* 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
[2022-04-12 08:00:14] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-04-12 08:00:14] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-12 08:00:14] [TRACE]   [OmnipathR] Cache locked: FALSE
[2022-04-12 08:00:14] [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`
[2022-04-12 08:00:14] [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`
[2022-04-12 08:00:14] [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`
[2022-04-12 08:00:16] [INFO]    [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:00:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2022-04-12 08:00:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`.
[2022-04-12 08:00:16] [INFO]    [OmnipathR] Download ready [key=f4de1f63d60f35d18bb262dd6de84d1cccd9cc97, version=1]
[2022-04-12 08:00:16] [INFO]    [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `started` to `ready`.
[2022-04-12 08:00:17] [SUCCESS] [OmnipathR] Downloaded 74513 interactions.
[2022-04-12 08:00:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:00:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:00:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:00:31] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:00:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2022-04-12 08:00:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2022-04-12 08:00:32] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2022-04-12 08:00:32] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2022-04-12 08:00:32] [SUCCESS] [OmnipathR] Downloaded 42248 enzyme-substrate relationships.
[2022-04-12 08:00:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:00:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:00:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:00:40] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 1/3); error: transfer closed with 6878172 bytes remaining to read
[2022-04-12 08:00:41] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
Quitting from lines 282-283 (bioc_workshop.Rmd) 
Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
transfer closed with 6878172 bytes remaining to read
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
Warning in for (opt in names(ohooks)) { :
  closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic)
[2022-04-12 08:00:43] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table (human)`.
[2022-04-12 08:00:43] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE)
[2022-04-12 08:00:43] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED)
[2022-04-12 08:00:43] [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`.
[2022-04-12 08:00:43] [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`
[2022-04-12 08:00:43] [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`.
[2022-04-12 08:00:43] [INFO]    [OmnipathR] Cache item `11eb810ae342ef823eec8d744d4ff3085012e1f4` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:00:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/11eb810ae342ef823eec8d744d4ff3085012e1f4-1.rds`.
[2022-04-12 08:00:43] [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`
[2022-04-12 08:00:43] [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`
[2022-04-12 08:00:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/11eb810ae342ef823eec8d744d4ff3085012e1f4-1.rds`.
[2022-04-12 08:00:54] [INFO]    [OmnipathR] Download ready [key=11eb810ae342ef823eec8d744d4ff3085012e1f4, version=1]
[2022-04-12 08:00:54] [INFO]    [OmnipathR] Cache item `11eb810ae342ef823eec8d744d4ff3085012e1f4` version 1: status changed from `started` to `ready`.
[2022-04-12 08:00:54] [SUCCESS] [OmnipathR] UniProt (www.uniprot.org): downloaded 20376 records
[2022-04-12 08:00:55] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table (human)`.
--- finished re-building ‘db_manager.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

[2022-04-12 08:01:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:01:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:01:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
Quitting from lines 43-48 (drug_targets.Rmd) 
Error: processing vignette 'drug_targets.Rmd' failed with diagnostics:
transfer closed with 6878172 bytes remaining to read
--- failed re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2022-04-12 08:01:08] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2022-04-12 08:01:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2022-04-12 08:01:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2022-04-12 08:01:32] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:01:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2022-04-12 08:01:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2022-04-12 08:01:33] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2022-04-12 08:01:33] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
Warning in for (i in seq_len(n)) { :
  closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic)
Warning in for (i in seq_len(n)) { :
  closing unused connection 5 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic)
[2022-04-12 08:01:36] [SUCCESS] [OmnipathR] Downloaded 80237 interactions.
[2022-04-12 08:03:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2022-04-12 08:03:14] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2022-04-12 08:03:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2022-04-12 08:03:33] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:03:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2022-04-12 08:03:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2022-04-12 08:03:34] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2022-04-12 08:03:34] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2022-04-12 08:03:34] [SUCCESS] [OmnipathR] Downloaded 204222 annotation records.
[2022-04-12 08:03:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2022-04-12 08:03:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2022-04-12 08:03:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2022-04-12 08:03:34] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:03:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2022-04-12 08:03:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2022-04-12 08:03:34] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2022-04-12 08:03:34] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2022-04-12 08:03:34] [SUCCESS] [OmnipathR] Downloaded 52 enzyme-substrate relationships.
--- finished re-building ‘extra_attrs.Rmd’

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

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

Attaching package: 'tidyr'

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

    crossing

Loading required package: supraHex
Loading required package: hexbin
[2022-04-12 08:03:37] [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`
[2022-04-12 08:03:37] [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`
[2022-04-12 08:03:37] [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`
[2022-04-12 08:03:43] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:03:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2022-04-12 08:03:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2022-04-12 08:03:43] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2022-04-12 08:03:43] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2022-04-12 08:03:44] [SUCCESS] [OmnipathR] Downloaded 14767 interactions.
[2022-04-12 08:03:45] [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`
[2022-04-12 08:03:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:03:45] [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`
[2022-04-12 08:03:46] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:03:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2022-04-12 08:03:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2022-04-12 08:03:46] [INFO]    [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1]
[2022-04-12 08:03:46] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`.
[2022-04-12 08:03:46] [SUCCESS] [OmnipathR] Downloaded 1263 interactions.
[2022-04-12 08:03:46] [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`
[2022-04-12 08:03:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:03:46] [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`
[2022-04-12 08:03:49] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:03:49] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2022-04-12 08:03:50] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2022-04-12 08:03:50] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2022-04-12 08:03:50] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2022-04-12 08:03:50] [SUCCESS] [OmnipathR] Downloaded 7468 interactions.
[2022-04-12 08:03:50] [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`
[2022-04-12 08:03:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:03:50] [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`
[2022-04-12 08:03:52] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:03:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2022-04-12 08:03:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2022-04-12 08:03:52] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2022-04-12 08:03:52] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2022-04-12 08:03:52] [SUCCESS] [OmnipathR] Downloaded 3013 interactions.
[2022-04-12 08:03:52] [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`
[2022-04-12 08:03:52] [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`
[2022-04-12 08:03:52] [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`
[2022-04-12 08:03:54] [INFO]    [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:03:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2022-04-12 08:03:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`.
[2022-04-12 08:03:54] [INFO]    [OmnipathR] Download ready [key=cde98994cdbb4dd0e43d69b43a01b3491332287d, version=1]
[2022-04-12 08:03:54] [INFO]    [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `started` to `ready`.
[2022-04-12 08:03:54] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2022-04-12 08:03:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2022-04-12 08:03:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2022-04-12 08:03:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2022-04-12 08:03:58] [INFO]    [OmnipathR] Cache item `8281969bb1ab7f3f99e3f1632559158df24b9a40` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:03:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8281969bb1ab7f3f99e3f1632559158df24b9a40-1.rds`.
[2022-04-12 08:03:59] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8281969bb1ab7f3f99e3f1632559158df24b9a40-1.rds`.
[2022-04-12 08:03:59] [INFO]    [OmnipathR] Download ready [key=8281969bb1ab7f3f99e3f1632559158df24b9a40, version=1]
[2022-04-12 08:03:59] [INFO]    [OmnipathR] Cache item `8281969bb1ab7f3f99e3f1632559158df24b9a40` version 1: status changed from `started` to `ready`.
[2022-04-12 08:03:59] [SUCCESS] [OmnipathR] Downloaded 27539 interactions.
[2022-04-12 08:03:59] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:03:59] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:03:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:04:00] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:04:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2022-04-12 08:04:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2022-04-12 08:04:00] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2022-04-12 08:04:00] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2022-04-12 08:04:00] [SUCCESS] [OmnipathR] Downloaded 728 interactions.
[2022-04-12 08:04:00] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2022-04-12 08:04:00] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2022-04-12 08:04:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2022-04-12 08:04:00] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:04:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2022-04-12 08:04:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2022-04-12 08:04:00] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2022-04-12 08:04:00] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2022-04-12 08:04:00] [SUCCESS] [OmnipathR] Downloaded 26 interactions.
[2022-04-12 08:04:00] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2022-04-12 08:04:00] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:04:01] [SUCCESS] [OmnipathR] Loaded 42248 enzyme-substrate relationships from cache.
[2022-04-12 08:04:01] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:04:01] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-04-12 08:04:01] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
Quitting from lines 436-470 (omnipath_intro.Rmd) 
Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
transfer closed with 6878172 bytes remaining to read
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2022-04-12 08:04:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2022-04-12 08:04:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2022-04-12 08:04:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2022-04-12 08:04:03] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:04:03] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2022-04-12 08:04:03] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2022-04-12 08:04:03] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2022-04-12 08:04:03] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2022-04-12 08:04:03] [SUCCESS] [OmnipathR] Downloaded 3516 annotation records.
[2022-04-12 08:04:03] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2022-04-12 08:04:03] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2022-04-12 08:04:03] [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`.
[2022-04-12 08:04:03] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:04:03] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2022-04-12 08:04:03] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2022-04-12 08:04:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2022-04-12 08:04:04] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2022-04-12 08:04:04] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2022-04-12 08:04:04] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2022-04-12 08:04:04] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2022-04-12 08:04:04] [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`
[2022-04-12 08:04:04] [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`
[2022-04-12 08:04:04] [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`
[2022-04-12 08:04:17] [INFO]    [OmnipathR] Cache item `ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:04:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2022-04-12 08:04:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41-1.rds`.
[2022-04-12 08:04:18] [INFO]    [OmnipathR] Download ready [key=ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41, version=1]
[2022-04-12 08:04:18] [INFO]    [OmnipathR] Cache item `ffaa4b7c994a4e5ce3a8d988ccdee2b0d8505c41` version 1: status changed from `started` to `ready`.
[2022-04-12 08:04:18] [SUCCESS] [OmnipathR] Downloaded 90360 interactions.
[2022-04-12 08:04:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2022-04-12 08:04:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2022-04-12 08:04:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2022-04-12 08:05:01] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2022-04-12 08:05:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2022-04-12 08:05:02] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2022-04-12 08:05:02] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:02] [SUCCESS] [OmnipathR] Downloaded 352707 annotation records.
Warning in for (i in seq_len(n)) { :
  closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic)
[2022-04-12 08:05:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=sec&license=academic`
[2022-04-12 08:05:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=sec&license=academic`
[2022-04-12 08:05:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=sec&license=academic`
[2022-04-12 08:05:05] [INFO]    [OmnipathR] Cache item `bff4a3e667dd430d687de100bd8432e1fadd5d3d` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bff4a3e667dd430d687de100bd8432e1fadd5d3d-1.rds`.
[2022-04-12 08:05:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bff4a3e667dd430d687de100bd8432e1fadd5d3d-1.rds`.
[2022-04-12 08:05:05] [INFO]    [OmnipathR] Download ready [key=bff4a3e667dd430d687de100bd8432e1fadd5d3d, version=1]
[2022-04-12 08:05:05] [INFO]    [OmnipathR] Cache item `bff4a3e667dd430d687de100bd8432e1fadd5d3d` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:05] [SUCCESS] [OmnipathR] Downloaded 9695 intercellular communication role records.
[2022-04-12 08:05:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 08:05:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 08:05:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 08:05:06] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 08:05:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 08:05:06] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2022-04-12 08:05:06] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:06] [SUCCESS] [OmnipathR] Downloaded 21325 intercellular communication role records.
[2022-04-12 08:05:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=pmtm&license=academic`
[2022-04-12 08:05:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=pmtm&license=academic`
[2022-04-12 08:05:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=pmtm&license=academic`
[2022-04-12 08:05:07] [INFO]    [OmnipathR] Cache item `37a6749854419bf778be37a7053bcaba8173aa40` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/37a6749854419bf778be37a7053bcaba8173aa40-1.rds`.
[2022-04-12 08:05:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/37a6749854419bf778be37a7053bcaba8173aa40-1.rds`.
[2022-04-12 08:05:07] [INFO]    [OmnipathR] Download ready [key=37a6749854419bf778be37a7053bcaba8173aa40, version=1]
[2022-04-12 08:05:07] [INFO]    [OmnipathR] Cache item `37a6749854419bf778be37a7053bcaba8173aa40` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:07] [SUCCESS] [OmnipathR] Downloaded 21198 intercellular communication role records.
[2022-04-12 08:05:07] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 08:05:07] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 08:05:07] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2022-04-12 08:05:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=sec&causality=trans&license=academic`
[2022-04-12 08:05:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=sec&causality=trans&license=academic`
[2022-04-12 08:05:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=sec&causality=trans&license=academic`
[2022-04-12 08:05:08] [INFO]    [OmnipathR] Cache item `1a787c9aceb59267b238ebd678a711c3fedf0d33` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1a787c9aceb59267b238ebd678a711c3fedf0d33-1.rds`.
[2022-04-12 08:05:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1a787c9aceb59267b238ebd678a711c3fedf0d33-1.rds`.
[2022-04-12 08:05:08] [INFO]    [OmnipathR] Download ready [key=1a787c9aceb59267b238ebd678a711c3fedf0d33, version=1]
[2022-04-12 08:05:08] [INFO]    [OmnipathR] Cache item `1a787c9aceb59267b238ebd678a711c3fedf0d33` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:08] [SUCCESS] [OmnipathR] Downloaded 14210 intercellular communication role records.
[2022-04-12 08:05:08] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 08:05:08] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 08:05:08] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2022-04-12 08:05:08] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=pmtm&causality=rec&license=academic`
[2022-04-12 08:05:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=pmtm&causality=rec&license=academic`
[2022-04-12 08:05:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=pmtm&causality=rec&license=academic`
[2022-04-12 08:05:09] [INFO]    [OmnipathR] Cache item `77083b97fe6cc7634b5082dc5f5aa90120f867f0` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/77083b97fe6cc7634b5082dc5f5aa90120f867f0-1.rds`.
[2022-04-12 08:05:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/77083b97fe6cc7634b5082dc5f5aa90120f867f0-1.rds`.
[2022-04-12 08:05:09] [INFO]    [OmnipathR] Download ready [key=77083b97fe6cc7634b5082dc5f5aa90120f867f0, version=1]
[2022-04-12 08:05:09] [INFO]    [OmnipathR] Cache item `77083b97fe6cc7634b5082dc5f5aa90120f867f0` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:09] [SUCCESS] [OmnipathR] Downloaded 26158 intercellular communication role records.
[2022-04-12 08:05:09] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 08:05:09] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 08:05:09] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2022-04-12 08:05:09] [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`
[2022-04-12 08:05:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2022-04-12 08:05:09] [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`
[2022-04-12 08:05:22] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2022-04-12 08:05:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2022-04-12 08:05:22] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2022-04-12 08:05:22] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:23] [SUCCESS] [OmnipathR] Downloaded 37689 interactions.
[2022-04-12 08:05:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2022-04-12 08:05:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2022-04-12 08:05:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2022-04-12 08:05:24] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2022-04-12 08:05:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2022-04-12 08:05:24] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2022-04-12 08:05:24] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:24] [SUCCESS] [OmnipathR] Downloaded 1145 annotation records.
[2022-04-12 08:05:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2022-04-12 08:05:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2022-04-12 08:05:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2022-04-12 08:05:24] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2022-04-12 08:05:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2022-04-12 08:05:24] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2022-04-12 08:05:24] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:24] [SUCCESS] [OmnipathR] Downloaded 1082 annotation records.
[2022-04-12 08:05:25] [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`
[2022-04-12 08:05:25] [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`
[2022-04-12 08:05:25] [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`
[2022-04-12 08:05:39] [INFO]    [OmnipathR] Cache item `fcb9b617e2cd1880fcda07c1509f5e941632e47b` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fcb9b617e2cd1880fcda07c1509f5e941632e47b-1.rds`.
[2022-04-12 08:05:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fcb9b617e2cd1880fcda07c1509f5e941632e47b-1.rds`.
[2022-04-12 08:05:39] [INFO]    [OmnipathR] Download ready [key=fcb9b617e2cd1880fcda07c1509f5e941632e47b, version=1]
[2022-04-12 08:05:39] [INFO]    [OmnipathR] Cache item `fcb9b617e2cd1880fcda07c1509f5e941632e47b` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:39] [SUCCESS] [OmnipathR] Downloaded 38240 interactions.
[2022-04-12 08:05:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2022-04-12 08:05:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2022-04-12 08:05:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=ligand&causality=trans&license=academic`
[2022-04-12 08:05:40] [INFO]    [OmnipathR] Cache item `b66455a04c1c3908ec8bb3b116a5ad645607e9bd` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b66455a04c1c3908ec8bb3b116a5ad645607e9bd-1.rds`.
[2022-04-12 08:05:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b66455a04c1c3908ec8bb3b116a5ad645607e9bd-1.rds`.
[2022-04-12 08:05:40] [INFO]    [OmnipathR] Download ready [key=b66455a04c1c3908ec8bb3b116a5ad645607e9bd, version=1]
[2022-04-12 08:05:40] [INFO]    [OmnipathR] Cache item `b66455a04c1c3908ec8bb3b116a5ad645607e9bd` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:40] [SUCCESS] [OmnipathR] Downloaded 8669 intercellular communication role records.
[2022-04-12 08:05:40] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 08:05:40] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 08:05:40] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2022-04-12 08:05:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2022-04-12 08:05:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2022-04-12 08:05:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&scope=generic&parent=receptor&causality=rec&license=academic`
[2022-04-12 08:05:46] [INFO]    [OmnipathR] Cache item `56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3-1.rds`.
[2022-04-12 08:05:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3-1.rds`.
[2022-04-12 08:05:46] [INFO]    [OmnipathR] Download ready [key=56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3, version=1]
[2022-04-12 08:05:46] [INFO]    [OmnipathR] Cache item `56fb848f2d07435e8feeceb21dbfaae5f9fc7cf3` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:46] [SUCCESS] [OmnipathR] Downloaded 20436 intercellular communication role records.
[2022-04-12 08:05:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2022-04-12 08:05:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2022-04-12 08:05:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2022-04-12 08:05:48] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2022-04-12 08:05:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2022-04-12 08:05:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2022-04-12 08:05:48] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2022-04-12 08:05:48] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2022-04-12 08:05:48] [SUCCESS] [OmnipathR] Downloaded 4617 interactions.
[2022-04-12 08:05:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2022-04-12 08:05:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2022-04-12 08:05:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
Quitting from lines 448-507 (paths.Rmd) 
Error: processing vignette 'paths.Rmd' failed with diagnostics:
transfer closed with 6031499 bytes remaining to read
--- failed re-building ‘paths.Rmd’

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

Error: Vignette re-building failed.
Execution halted