[ Started: 2023-09-08 02:00:42 CEST ]
[ OmnipathR v3.6.6 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2023-09-08 02:00:51] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-09-08 02:00:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-09-08 02:00:51] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-09-08 02:00:51] [TRACE]   [OmnipathR] Contains 1 files.
[2023-09-08 02:00:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-09-08 02:00:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-09-08 02:00:51] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-09-08 02:00:51] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-09-08 02:00:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-09-08 02:00:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-09-08 02:00:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-09-08 02:00:51] [WARN]    [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
[2023-09-08 02:00:56] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-09-08 02:00:56] [WARN]    [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-09-08 02:01:01] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-09-08 02:01:01] [ERROR]   [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.

Quitting from lines 225-227 [network] (bioc_workshop.Rmd)
Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
Warning in gsub(chunk.begin, "\\1", line) :
  closing unused connection 5 (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)
Warning in gsub(chunk.begin, "\\1", line) :
  closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic)
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2023-09-08 02:01:02] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE)
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Loading database `Ensembl organism names`.
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2023-09-08 02:01:02] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2023-09-08 02:01:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2023-09-08 02:01:02] [TRACE]   [OmnipathR] HTTP 200
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Loaded database `Ensembl organism names`.
[2023-09-08 02:01:02] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED)
[2023-09-08 02:01:02] [TRACE]   [OmnipathR] Looking up in cache: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Cache record does not exist: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-09-08 02:01:02] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`.
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:01:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`.
[2023-09-08 02:01:02] [INFO]    [OmnipathR] Retrieving URL: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-09-08 02:01:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-09-08 02:01:02] [WARN]    [OmnipathR] Failed to download `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` (attempt 1/3); error: Could not resolve host: legacy.uniprot.org
[2023-09-08 02:01:07] [TRACE]   [OmnipathR] Attempt 2/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-09-08 02:01:07] [WARN]    [OmnipathR] Failed to download `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` (attempt 2/3); error: Could not resolve host: legacy.uniprot.org
[2023-09-08 02:01:13] [TRACE]   [OmnipathR] Attempt 3/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`
[2023-09-08 02:01:13] [ERROR]   [OmnipathR] Failed to download `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` (attempt 3/3); error: Could not resolve host: legacy.uniprot.org
[2023-09-08 02:01:13] [TRACE]   [OmnipathR] Failed download attempt: `Could not resolve host: legacy.uniprot.org`.

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

--- re-building ‘drug_targets.Rmd’ using rmarkdown
Warning in for (i in 1L:d2) { :
  closing unused connection 5 (https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no)
Warning in for (i in 1L:d2) { :
  closing unused connection 4 (https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no)
[2023-09-08 02:01:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:01:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:01:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:01:13] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:01:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-09-08 02:01:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2023-09-08 02:01:14] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2023-09-08 02:01:14] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2023-09-08 02:01:16] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
Warning: closing unused connection 7 (https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no)
Warning: closing unused connection 6 (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)
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2023-09-08 02:01:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-09-08 02:01:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-09-08 02:01:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-09-08 02:01:21] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:01:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-09-08 02:01:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2023-09-08 02:01:22] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2023-09-08 02:01:22] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2023-09-08 02:01:31] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2023-09-08 02:05:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-09-08 02:05:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-09-08 02:05:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2023-09-08 02:05:17] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:05:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2023-09-08 02:05:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2023-09-08 02:05:18] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2023-09-08 02:05:18] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2023-09-08 02:05:18] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2023-09-08 02:05:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-09-08 02:05:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-09-08 02:05:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2023-09-08 02:05:18] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:05:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2023-09-08 02:05:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2023-09-08 02:05:18] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2023-09-08 02:05:18] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2023-09-08 02:05:18] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships.
--- finished re-building ‘extra_attrs.Rmd’

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

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2023-09-08 02:05:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:22] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:05:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2023-09-08 02:05:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2023-09-08 02:05:22] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2023-09-08 02:05:22] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2023-09-08 02:05:24] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2023-09-08 02:05:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:28] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:05:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2023-09-08 02:05:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`.
[2023-09-08 02:05:28] [INFO]    [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1]
[2023-09-08 02:05:28] [INFO]    [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`.
[2023-09-08 02:05:28] [SUCCESS] [OmnipathR] Downloaded 1532 interactions.
[2023-09-08 02:05:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:29] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:05:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2023-09-08 02:05:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2023-09-08 02:05:29] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2023-09-08 02:05:29] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2023-09-08 02:05:29] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2023-09-08 02:05:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-09-08 02:05:30] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:05:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2023-09-08 02:05:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2023-09-08 02:05:30] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2023-09-08 02:05:30] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2023-09-08 02:05:30] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2023-09-08 02:05:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-09-08 02:05:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-09-08 02:05:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-09-08 02:05:30] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-09-08 02:05:35] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-09-08 02:05:35] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-09-08 02:05:40] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-09-08 02:05:41] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: HTTP error 500.

Quitting from lines 339-359 [dorothea] (omnipath_intro.Rmd)
Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2023-09-08 02:05:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-09-08 02:05:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-09-08 02:05:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2023-09-08 02:05:41] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:05:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2023-09-08 02:05:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2023-09-08 02:05:41] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
Warning in .Internal(eval(expr, envir, enclos)) :
  closing unused connection 5 (https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic)
Warning in .Internal(eval(expr, envir, enclos)) :
  closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic)
[2023-09-08 02:05:41] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2023-09-08 02:05:41] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2023-09-08 02:05:41] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2023-09-08 02:05:41] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-09-08 02:05:41] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2023-09-08 02:05:41] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2023-09-08 02:05:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2023-09-08 02:05:41] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-09-08 02:05:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2023-09-08 02:05:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2023-09-08 02:05:41] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2023-09-08 02:05:41] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2023-09-08 02:05:41] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2023-09-08 02:05:41] [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`
[2023-09-08 02:05:41] [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`
[2023-09-08 02:05:41] [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`
[2023-09-08 02:05:42] [WARN]    [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
[2023-09-08 02:05:47] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-09-08 02:05:47] [WARN]    [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-09-08 02:05:52] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2023-09-08 02:05:52] [ERROR]   [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.

Quitting from lines 88-97 [tfs-from-network] (paths.Rmd)
Error: processing vignette 'paths.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘paths.Rmd’

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

Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-09-08 02:05:52 CEST ]