05:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2021-11-28 12:05:17] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2021-11-28 12:05:17] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2021-11-28 12:05:17] [SUCCESS] [OmnipathR] Downloaded 2444 annotation records.
[2021-11-28 12:05:17] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2021-11-28 12:05:17] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:05:17] [SUCCESS] [OmnipathR] Loaded 39742 interactions from cache.
[2021-11-28 12:05:18] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2021-11-28 12:05:18] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2021-11-28 12:05:18] [SUCCESS] [OmnipathR] Loaded 2444 annotation records from cache.
[2021-11-28 12:05:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2021-11-28 12:05:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2021-11-28 12:05:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2021-11-28 12:05:32] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:05:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2021-11-28 12:05:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2021-11-28 12:05:34] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2021-11-28 12:05:34] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2021-11-28 12:05:34] [SUCCESS] [OmnipathR] Downloaded 323304 intercellular communication role records.
[2021-11-28 12:05:35] [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`
[2021-11-28 12:05:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2021-11-28 12:05:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2021-11-28 12:05:39] [INFO]    [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:05:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2021-11-28 12:05:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2021-11-28 12:05:40] [INFO]    [OmnipathR] Download ready [key=498f91238951df23d4d71705063f40254eddbfbf, version=1]
[2021-11-28 12:05:40] [INFO]    [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `started` to `ready`.
[2021-11-28 12:05:40] [SUCCESS] [OmnipathR] Downloaded 40409 interactions.
[2021-11-28 12:05:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2021-11-28 12:05:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2021-11-28 12:05:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2021-11-28 12:05:42] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:05:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2021-11-28 12:05:42] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2021-11-28 12:05:42] [INFO]    [OmnipathR] Download ready [key=1ac430724a20c137fc374a8499adabb468a12835, version=1]
[2021-11-28 12:05:42] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `started` to `ready`.
[2021-11-28 12:05:42] [SUCCESS] [OmnipathR] Downloaded 27897 intercellular communication role records.
[2021-11-28 12:05:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-11-28 12:05:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-11-28 12:05:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-11-28 12:05:43] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:05:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-11-28 12:05:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-11-28 12:05:44] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2021-11-28 12:05:44] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2021-11-28 12:05:44] [SUCCESS] [OmnipathR] Downloaded 21323 intercellular communication role records.
[2021-11-28 12:05:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2021-11-28 12:05:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2021-11-28 12:05:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2021-11-28 12:05:45] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:05:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2021-11-28 12:05:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2021-11-28 12:05:46] [INFO]    [OmnipathR] Download ready [key=552757063f9934c7b745a9c4247c3b5282a66c88, version=1]
[2021-11-28 12:05:46] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `started` to `ready`.
[2021-11-28 12:05:46] [SUCCESS] [OmnipathR] Downloaded 43921 intercellular communication role records.
[2021-11-28 12:05:51] [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`
[2021-11-28 12:05:51] [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`
[2021-11-28 12:05:51] [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`
[2021-11-28 12:05:56] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:05:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2021-11-28 12:05:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2021-11-28 12:05:57] [INFO]    [OmnipathR] Download ready [key=3098404926bc0cf155d043ff0c6efe64e3424b74, version=1]
[2021-11-28 12:05:57] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `started` to `ready`.
[2021-11-28 12:05:58] [SUCCESS] [OmnipathR] Downloaded 79979 interactions.
[2021-11-28 12:05:58] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2021-11-28 12:05:58] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2021-11-28 12:05:58] [SUCCESS] [OmnipathR] Loaded 27897 intercellular communication role records from cache.
[2021-11-28 12:05:58] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2021-11-28 12:05:58] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2021-11-28 12:05:58] [SUCCESS] [OmnipathR] Loaded 43921 intercellular communication role records from cache.
[2021-11-28 12:06:25] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2021-11-28 12:06:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2021-11-28 12:06:26] [SUCCESS] [OmnipathR] Loaded 323304 intercellular communication role records from cache.
[2021-11-28 12:06:26] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-11-28 12:06:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-11-28 12:06:26] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-11-28 12:06:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2021-11-28 12:06:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2021-11-28 12:06:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2021-11-28 12:06:27] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:06:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2021-11-28 12:06:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2021-11-28 12:06:27] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2021-11-28 12:06:27] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2021-11-28 12:06:27] [SUCCESS] [OmnipathR] Downloaded 1097 records.
[2021-11-28 12:06:27] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2021-11-28 12:06:27] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE)
[2021-11-28 12:06:27] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED)
[2021-11-28 12:06:27] [TRACE]   [OmnipathR] Looking up in cache: `https://www.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2021-11-28 12:06:27] [INFO]    [OmnipathR] Cache record does not exist: `https://www.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2021-11-28 12:06:27] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://www.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2021-11-28 12:06:27] [INFO]    [OmnipathR] Cache item `11eb810ae342ef823eec8d744d4ff3085012e1f4` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:06:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/11eb810ae342ef823eec8d744d4ff3085012e1f4-1.rds`.
[2021-11-28 12:06:27] [INFO]    [OmnipathR] Retrieving URL: `https://www.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2021-11-28 12:06:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2021-11-28 12:06:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/11eb810ae342ef823eec8d744d4ff3085012e1f4-1.rds`.
[2021-11-28 12:06:38] [INFO]    [OmnipathR] Download ready [key=11eb810ae342ef823eec8d744d4ff3085012e1f4, version=1]
[2021-11-28 12:06:38] [INFO]    [OmnipathR] Cache item `11eb810ae342ef823eec8d744d4ff3085012e1f4` version 1: status changed from `started` to `ready`.
[2021-11-28 12:06:38] [SUCCESS] [OmnipathR] UniProt (www.uniprot.org): downloaded 20375 records
[2021-11-28 12:06:38] [INFO]    [OmnipathR] Looking up in cache `http://purl.obolibrary.org/obo/go/go-basic.obo`: key=663f8a0321e09c16870d151bd7559c9385d22288, no version available.
[2021-11-28 12:06:38] [INFO]    [OmnipathR] Created new version for cache record 663f8a0321e09c16870d151bd7559c9385d22288: version 1.
[2021-11-28 12:06:38] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo
[2021-11-28 12:06:38] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/go/go-basic.obo`
[2021-11-28 12:06:38] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/go/go-basic.obo`
[2021-11-28 12:06:39] [TRACE]   [OmnipathR] HTTP 200
[2021-11-28 12:06:40] [TRACE]   [OmnipathR] HTTP 200
[2021-11-28 12:06:40] [INFO]    [OmnipathR] Download ready [key=663f8a0321e09c16870d151bd7559c9385d22288, version=1]
[2021-11-28 12:06:40] [INFO]    [OmnipathR] Cache item `663f8a0321e09c16870d151bd7559c9385d22288` version 1: status changed from `unknown` to `ready`.
[2021-11-28 12:06:40] [TRACE]   [OmnipathR] Processing OBO file `/home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2021-11-28 12:06:43] [TRACE]   [OmnipathR] Finished processing OBO file `/home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2021-11-28 12:06:43] [TRACE]   [OmnipathR] Converting ontology relations from table to graph.
[2021-11-28 12:06:44] [INFO]    [OmnipathR] Loading database `Gene Ontology (basic)`.
[2021-11-28 12:06:44] [INFO]    [OmnipathR] Looking up in cache `http://purl.obolibrary.org/obo/go/go-basic.obo`: key=663f8a0321e09c16870d151bd7559c9385d22288, latest version=1.
[2021-11-28 12:06:44] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo
[2021-11-28 12:06:44] [TRACE]   [OmnipathR] Processing OBO file `/home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2021-11-28 12:06:47] [TRACE]   [OmnipathR] Finished processing OBO file `/home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`.
[2021-11-28 12:06:47] [INFO]    [OmnipathR] Loaded database `Gene Ontology (basic)`.
--- finished re-building ‘bioc_workshop.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

[2021-11-28 12:06:48] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2021-11-28 12:06:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:06:49] [SUCCESS] [OmnipathR] Loaded 39742 interactions from cache.
The magick package is required to crop "/tmp/RtmpY4gI6C/Rbuildd1249532123/OmnipathR/vignettes/drug_targets_files/figure-html/unnamed-chunk-12-1.png" but not available.
--- finished re-building ‘drug_targets.Rmd’

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

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown

Attaching package: 'tidyr'

The following object is masked from 'package:igraph':

    crossing

Loading required package: supraHex
Loading required package: hexbin
[2021-11-28 12:06:54] [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`
[2021-11-28 12:06:54] [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`
[2021-11-28 12:06:54] [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`
[2021-11-28 12:06:56] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:06:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2021-11-28 12:06:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2021-11-28 12:06:57] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2021-11-28 12:06:57] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2021-11-28 12:06:57] [SUCCESS] [OmnipathR] Downloaded 14487 interactions.
[2021-11-28 12:06:58] [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`
[2021-11-28 12:06:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:06:58] [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`
[2021-11-28 12:06:59] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:06:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2021-11-28 12:06:59] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2021-11-28 12:06:59] [INFO]    [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1]
[2021-11-28 12:06:59] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`.
[2021-11-28 12:06:59] [SUCCESS] [OmnipathR] Downloaded 1253 interactions.
[2021-11-28 12:06:59] [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`
[2021-11-28 12:06:59] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:06:59] [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`
[2021-11-28 12:07:01] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2021-11-28 12:07:01] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2021-11-28 12:07:01] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2021-11-28 12:07:01] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:01] [SUCCESS] [OmnipathR] Downloaded 9855 interactions.
[2021-11-28 12:07:01] [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`
[2021-11-28 12:07:01] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:07:01] [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`
[2021-11-28 12:07:02] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2021-11-28 12:07:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2021-11-28 12:07:02] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2021-11-28 12:07:02] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:02] [SUCCESS] [OmnipathR] Downloaded 3001 interactions.
[2021-11-28 12:07:03] [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`
[2021-11-28 12:07:03] [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`
[2021-11-28 12:07:03] [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`
[2021-11-28 12:07:04] [INFO]    [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2021-11-28 12:07:04] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2021-11-28 12:07:04] [INFO]    [OmnipathR] Download ready [key=cde98994cdbb4dd0e43d69b43a01b3491332287d, version=1]
[2021-11-28 12:07:04] [INFO]    [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:04] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2021-11-28 12:07:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:07:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:07:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-11-28 12:07:05] [INFO]    [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2021-11-28 12:07:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2021-11-28 12:07:05] [INFO]    [OmnipathR] Download ready [key=fc18df7465bfc9f5b72d079bc3dc9408636597cc, version=1]
[2021-11-28 12:07:05] [INFO]    [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:05] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
Quitting from lines 364-377 (omnipath_intro.Rmd) 
Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
non-character argument
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2021-11-28 12:07:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2021-11-28 12:07:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2021-11-28 12:07:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2021-11-28 12:07:05] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2021-11-28 12:07:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2021-11-28 12:07:05] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2021-11-28 12:07:05] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:05] [SUCCESS] [OmnipathR] Downloaded 3517 annotation records.
[2021-11-28 12:07:05] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2021-11-28 12:07:05] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2021-11-28 12:07:05] [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`.
[2021-11-28 12:07:06] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2021-11-28 12:07:06] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2021-11-28 12:07:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2021-11-28 12:07:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2021-11-28 12:07:06] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2021-11-28 12:07:06] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:06] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2021-11-28 12:07:06] [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`
[2021-11-28 12:07:06] [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`
[2021-11-28 12:07:06] [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`
[2021-11-28 12:07:12] [INFO]    [OmnipathR] Cache item `ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2021-11-28 12:07:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2021-11-28 12:07:12] [INFO]    [OmnipathR] Download ready [key=ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41, version=1]
[2021-11-28 12:07:12] [INFO]    [OmnipathR] Cache item `ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:13] [SUCCESS] [OmnipathR] Downloaded 62554 interactions.
[2021-11-28 12:07:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2021-11-28 12:07:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2021-11-28 12:07:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2021-11-28 12:07:23] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2021-11-28 12:07:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2021-11-28 12:07:24] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2021-11-28 12:07:24] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:24] [SUCCESS] [OmnipathR] Downloaded 351307 annotation records.
[2021-11-28 12:07:25] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=sec&license=academic`
[2021-11-28 12:07:25] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=sec&license=academic`
[2021-11-28 12:07:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=sec&license=academic`
[2021-11-28 12:07:25] [INFO]    [OmnipathR] Cache item `bff4a3e667dd430d687de100bd8432e1fadd5d3d` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bff4a3e667dd430d687de100bd8432e1fadd5d3d-1.rds`.
[2021-11-28 12:07:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bff4a3e667dd430d687de100bd8432e1fadd5d3d-1.rds`.
[2021-11-28 12:07:25] [INFO]    [OmnipathR] Download ready [key=bff4a3e667dd430d687de100bd8432e1fadd5d3d, version=1]
[2021-11-28 12:07:26] [INFO]    [OmnipathR] Cache item `bff4a3e667dd430d687de100bd8432e1fadd5d3d` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:26] [SUCCESS] [OmnipathR] Downloaded 9693 intercellular communication role records.
[2021-11-28 12:07:26] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-11-28 12:07:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-11-28 12:07:26] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-11-28 12:07:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=pmtm&license=academic`
[2021-11-28 12:07:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=pmtm&license=academic`
[2021-11-28 12:07:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=pmtm&license=academic`
[2021-11-28 12:07:27] [INFO]    [OmnipathR] Cache item `37a6749854419bf778be37a7053bcaba8173aa40` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/37a6749854419bf778be37a7053bcaba8173aa40-1.rds`.
[2021-11-28 12:07:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/37a6749854419bf778be37a7053bcaba8173aa40-1.rds`.
[2021-11-28 12:07:27] [INFO]    [OmnipathR] Download ready [key=37a6749854419bf778be37a7053bcaba8173aa40, version=1]
[2021-11-28 12:07:27] [INFO]    [OmnipathR] Cache item `37a6749854419bf778be37a7053bcaba8173aa40` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:27] [SUCCESS] [OmnipathR] Downloaded 21257 intercellular communication role records.
[2021-11-28 12:07:27] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-11-28 12:07:27] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-11-28 12:07:27] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-11-28 12:07:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=sec&causality=trans&license=academic`
[2021-11-28 12:07:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=sec&causality=trans&license=academic`
[2021-11-28 12:07:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=sec&causality=trans&license=academic`
[2021-11-28 12:07:28] [INFO]    [OmnipathR] Cache item `1a787c9aceb59267b238ebd678a711c3fedf0d33` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1a787c9aceb59267b238ebd678a711c3fedf0d33-1.rds`.
[2021-11-28 12:07:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1a787c9aceb59267b238ebd678a711c3fedf0d33-1.rds`.
[2021-11-28 12:07:28] [INFO]    [OmnipathR] Download ready [key=1a787c9aceb59267b238ebd678a711c3fedf0d33, version=1]
[2021-11-28 12:07:28] [INFO]    [OmnipathR] Cache item `1a787c9aceb59267b238ebd678a711c3fedf0d33` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:28] [SUCCESS] [OmnipathR] Downloaded 14205 intercellular communication role records.
[2021-11-28 12:07:29] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-11-28 12:07:29] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-11-28 12:07:29] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-11-28 12:07:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=pmtm&causality=rec&license=academic`
[2021-11-28 12:07:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=pmtm&causality=rec&license=academic`
[2021-11-28 12:07:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=pmtm&causality=rec&license=academic`
[2021-11-28 12:07:30] [INFO]    [OmnipathR] Cache item `77083b97fe6cc7634b5082dc5f5aa90120f867f0` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/77083b97fe6cc7634b5082dc5f5aa90120f867f0-1.rds`.
[2021-11-28 12:07:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/77083b97fe6cc7634b5082dc5f5aa90120f867f0-1.rds`.
[2021-11-28 12:07:30] [INFO]    [OmnipathR] Download ready [key=77083b97fe6cc7634b5082dc5f5aa90120f867f0, version=1]
[2021-11-28 12:07:30] [INFO]    [OmnipathR] Cache item `77083b97fe6cc7634b5082dc5f5aa90120f867f0` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:30] [SUCCESS] [OmnipathR] Downloaded 26220 intercellular communication role records.
[2021-11-28 12:07:30] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-11-28 12:07:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-11-28 12:07:30] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-11-28 12:07:30] [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`
[2021-11-28 12:07:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2021-11-28 12:07:30] [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`
[2021-11-28 12:07:34] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2021-11-28 12:07:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2021-11-28 12:07:35] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2021-11-28 12:07:35] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:35] [SUCCESS] [OmnipathR] Downloaded 37564 interactions.
[2021-11-28 12:07:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2021-11-28 12:07:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2021-11-28 12:07:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2021-11-28 12:07:36] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2021-11-28 12:07:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2021-11-28 12:07:36] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2021-11-28 12:07:36] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:36] [SUCCESS] [OmnipathR] Downloaded 1145 annotation records.
[2021-11-28 12:07:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2021-11-28 12:07:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2021-11-28 12:07:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2021-11-28 12:07:37] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2021-11-28 12:07:37] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2021-11-28 12:07:37] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2021-11-28 12:07:37] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:37] [SUCCESS] [OmnipathR] Downloaded 1082 annotation records.
[2021-11-28 12:07:37] [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`
[2021-11-28 12:07:37] [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`
[2021-11-28 12:07:37] [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`
[2021-11-28 12:07:41] [INFO]    [OmnipathR] Cache item `fcb9b617e2cd1880fcda07c1509f5e941632e47b` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fcb9b617e2cd1880fcda07c1509f5e941632e47b-1.rds`.
[2021-11-28 12:07:42] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fcb9b617e2cd1880fcda07c1509f5e941632e47b-1.rds`.
[2021-11-28 12:07:42] [INFO]    [OmnipathR] Download ready [key=fcb9b617e2cd1880fcda07c1509f5e941632e47b, version=1]
[2021-11-28 12:07:42] [INFO]    [OmnipathR] Cache item `fcb9b617e2cd1880fcda07c1509f5e941632e47b` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:42] [SUCCESS] [OmnipathR] Downloaded 38115 interactions.
[2021-11-28 12:07:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2021-11-28 12:07:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2021-11-28 12:07:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2021-11-28 12:07:43] [INFO]    [OmnipathR] Cache item `b66455a04c1c3908ec8bb3b116a5ad645607e9bd` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b66455a04c1c3908ec8bb3b116a5ad645607e9bd-1.rds`.
[2021-11-28 12:07:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b66455a04c1c3908ec8bb3b116a5ad645607e9bd-1.rds`.
[2021-11-28 12:07:43] [INFO]    [OmnipathR] Download ready [key=b66455a04c1c3908ec8bb3b116a5ad645607e9bd, version=1]
[2021-11-28 12:07:43] [INFO]    [OmnipathR] Cache item `b66455a04c1c3908ec8bb3b116a5ad645607e9bd` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:43] [SUCCESS] [OmnipathR] Downloaded 8667 intercellular communication role records.
[2021-11-28 12:07:44] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-11-28 12:07:44] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-11-28 12:07:44] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-11-28 12:07:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2021-11-28 12:07:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2021-11-28 12:07:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2021-11-28 12:07:45] [INFO]    [OmnipathR] Cache item `56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3-1.rds`.
[2021-11-28 12:07:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3-1.rds`.
[2021-11-28 12:07:45] [INFO]    [OmnipathR] Download ready [key=56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3, version=1]
[2021-11-28 12:07:45] [INFO]    [OmnipathR] Cache item `56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:45] [SUCCESS] [OmnipathR] Downloaded 20431 intercellular communication role records.
[2021-11-28 12:07:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2021-11-28 12:07:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2021-11-28 12:07:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2021-11-28 12:07:47] [INFO]    [OmnipathR] Cache item `f100eb9a673f67d563f3064546939882685ef470` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f100eb9a673f67d563f3064546939882685ef470-1.rds`.
[2021-11-28 12:07:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f100eb9a673f67d563f3064546939882685ef470-1.rds`.
[2021-11-28 12:07:47] [INFO]    [OmnipathR] Download ready [key=f100eb9a673f67d563f3064546939882685ef470, version=1]
[2021-11-28 12:07:47] [INFO]    [OmnipathR] Cache item `f100eb9a673f67d563f3064546939882685ef470` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:47] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2021-11-28 12:07:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2021-11-28 12:07:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-11-28 12:07:47] [SUCCESS] [OmnipathR] Loaded 72383 annotation records from cache.
[2021-11-28 12:07:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2021-11-28 12:07:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2021-11-28 12:07:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2021-11-28 12:07:48] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2021-11-28 12:07:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2021-11-28 12:07:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2021-11-28 12:07:48] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2021-11-28 12:07:48] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2021-11-28 12:07:48] [SUCCESS] [OmnipathR] Downloaded 1988 annotation records.
[2021-11-28 12:07:54] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2021-11-28 12:07:54] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-11-28 12:07:54] [SUCCESS] [OmnipathR] Loaded 72383 annotation records from cache.
[2021-11-28 12:07:54] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2021-11-28 12:07:54] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2021-11-28 12:07:54] [SUCCESS] [OmnipathR] Loaded 1988 annotation records from cache.
Quitting from lines 446-503 (paths.Rmd) 
Error: processing vignette 'paths.Rmd' failed with diagnostics:
Must group by variables found in `.data`.
* Column `n_resources` is not found.
--- failed re-building ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘omnipath_intro.Rmd’ ‘paths.Rmd’

Error: Vignette re-building failed.
Execution halted