* 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
[2021-12-28 12:00:12] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2021-12-28 12:00:12] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2021-12-28 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`
[2021-12-28 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`
[2021-12-28 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`
[2021-12-28 12:00:16] [INFO]    [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:00:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2021-12-28 12:00:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2021-12-28 12:00:16] [INFO]    [OmnipathR] Download ready [key=f4de1f63d60f35d18bb262dd6de84d1cccd9cc97, version=1]
[2021-12-28 12:00:16] [INFO]    [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `started` to `ready`.
[2021-12-28 12:00:17] [SUCCESS] [OmnipathR] Downloaded 62752 interactions.
[2021-12-28 12:00:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:00:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:00:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:00:23] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:00:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2021-12-28 12:00:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2021-12-28 12:00:23] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2021-12-28 12:00:23] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2021-12-28 12:00:23] [SUCCESS] [OmnipathR] Downloaded 42162 enzyme-substrate relationships.
[2021-12-28 12:00:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:00:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:00:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:00:26] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:00:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2021-12-28 12:00:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2021-12-28 12:00:27] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2021-12-28 12:00:27] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2021-12-28 12:00:27] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2021-12-28 12:00:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2021-12-28 12:00:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2021-12-28 12:00:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2021-12-28 12:00:29] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:00:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2021-12-28 12:00:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2021-12-28 12:00:30] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2021-12-28 12:00:30] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2021-12-28 12:00:30] [SUCCESS] [OmnipathR] Downloaded 32535 protein complexes.
[2021-12-28 12:00:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-12-28 12:00:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-12-28 12:00:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-12-28 12:00:32] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:00:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2021-12-28 12:00:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2021-12-28 12:00:32] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2021-12-28 12:00:32] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2021-12-28 12:00:32] [SUCCESS] [OmnipathR] Downloaded 72383 annotation records.
[2021-12-28 12:00:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2021-12-28 12:00:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2021-12-28 12:00:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2021-12-28 12:00:33] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:00:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2021-12-28 12:00:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2021-12-28 12:00:33] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2021-12-28 12:00:33] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2021-12-28 12:00:33] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2021-12-28 12:00:33] [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.
[2021-12-28 12:00:33] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2021-12-28 12:00:33] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-12-28 12:00:33] [SUCCESS] [OmnipathR] Loaded 72383 annotation records from cache.
[2021-12-28 12:00:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&license=academic`
[2021-12-28 12:00:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&license=academic`
[2021-12-28 12:00:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&license=academic`
Quitting from lines 346-351 (bioc_workshop.Rmd) 
Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
transfer closed with 784861312 bytes remaining to read
--- failed 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

[2021-12-28 12:01:52] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2021-12-28 12:01:52] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:01:52] [SUCCESS] [OmnipathR] Loaded 39742 interactions from cache.
The magick package is required to crop "/tmp/Rtmp9lZQsQ/Rbuild3d35c2dc36082/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
[2021-12-28 12:01:58] [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`
[2021-12-28 12:01:58] [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`
[2021-12-28 12:01:58] [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`
[2021-12-28 12:02:03] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:03] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2021-12-28 12:02:03] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2021-12-28 12:02:03] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2021-12-28 12:02:03] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:03] [SUCCESS] [OmnipathR] Downloaded 14487 interactions.
[2021-12-28 12:02:04] [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`
[2021-12-28 12:02:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:02:04] [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`
[2021-12-28 12:02:05] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2021-12-28 12:02:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2021-12-28 12:02:05] [INFO]    [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1]
[2021-12-28 12:02:05] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:05] [SUCCESS] [OmnipathR] Downloaded 1253 interactions.
[2021-12-28 12:02:05] [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`
[2021-12-28 12:02:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:02:05] [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`
[2021-12-28 12:02:07] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2021-12-28 12:02:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2021-12-28 12:02:07] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2021-12-28 12:02:07] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:07] [SUCCESS] [OmnipathR] Downloaded 9855 interactions.
[2021-12-28 12:02:07] [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`
[2021-12-28 12:02:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:02:07] [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`
[2021-12-28 12:02:08] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2021-12-28 12:02:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2021-12-28 12:02:09] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2021-12-28 12:02:09] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:09] [SUCCESS] [OmnipathR] Downloaded 3001 interactions.
[2021-12-28 12:02:09] [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`
[2021-12-28 12:02:09] [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`
[2021-12-28 12:02:09] [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`
[2021-12-28 12:02:10] [INFO]    [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2021-12-28 12:02:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2021-12-28 12:02:10] [INFO]    [OmnipathR] Download ready [key=cde98994cdbb4dd0e43d69b43a01b3491332287d, version=1]
[2021-12-28 12:02:10] [INFO]    [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:10] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2021-12-28 12:02:10] [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`
[2021-12-28 12:02:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:02:10] [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`
[2021-12-28 12:02:10] [INFO]    [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2021-12-28 12:02:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2021-12-28 12:02:10] [INFO]    [OmnipathR] Download ready [key=fc18df7465bfc9f5b72d079bc3dc9408636597cc, version=1]
[2021-12-28 12:02:10] [INFO]    [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:10] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2021-12-28 12:02:11] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2021-12-28 12:02:11] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:02:11] [SUCCESS] [OmnipathR] Loaded 42162 enzyme-substrate relationships from cache.
[2021-12-28 12:02:11] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2021-12-28 12:02:11] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:02:11] [SUCCESS] [OmnipathR] Loaded 39742 interactions from cache.
[2021-12-28 12:02:12] [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`
[2021-12-28 12:02:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:02:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2021-12-28 12:02:14] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2021-12-28 12:02:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2021-12-28 12:02:14] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2021-12-28 12:02:14] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:14] [SUCCESS] [OmnipathR] Downloaded 17416 enzyme-substrate relationships.
[2021-12-28 12:02:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2021-12-28 12:02:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2021-12-28 12:02:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2021-12-28 12:02:15] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2021-12-28 12:02:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2021-12-28 12:02:16] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2021-12-28 12:02:16] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:16] [SUCCESS] [OmnipathR] Downloaded 7190 protein complexes.
[2021-12-28 12:02:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2021-12-28 12:02:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2021-12-28 12:02:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:PARP1_WRN_XRCC5_XRCC6&license=academic`
[2021-12-28 12:02:17] [INFO]    [OmnipathR] Cache item `929c2072937af212fa00922d04d210172bd315c8` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/929c2072937af212fa00922d04d210172bd315c8-1.rds`.
[2021-12-28 12:02:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/929c2072937af212fa00922d04d210172bd315c8-1.rds`.
[2021-12-28 12:02:17] [INFO]    [OmnipathR] Download ready [key=929c2072937af212fa00922d04d210172bd315c8, version=1]
[2021-12-28 12:02:17] [INFO]    [OmnipathR] Cache item `929c2072937af212fa00922d04d210172bd315c8` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:17] [SUCCESS] [OmnipathR] Downloaded 39 annotation records.
[2021-12-28 12:02:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2021-12-28 12:02:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2021-12-28 12:02:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2021-12-28 12:02:18] [INFO]    [OmnipathR] Cache item `20cd5eb55475c83ea15e2d2ddb162dcdd528116f` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20cd5eb55475c83ea15e2d2ddb162dcdd528116f-1.rds`.
[2021-12-28 12:02:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20cd5eb55475c83ea15e2d2ddb162dcdd528116f-1.rds`.
[2021-12-28 12:02:18] [INFO]    [OmnipathR] Download ready [key=20cd5eb55475c83ea15e2d2ddb162dcdd528116f, version=1]
[2021-12-28 12:02:18] [INFO]    [OmnipathR] Cache item `20cd5eb55475c83ea15e2d2ddb162dcdd528116f` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:18] [SUCCESS] [OmnipathR] Downloaded 7 annotation records.
[2021-12-28 12:02:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2021-12-28 12:02:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2021-12-28 12:02:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=PARP1,WRN,XRCC5,XRCC6&license=academic`
[2021-12-28 12:02:18] [INFO]    [OmnipathR] Cache item `acaa653138834ed8b6d7d52ce1b3529953f720a2` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/acaa653138834ed8b6d7d52ce1b3529953f720a2-1.rds`.
[2021-12-28 12:02:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/acaa653138834ed8b6d7d52ce1b3529953f720a2-1.rds`.
[2021-12-28 12:02:18] [INFO]    [OmnipathR] Download ready [key=acaa653138834ed8b6d7d52ce1b3529953f720a2, version=1]
[2021-12-28 12:02:18] [INFO]    [OmnipathR] Cache item `acaa653138834ed8b6d7d52ce1b3529953f720a2` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:18] [SUCCESS] [OmnipathR] Downloaded 28 annotation records.
[2021-12-28 12:02:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2021-12-28 12:02:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2021-12-28 12:02:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2021-12-28 12:02:19] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2021-12-28 12:02:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2021-12-28 12:02:19] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2021-12-28 12:02:19] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:19] [SUCCESS] [OmnipathR] Downloaded 2444 annotation records.
[2021-12-28 12:02:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2021-12-28 12:02:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2021-12-28 12:02:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2021-12-28 12:02:19] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2021-12-28 12:02:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2021-12-28 12:02:20] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2021-12-28 12:02:20] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:20] [SUCCESS] [OmnipathR] Downloaded 1097 records.
[2021-12-28 12:02:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2021-12-28 12:02:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2021-12-28 12:02:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2021-12-28 12:02:31] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2021-12-28 12:02:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2021-12-28 12:02:32] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2021-12-28 12:02:32] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:32] [SUCCESS] [OmnipathR] Downloaded 231008 intercellular communication role records.
[2021-12-28 12:02:34] [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`
[2021-12-28 12:02:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2021-12-28 12:02:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2021-12-28 12:02:37] [INFO]    [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2021-12-28 12:02:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`.
[2021-12-28 12:02:38] [INFO]    [OmnipathR] Download ready [key=498f91238951df23d4d71705063f40254eddbfbf, version=1]
[2021-12-28 12:02:38] [INFO]    [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:38] [SUCCESS] [OmnipathR] Downloaded 40409 interactions.
[2021-12-28 12:02:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2021-12-28 12:02:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2021-12-28 12:02:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2021-12-28 12:02:39] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2021-12-28 12:02:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2021-12-28 12:02:39] [INFO]    [OmnipathR] Download ready [key=1ac430724a20c137fc374a8499adabb468a12835, version=1]
[2021-12-28 12:02:39] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:39] [SUCCESS] [OmnipathR] Downloaded 27897 intercellular communication role records.
[2021-12-28 12:02:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-12-28 12:02:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-12-28 12:02:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-12-28 12:02:41] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-12-28 12:02:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-12-28 12:02:41] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2021-12-28 12:02:41] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:41] [SUCCESS] [OmnipathR] Downloaded 21323 intercellular communication role records.
[2021-12-28 12:02:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2021-12-28 12:02:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2021-12-28 12:02:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2021-12-28 12:02:42] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:02:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2021-12-28 12:02:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2021-12-28 12:02:43] [INFO]    [OmnipathR] Download ready [key=552757063f9934c7b745a9c4247c3b5282a66c88, version=1]
[2021-12-28 12:02:43] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `started` to `ready`.
[2021-12-28 12:02:43] [SUCCESS] [OmnipathR] Downloaded 43921 intercellular communication role records.
[2021-12-28 12:02:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2021-12-28 12:02:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2021-12-28 12:02:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2021-12-28 12:03:02] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:03:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2021-12-28 12:03:04] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2021-12-28 12:03:04] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2021-12-28 12:03:04] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2021-12-28 12:03:05] [SUCCESS] [OmnipathR] Downloaded 323304 intercellular communication role records.
[2021-12-28 12:03:06] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-12-28 12:03:06] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-12-28 12:03:06] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-12-28 12:03:06] [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`
[2021-12-28 12:03:06] [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`
[2021-12-28 12:03:06] [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`
[2021-12-28 12:03:11] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:03:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2021-12-28 12:03:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2021-12-28 12:03:12] [INFO]    [OmnipathR] Download ready [key=3098404926bc0cf155d043ff0c6efe64e3424b74, version=1]
[2021-12-28 12:03:12] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `started` to `ready`.
[2021-12-28 12:03:13] [SUCCESS] [OmnipathR] Downloaded 79979 interactions.
[2021-12-28 12:03:13] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2021-12-28 12:03:13] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2021-12-28 12:03:13] [SUCCESS] [OmnipathR] Loaded 27897 intercellular communication role records from cache.
[2021-12-28 12:03:13] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2021-12-28 12:03:13] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2021-12-28 12:03:13] [SUCCESS] [OmnipathR] Loaded 43921 intercellular communication role records from cache.
--- finished re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2021-12-28 12:03:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2021-12-28 12:03:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2021-12-28 12:03:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2021-12-28 12:03:40] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:03:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2021-12-28 12:03:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2021-12-28 12:03:40] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2021-12-28 12:03:40] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2021-12-28 12:03:40] [SUCCESS] [OmnipathR] Downloaded 3517 annotation records.
[2021-12-28 12:03:40] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2021-12-28 12:03:40] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2021-12-28 12:03:40] [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`.
[2021-12-28 12:03:40] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:03:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2021-12-28 12:03:40] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2021-12-28 12:03:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2021-12-28 12:03:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2021-12-28 12:03:41] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2021-12-28 12:03:41] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2021-12-28 12:03:41] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2021-12-28 12:03:41] [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`
[2021-12-28 12:03:41] [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`
[2021-12-28 12:03:41] [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`
[2021-12-28 12:03:44] [INFO]    [OmnipathR] Cache item `ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:03:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2021-12-28 12:03:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2021-12-28 12:03:44] [INFO]    [OmnipathR] Download ready [key=ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41, version=1]
[2021-12-28 12:03:44] [INFO]    [OmnipathR] Cache item `ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41` version 1: status changed from `started` to `ready`.
[2021-12-28 12:03:45] [SUCCESS] [OmnipathR] Downloaded 62554 interactions.
[2021-12-28 12:03:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2021-12-28 12:03:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2021-12-28 12:03:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2021-12-28 12:03:52] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:03:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2021-12-28 12:03:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2021-12-28 12:03:53] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2021-12-28 12:03:53] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2021-12-28 12:03:53] [SUCCESS] [OmnipathR] Downloaded 351307 annotation records.
[2021-12-28 12:03:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=sec&license=academic`
[2021-12-28 12:03:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=sec&license=academic`
[2021-12-28 12:03:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=sec&license=academic`
[2021-12-28 12:03:55] [INFO]    [OmnipathR] Cache item `bff4a3e667dd430d687de100bd8432e1fadd5d3d` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:03:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bff4a3e667dd430d687de100bd8432e1fadd5d3d-1.rds`.
[2021-12-28 12:03:55] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bff4a3e667dd430d687de100bd8432e1fadd5d3d-1.rds`.
[2021-12-28 12:03:55] [INFO]    [OmnipathR] Download ready [key=bff4a3e667dd430d687de100bd8432e1fadd5d3d, version=1]
[2021-12-28 12:03:55] [INFO]    [OmnipathR] Cache item `bff4a3e667dd430d687de100bd8432e1fadd5d3d` version 1: status changed from `started` to `ready`.
[2021-12-28 12:03:55] [SUCCESS] [OmnipathR] Downloaded 9693 intercellular communication role records.
[2021-12-28 12:03:55] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-12-28 12:03:55] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-12-28 12:03:55] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-12-28 12:03:55] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=pmtm&license=academic`
[2021-12-28 12:03:55] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=pmtm&license=academic`
[2021-12-28 12:03:55] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=pmtm&license=academic`
[2021-12-28 12:03:56] [INFO]    [OmnipathR] Cache item `37a6749854419bf778be37a7053bcaba8173aa40` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:03:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/37a6749854419bf778be37a7053bcaba8173aa40-1.rds`.
[2021-12-28 12:03:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/37a6749854419bf778be37a7053bcaba8173aa40-1.rds`.
[2021-12-28 12:03:56] [INFO]    [OmnipathR] Download ready [key=37a6749854419bf778be37a7053bcaba8173aa40, version=1]
[2021-12-28 12:03:56] [INFO]    [OmnipathR] Cache item `37a6749854419bf778be37a7053bcaba8173aa40` version 1: status changed from `started` to `ready`.
[2021-12-28 12:03:56] [SUCCESS] [OmnipathR] Downloaded 21257 intercellular communication role records.
[2021-12-28 12:03:56] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-12-28 12:03:56] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-12-28 12:03:56] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-12-28 12:03:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=sec&causality=trans&license=academic`
[2021-12-28 12:03:56] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=sec&causality=trans&license=academic`
[2021-12-28 12:03:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=sec&causality=trans&license=academic`
[2021-12-28 12:03:57] [INFO]    [OmnipathR] Cache item `1a787c9aceb59267b238ebd678a711c3fedf0d33` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:03:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1a787c9aceb59267b238ebd678a711c3fedf0d33-1.rds`.
[2021-12-28 12:03:58] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1a787c9aceb59267b238ebd678a711c3fedf0d33-1.rds`.
[2021-12-28 12:03:58] [INFO]    [OmnipathR] Download ready [key=1a787c9aceb59267b238ebd678a711c3fedf0d33, version=1]
[2021-12-28 12:03:58] [INFO]    [OmnipathR] Cache item `1a787c9aceb59267b238ebd678a711c3fedf0d33` version 1: status changed from `started` to `ready`.
[2021-12-28 12:03:58] [SUCCESS] [OmnipathR] Downloaded 14205 intercellular communication role records.
[2021-12-28 12:03:58] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-12-28 12:03:58] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-12-28 12:03:58] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-12-28 12:03:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=pmtm&causality=rec&license=academic`
[2021-12-28 12:03:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=pmtm&causality=rec&license=academic`
[2021-12-28 12:03:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=pmtm&causality=rec&license=academic`
[2021-12-28 12:03:59] [INFO]    [OmnipathR] Cache item `77083b97fe6cc7634b5082dc5f5aa90120f867f0` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:03:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/77083b97fe6cc7634b5082dc5f5aa90120f867f0-1.rds`.
[2021-12-28 12:03:59] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/77083b97fe6cc7634b5082dc5f5aa90120f867f0-1.rds`.
[2021-12-28 12:03:59] [INFO]    [OmnipathR] Download ready [key=77083b97fe6cc7634b5082dc5f5aa90120f867f0, version=1]
[2021-12-28 12:03:59] [INFO]    [OmnipathR] Cache item `77083b97fe6cc7634b5082dc5f5aa90120f867f0` version 1: status changed from `started` to `ready`.
[2021-12-28 12:03:59] [SUCCESS] [OmnipathR] Downloaded 26220 intercellular communication role records.
[2021-12-28 12:04:00] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-12-28 12:04:00] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-12-28 12:04:00] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-12-28 12:04:00] [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`
[2021-12-28 12:04:00] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2021-12-28 12:04:00] [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`
[2021-12-28 12:04:03] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:04:03] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2021-12-28 12:04:03] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2021-12-28 12:04:03] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2021-12-28 12:04:03] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2021-12-28 12:04:04] [SUCCESS] [OmnipathR] Downloaded 37564 interactions.
[2021-12-28 12:04:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2021-12-28 12:04:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2021-12-28 12:04:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2021-12-28 12:04:05] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:04:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2021-12-28 12:04:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2021-12-28 12:04:05] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2021-12-28 12:04:05] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2021-12-28 12:04:05] [SUCCESS] [OmnipathR] Downloaded 1145 annotation records.
[2021-12-28 12:04:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2021-12-28 12:04:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2021-12-28 12:04:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2021-12-28 12:04:05] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:04:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2021-12-28 12:04:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2021-12-28 12:04:05] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2021-12-28 12:04:05] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2021-12-28 12:04:05] [SUCCESS] [OmnipathR] Downloaded 1082 annotation records.
[2021-12-28 12:04:06] [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`
[2021-12-28 12:04:06] [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`
[2021-12-28 12:04:06] [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`
[2021-12-28 12:04:10] [INFO]    [OmnipathR] Cache item `fcb9b617e2cd1880fcda07c1509f5e941632e47b` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:04:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fcb9b617e2cd1880fcda07c1509f5e941632e47b-1.rds`.
[2021-12-28 12:04:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fcb9b617e2cd1880fcda07c1509f5e941632e47b-1.rds`.
[2021-12-28 12:04:10] [INFO]    [OmnipathR] Download ready [key=fcb9b617e2cd1880fcda07c1509f5e941632e47b, version=1]
[2021-12-28 12:04:10] [INFO]    [OmnipathR] Cache item `fcb9b617e2cd1880fcda07c1509f5e941632e47b` version 1: status changed from `started` to `ready`.
[2021-12-28 12:04:11] [SUCCESS] [OmnipathR] Downloaded 38115 interactions.
[2021-12-28 12:04:11] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2021-12-28 12:04:11] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2021-12-28 12:04:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2021-12-28 12:04:12] [INFO]    [OmnipathR] Cache item `b66455a04c1c3908ec8bb3b116a5ad645607e9bd` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:04:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b66455a04c1c3908ec8bb3b116a5ad645607e9bd-1.rds`.
[2021-12-28 12:04:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b66455a04c1c3908ec8bb3b116a5ad645607e9bd-1.rds`.
[2021-12-28 12:04:12] [INFO]    [OmnipathR] Download ready [key=b66455a04c1c3908ec8bb3b116a5ad645607e9bd, version=1]
[2021-12-28 12:04:12] [INFO]    [OmnipathR] Cache item `b66455a04c1c3908ec8bb3b116a5ad645607e9bd` version 1: status changed from `started` to `ready`.
[2021-12-28 12:04:12] [SUCCESS] [OmnipathR] Downloaded 8667 intercellular communication role records.
[2021-12-28 12:04:12] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2021-12-28 12:04:12] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2021-12-28 12:04:12] [SUCCESS] [OmnipathR] Loaded 21323 intercellular communication role records from cache.
[2021-12-28 12:04:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2021-12-28 12:04:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2021-12-28 12:04:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2021-12-28 12:04:13] [INFO]    [OmnipathR] Cache item `56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:04:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3-1.rds`.
[2021-12-28 12:04:13] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3-1.rds`.
[2021-12-28 12:04:13] [INFO]    [OmnipathR] Download ready [key=56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3, version=1]
[2021-12-28 12:04:13] [INFO]    [OmnipathR] Cache item `56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3` version 1: status changed from `started` to `ready`.
[2021-12-28 12:04:13] [SUCCESS] [OmnipathR] Downloaded 20431 intercellular communication role records.
[2021-12-28 12:04:14] [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`
[2021-12-28 12:04:14] [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`
[2021-12-28 12:04:14] [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`
[2021-12-28 12:04:15] [INFO]    [OmnipathR] Cache item `f100eb9a673f67d563f3064546939882685ef470` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:04:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f100eb9a673f67d563f3064546939882685ef470-1.rds`.
[2021-12-28 12:04:15] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f100eb9a673f67d563f3064546939882685ef470-1.rds`.
[2021-12-28 12:04:15] [INFO]    [OmnipathR] Download ready [key=f100eb9a673f67d563f3064546939882685ef470, version=1]
[2021-12-28 12:04:15] [INFO]    [OmnipathR] Cache item `f100eb9a673f67d563f3064546939882685ef470` version 1: status changed from `started` to `ready`.
[2021-12-28 12:04:15] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2021-12-28 12:04:16] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2021-12-28 12:04:16] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-12-28 12:04:16] [SUCCESS] [OmnipathR] Loaded 72383 annotation records from cache.
[2021-12-28 12:04:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2021-12-28 12:04:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2021-12-28 12:04:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2021-12-28 12:04:16] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2021-12-28 12:04:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2021-12-28 12:04:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2021-12-28 12:04:16] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2021-12-28 12:04:16] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2021-12-28 12:04:16] [SUCCESS] [OmnipathR] Downloaded 1988 annotation records.
[2021-12-28 12:04:21] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2021-12-28 12:04:21] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2021-12-28 12:04:21] [SUCCESS] [OmnipathR] Loaded 72383 annotation records from cache.
[2021-12-28 12:04:21] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2021-12-28 12:04:21] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2021-12-28 12:04:21] [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:
  ‘bioc_workshop.Rmd’ ‘paths.Rmd’

Error: Vignette re-building failed.
In addition: Warning messages:
1: In get(as.character(FUN), mode = "function", envir = envir) :
  closing unused connection 4 (https://omnipathdb.org/annotations?resources=HPA_tissue&license=academic)
2: The label(s) fig:fig1 not found 
3: The label(s) fig:fig2 not found 
4: The label(s) fig:fig3 not found 
5: The label(s) fig:fig4 not found 
Execution halted