[ Started: 2023-06-17 22:52:33 CEST ]
[ wppi v1.6.0 for BioC-3.16 from https://github.com/AnaGalhoz37/wppi@main ]

* 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
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:41] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Contains 1 files.
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-06-17 22:52:41] [INFO]    [wppi] Executing WPPI workflow.
[2023-06-17 22:52:41] [INFO]    [wppi] Collecting database knowledge.
[2023-06-17 22:52:41] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-06-17 22:52:42] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-06-17 22:52:42] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-06-17 22:52:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:42] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2023-06-17 22:52:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-06-17 22:52:42] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-06-17 22:52:42] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-06-17 22:52:44] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:44] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2023-06-17 22:52:44] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 293469 records
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2023-06-17 22:52:44] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:44] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2023-06-17 22:52:44] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-06-17 22:52:44] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-06-17 22:52:50] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2023-06-17 22:52:50] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2023-06-17 22:52:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:50] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2023-06-17 22:52:50] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 632318 records
[2023-06-17 22:52:50] [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`
[2023-06-17 22:52:50] [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`
[2023-06-17 22:52:50] [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`
[2023-06-17 22:52:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:51] [INFO]    [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `unknown` to `started`.
[2023-06-17 22:52:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`.
[2023-06-17 22:52:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`.
[2023-06-17 22:52:51] [INFO]    [OmnipathR] Download ready [key=14b0e2906349bc073c3b72851e073e2886a90093, version=1]
[2023-06-17 22:52:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-17 22:52:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-17 22:52:51] [INFO]    [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `started` to `ready`.
[2023-06-17 22:52:54] [SUCCESS] [OmnipathR] Downloaded 80536 interactions.
[2023-06-17 22:52:54] [INFO]    [wppi] Finished collecting database knowledge.
[2023-06-17 22:52:54] [INFO]    [wppi] Using all HPO annotations available.
[2023-06-17 22:52:54] [INFO]    [wppi] Calculating weighted adjacency matrix.
[2023-06-17 22:52:54] [INFO]    [wppi] Preprocessing annotations (Gene Ontology).
[2023-06-17 22:52:54] [INFO]    [wppi] Preprocessing annotations (Human Phenotype Ontology).
[2023-06-17 22:52:54] [INFO]    [wppi] Graph size: 226 nodes and 2690 edges; GO: 3358 terms, 225 genes, 9701 annotations; HPO: 2622 terms, 112 genes, 7958 annotations.
[2023-06-17 22:52:58] [INFO]    [wppi] Finished calculating weighted adjacency matrix.
[2023-06-17 22:52:58] [INFO]    [wppi] Performing random walk with restart (restart probablilty: 0.4, threshold: 1e-05, number of genes: 226).
[2023-06-17 22:53:01] [INFO]    [wppi] Calculating WPPI gene scores (genes of interest: 8, genes in network: 226).
[2023-06-17 22:53:01] [SUCCESS] [wppi] WPPI workflow completed.
[2023-06-17 22:53:01] [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`
[2023-06-17 22:53:01] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-06-17 22:53:01] [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`
[2023-06-17 22:53:02] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-06-17 22:53:07] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-06-17 22:53:07] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-06-17 22:53:12] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-06-17 22:53:12] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 3/3); error: HTTP error 500.

Quitting from lines 117-118 [database-knowledge-omnipath] (wppi_workflow.Rmd)
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘wppi_workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-06-17 22:53:12 CEST ]