[ Started: 2023-01-09 01:19:52 CET ]
[ wppi v1.6.0 for BioC-3.16 from https://github.com/AnaGalhoz37/wppi@main ]

* using log directory ‘/home/omnipath/testing/bioc/wppi/bioc-3.16/2023-01-09_0118/wppi/wppi.Rcheck’
* using R version 4.2.2 Patched (2022-11-10 r83330)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘wppi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2023-01-09 01:20:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:20:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:20:21] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:20:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-01-09 01:20:21] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:20:21] [TRACE]   [OmnipathR] Contains 1 files.
[2023-01-09 01:20:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-01-09 01:20:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:20:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:20:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:20:22] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-01-09 01:20:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-01-09 01:20:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:20:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-01-09 01:20:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:20:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-01-09 01:20:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:20:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-01-09 01:20:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:20:22] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘wppi_workflow.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:19] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Contains 4 files.
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:19] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-01-09 01:22:20] [INFO]    [wppi] Executing WPPI workflow.
[2023-01-09 01:22:20] [INFO]    [wppi] Collecting database knowledge.
[2023-01-09 01:22:20] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-01-09 01:22:20] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-01-09 01:22:20] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-01-09 01:22:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:20] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2023-01-09 01:22:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-01-09 01:22:20] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-01-09 01:22:20] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-01-09 01:22:22] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:22] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2023-01-09 01:22:22] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 268056 records
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2023-01-09 01:22:22] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:22] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2023-01-09 01:22:22] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-01-09 01:22:22] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-01-09 01:22:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2023-01-09 01:22:27] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2023-01-09 01:22:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:27] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2023-01-09 01:22:28] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 626136 records
[2023-01-09 01:22:28] [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`
[2023-01-09 01:22:28] [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`
[2023-01-09 01:22:28] [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`
[2023-01-09 01:22:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:28] [INFO]    [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `unknown` to `started`.
[2023-01-09 01:22:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`.
[2023-01-09 01:22:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`.
[2023-01-09 01:22:29] [INFO]    [OmnipathR] Download ready [key=14b0e2906349bc073c3b72851e073e2886a90093, version=1]
[2023-01-09 01:22:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:22:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:22:29] [INFO]    [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `started` to `ready`.
[2023-01-09 01:22:31] [SUCCESS] [OmnipathR] Downloaded 77462 interactions.
[2023-01-09 01:22:31] [INFO]    [wppi] Finished collecting database knowledge.
[2023-01-09 01:22:31] [INFO]    [wppi] Using all HPO annotations available.
[2023-01-09 01:22:31] [INFO]    [wppi] Calculating weighted adjacency matrix.
[2023-01-09 01:22:31] [INFO]    [wppi] Preprocessing annotations (Gene Ontology).
[2023-01-09 01:22:31] [INFO]    [wppi] Preprocessing annotations (Human Phenotype Ontology).
[2023-01-09 01:22:31] [INFO]    [wppi] Graph size: 225 nodes and 2598 edges; GO: 3370 terms, 224 genes, 9750 annotations; HPO: 2497 terms, 112 genes, 7251 annotations.
[2023-01-09 01:22:35] [INFO]    [wppi] Finished calculating weighted adjacency matrix.
[2023-01-09 01:22:35] [INFO]    [wppi] Performing random walk with restart (restart probablilty: 0.4, threshold: 1e-05, number of genes: 225).
[2023-01-09 01:22:38] [INFO]    [wppi] Calculating WPPI gene scores (genes of interest: 8, genes in network: 225).
[2023-01-09 01:22:38] [SUCCESS] [wppi] WPPI workflow completed.
[2023-01-09 01:22:38] [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`
[2023-01-09 01:22:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-01-09 01:22:38] [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`
[2023-01-09 01:22:38] [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.
[2023-01-09 01:22:43] [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`
[2023-01-09 01:22:43] [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.
[2023-01-09 01:22:48] [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`
[2023-01-09 01:22:49] [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 (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

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/omnipath/testing/bioc/wppi/bioc-3.16/2023-01-09_0118/wppi/wppi.Rcheck/00check.log’
for details.

[ Finished: 2023-01-09 01:22:51 CET ]