[ Started: 2024-03-27 12:59:41 CET ]
[ wppi v1.6.0 for BioC-3.18 from https://github.com/AnaGalhoz37/wppi@main (9b574a4 2022-11-02 08:18:02) ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘wppi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:49] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:49] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-03-27 12:59:49] [INFO]    [wppi] Executing WPPI workflow.
[2024-03-27 12:59:49] [INFO]    [wppi] Collecting database knowledge.
[2024-03-27 12:59:50] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2024-03-27 12:59:50] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-03-27 12:59:50] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2024-03-27 12:59:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:50] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2024-03-27 12:59:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2024-03-27 12:59:50] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-03-27 12:59:50] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2024-03-27 12:59:52] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:52] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2024-03-27 12:59:52] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 305238 records
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2024-03-27 12:59:52] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:52] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2024-03-27 12:59:52] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-03-27 12:59:52] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-03-27 12:59:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2024-03-27 12:59:57] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2024-03-27 12:59:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:57] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2024-03-27 12:59:58] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 638732 records
[2024-03-27 12:59:58] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:58] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:58] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-03-27 12:59:58] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] HTTP 200
[2024-03-27 12:59:58] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:58] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-03-27 12:59:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:58] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-03-27 12:59:58] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 12:59:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 12:59:59] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-03-27 12:59:59] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-03-27 12:59:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:59:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:59:59] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-03-27 12:59:59] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-03-27 12:59:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-03-27 12:59:59] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-03-27 12:59:59] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-03-27 12:59:59] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-03-27 12:59:59] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-03-27 12:59:59] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-03-27 12:59:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-03-27 12:59:59] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 1/3); error: Failed to connect to omnipathdb.org port 443 after 34 ms: Connection refused
[2024-03-27 13:00:04] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-03-27 13:00:04] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 2/3); error: Failed to connect to omnipathdb.org port 443 after 34 ms: Connection refused
[2024-03-27 13:00:09] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-03-27 13:00:09] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 3/3); error: Failed to connect to omnipathdb.org port 443 after 23 ms: Connection refused
[2024-03-27 13:00:09] [WARN]    [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`; error: Failed to connect to omnipathdb.org port 443 after 23 ms: Connection refused
[2024-03-27 13:00:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-03-27 13:00:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 13:00:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 13:00:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 13:00:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 13:00:09] [INFO]    [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `unknown` to `started`.
[2024-03-27 13:00:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`.
[2024-03-27 13:00:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`.
[2024-03-27 13:00:09] [INFO]    [OmnipathR] Download ready [key=14b0e2906349bc073c3b72851e073e2886a90093, version=1]
[2024-03-27 13:00:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 13:00:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 13:00:09] [INFO]    [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `started` to `ready`.

Quitting from lines 80-102 [workflow] (wppi_workflow.Rmd)
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
no applicable method for 'mutate' applied to an object of class "list"
--- failed re-building ‘wppi_workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘wppi_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2024-03-27 13:00:09 CET ]