[ Started: 2023-09-25 00:33:13 CEST ] [ wppi v1.6.0 for BioC-3.17 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 Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2023-09-25 00:33:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:33:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:21] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-09-25 00:33:21] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-09-25 00:33:21] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-09-25 00:33:21] [TRACE] [OmnipathR] Contains 1 files. [2023-09-25 00:33:21] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-09-25 00:33:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:33:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-09-25 00:33:21] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-09-25 00:33:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-09-25 00:33:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-09-25 00:33:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-09-25 00:33:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-09-25 00:33:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:21] [TRACE] [OmnipathR] Cache locked: FALSE [2023-09-25 00:33:22] [INFO] [wppi] Executing WPPI workflow. [2023-09-25 00:33:22] [INFO] [wppi] Collecting database knowledge. [2023-09-25 00:33:22] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2023-09-25 00:33:22] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2023-09-25 00:33:22] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2023-09-25 00:33:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:33:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:33:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:22] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`. [2023-09-25 00:33:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2023-09-25 00:33:22] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2023-09-25 00:33:22] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2023-09-25 00:33:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2023-09-25 00:33:24] [INFO] [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1] [2023-09-25 00:33:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:33:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:24] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`. [2023-09-25 00:33:24] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 298384 records [2023-09-25 00:33:24] [TRACE] [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2023-09-25 00:33:24] [INFO] [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2023-09-25 00:33:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2023-09-25 00:33:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:33:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:33:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:24] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`. [2023-09-25 00:33:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2023-09-25 00:33:24] [INFO] [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2023-09-25 00:33:24] [TRACE] [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2023-09-25 00:33:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2023-09-25 00:33:29] [INFO] [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1] [2023-09-25 00:33:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:33:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:33:29] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`. [2023-09-25 00:33:30] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 633586 records [2023-09-25 00:33:30] [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` [2023-09-25 00:33:30] [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` [2023-09-25 00:33:30] [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` [2023-09-25 00:33:30] [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` [2023-09-25 00:33:30] [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` [2023-09-25 00:33:30] [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` [2023-09-25 00:33:30] [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` [2023-09-25 00:33:32] [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: Empty reply from server [2023-09-25 00:33:37] [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` [2023-09-25 00:33:39] [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: Empty reply from server [2023-09-25 00:33:44] [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` [2023-09-25 00:33:46] [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: Empty reply from server [2023-09-25 00:33:46] [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: Empty reply from server [2023-09-25 00:33:46] [TRACE] [OmnipathR] Attempting `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` [2023-09-25 00:33:46] [INFO] [OmnipathR] Retrieving URL: `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` [2023-09-25 00:33:46] [TRACE] [OmnipathR] Attempt 1/3: `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` [2023-09-25 00:33:47] [WARN] [OmnipathR] Failed to download `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` (attempt 1/3); error: Empty reply from server [2023-09-25 00:33:52] [TRACE] [OmnipathR] Attempt 2/3: `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` [2023-09-25 00:33:54] [WARN] [OmnipathR] Failed to download `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` (attempt 2/3); error: transfer closed with outstanding read data remaining [2023-09-25 00:33:59] [TRACE] [OmnipathR] Attempt 3/3: `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` [2023-09-25 00:34:02] [INFO] [OmnipathR] Successfully retrieved: `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` [2023-09-25 00:34:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:34:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:34:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:34:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:34:02] [INFO] [OmnipathR] Cache item `1872cd8397bd484fd1edd7f063ad5dfe0006f3fd` version 1: status changed from `unknown` to `started`. [2023-09-25 00:34:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1872cd8397bd484fd1edd7f063ad5dfe0006f3fd-1.rds`. [2023-09-25 00:34:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1872cd8397bd484fd1edd7f063ad5dfe0006f3fd-1.rds`. [2023-09-25 00:34:02] [INFO] [OmnipathR] Download ready [key=1872cd8397bd484fd1edd7f063ad5dfe0006f3fd, version=1] [2023-09-25 00:34:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-09-25 00:34:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-09-25 00:34:02] [INFO] [OmnipathR] Cache item `1872cd8397bd484fd1edd7f063ad5dfe0006f3fd` version 1: status changed from `started` to `ready`. Warning in if (missing(...)) { : closing unused connection 8 (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) [2023-09-25 00:34:04] [SUCCESS] [OmnipathR] Downloaded 80536 interactions. [2023-09-25 00:34:04] [INFO] [wppi] Finished collecting database knowledge. [2023-09-25 00:34:04] [INFO] [wppi] Using all HPO annotations available. [2023-09-25 00:34:04] [INFO] [wppi] Calculating weighted adjacency matrix. [2023-09-25 00:34:04] [INFO] [wppi] Preprocessing annotations (Gene Ontology). [2023-09-25 00:34:05] [INFO] [wppi] Preprocessing annotations (Human Phenotype Ontology). [2023-09-25 00:34:05] [INFO] [wppi] Graph size: 226 nodes and 2690 edges; GO: 3335 terms, 225 genes, 9660 annotations; HPO: 2641 terms, 113 genes, 8098 annotations. [2023-09-25 00:34:09] [INFO] [wppi] Finished calculating weighted adjacency matrix. [2023-09-25 00:34:09] [INFO] [wppi] Performing random walk with restart (restart probablilty: 0.4, threshold: 1e-05, number of genes: 226). [2023-09-25 00:34:12] [INFO] [wppi] Calculating WPPI gene scores (genes of interest: 8, genes in network: 226). [2023-09-25 00:34:12] [SUCCESS] [wppi] WPPI workflow completed. [2023-09-25 00:34:12] [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` [2023-09-25 00:34:12] [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` [2023-09-25 00:34:12] [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` [2023-09-25 00:34:12] [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` [2023-09-25 00:34:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2023-09-25 00:34:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2023-09-25 00:34:12] [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` [2023-09-25 00:34:13] [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: transfer closed with outstanding read data remaining [2023-09-25 00:34:18] [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` [2023-09-25 00:34:19] [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: transfer closed with outstanding read data remaining [2023-09-25 00:34:24] [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` [2023-09-25 00:34:25] [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: transfer closed with outstanding read data remaining [2023-09-25 00:34:25] [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: transfer closed with outstanding read data remaining [2023-09-25 00:34:25] [TRACE] [OmnipathR] Attempting `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2023-09-25 00:34:25] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2023-09-25 00:34:25] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2023-09-25 00:34:27] [WARN] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 1/3); error: transfer closed with outstanding read data remaining [2023-09-25 00:34:32] [TRACE] [OmnipathR] Attempt 2/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2023-09-25 00:34:33] [WARN] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 2/3); error: transfer closed with outstanding read data remaining [2023-09-25 00:34:38] [TRACE] [OmnipathR] Attempt 3/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2023-09-25 00:34:40] [ERROR] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 3/3); error: transfer closed with outstanding read data remaining [2023-09-25 00:34:40] [WARN] [OmnipathR] Failed to download: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`; error: transfer closed with outstanding read data remaining 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 "NULL" --- failed re-building ‘wppi_workflow.Rmd’ SUMMARY: processing the following file failed: ‘wppi_workflow.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2023-09-25 00:34:40 CEST ]