Multiple platform build/check report for BioC 3.20 - BUILD results for wppi on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4494
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4395
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
BUILD results for wppi on palomino8

To the developers/maintainers of the wppi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: wppi
Version: 1.14.0
Command: chmod a+r wppi -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data wppi
StartedAt: 2025-01-23 22:51:30 -0500 (Thu, 23 Jan 2025)
EndedAt: 2025-01-23 22:52:35 -0500 (Thu, 23 Jan 2025)
EllapsedTime: 65.1 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r wppi -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data wppi
###
##############################################################################
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* checking for file 'wppi/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
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:52] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:52] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:52] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-01-23 22:51:53] [INFO]    [wppi] Executing WPPI workflow.
[2025-01-23 22:51:53] [INFO]    [wppi] Collecting database knowledge.
[2025-01-23 22:51:53] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-01-23 22:51:53] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-01-23 22:51:53] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-01-23 22:51:53] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:53] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:53] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-01-23 22:51:53] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-01-23 22:51:53] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-01-23 22:51:53] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-01-23 22:51:55] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:55] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-01-23 22:51:55] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 316589 records
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-01-23 22:51:55] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:51:55] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-01-23 22:51:55] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-01-23 22:51:55] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-01-23 22:52:05] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-01-23 22:52:05] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2025-01-23 22:52:05] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:05] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2025-01-23 22:52:06] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 782823 records
[2025-01-23 22:52:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2025-01-23 22:52:06] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-23 22:52:06] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:06] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-23 22:52:06] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:06] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-23 22:52:06] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-23 22:52:06] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-23 22:52:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-23 22:52:07] [TRACE]   [OmnipathR] HTTP 200
[2025-01-23 22:52:07] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-01-23 22:52:07] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:07] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-01-23 22:52:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-23 22:52:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-01-23 22:52:07] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-23 22:52:08] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:08] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:08] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-01-23 22:52:08] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-23 22:52:08] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-01-23 22:52:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-01-23 22:52:09] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-23 22:52:09] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-01-23 22:52:09] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:09] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-01-23 22:52:09] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-01-23 22:52:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-01-23 22:52:09] [TRACE]   [OmnipathR] Orthology targets: 
[2025-01-23 22:52:09] [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`
[2025-01-23 22:52:09] [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`
[2025-01-23 22:52:09] [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`
[2025-01-23 22:52:09] [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`
[2025-01-23 22:52:09] [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`
[2025-01-23 22:52:09] [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`
[2025-01-23 22:52:09] [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`
[2025-01-23 22:52:10] [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`
[2025-01-23 22:52:10] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:10] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:10] [INFO]    [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `unknown` to `started`.
[2025-01-23 22:52:10] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`.
[2025-01-23 22:52:10] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`.
[2025-01-23 22:52:10] [INFO]    [OmnipathR] Download ready [key=14b0e2906349bc073c3b72851e073e2886a90093, version=1]
[2025-01-23 22:52:10] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:10] [INFO]    [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `started` to `ready`.
[2025-01-23 22:52:13] [SUCCESS] [OmnipathR] Downloaded 80536 interactions.
[2025-01-23 22:52:13] [INFO]    [wppi] Finished collecting database knowledge.
[2025-01-23 22:52:13] [INFO]    [wppi] Using all HPO annotations available.
[2025-01-23 22:52:14] [INFO]    [wppi] Calculating weighted adjacency matrix.
[2025-01-23 22:52:14] [INFO]    [wppi] Preprocessing annotations (Gene Ontology).
[2025-01-23 22:52:14] [INFO]    [wppi] Preprocessing annotations (Human Phenotype Ontology).
[2025-01-23 22:52:14] [INFO]    [wppi] Graph size: 226 nodes and 2690 edges; GO: 3449 terms, 225 genes, 10845 annotations; HPO: 2729 terms, 116 genes, 8429 annotations.
[2025-01-23 22:52:19] [INFO]    [wppi] Finished calculating weighted adjacency matrix.
[2025-01-23 22:52:19] [INFO]    [wppi] Performing random walk with restart (restart probablilty: 0.4, threshold: 1e-05, number of genes: 226).
[2025-01-23 22:52:23] [INFO]    [wppi] Calculating WPPI gene scores (genes of interest: 8, genes in network: 226).
[2025-01-23 22:52:23] [SUCCESS] [wppi] WPPI workflow completed.
[2025-01-23 22:52:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2025-01-23 22:52:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-01-23 22:52:23] [TRACE]   [OmnipathR] Orthology targets: 
[2025-01-23 22:52:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-01-23 22:52:23] [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`
[2025-01-23 22:52:23] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-01-23 22:52:23] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-01-23 22:52:23] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-01-23 22:52:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-01-23 22:52:23] [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`
[2025-01-23 22:52:23] [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: cannot open the connection
[2025-01-23 22:52:28] [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`
[2025-01-23 22:52:28] [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: cannot open the connection
[2025-01-23 22:52:33] [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`
[2025-01-23 22:52:34] [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: cannot open the connection
[2025-01-23 22:52:34] [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`; error: cannot open the connection
[2025-01-23 22:52:34] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-01-23 22:52:34] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:34] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:34] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2025-01-23 22:52:34] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-01-23 22:52:34] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-01-23 22:52:34] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2025-01-23 22:52:34] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 22:52:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 22:52:34] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.

Quitting from lines 117-118 [database-knowledge-omnipath] (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