[ Started: 2025-03-03 00:09:40 CET ] [ OmnipathR v3.14.0 for BioC-3.20 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_20 (3c7d7f1 2024-10-29 10:41:00) ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2025-03-03 00:09:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:09:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:52] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-03 00:09:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-03 00:09:52] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-03 00:09:52] [TRACE] [OmnipathR] Contains 1 files. [2025-03-03 00:09:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-03 00:09:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:09:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-03 00:09:52] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-03 00:09:52] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpioWoIh/Rinst29903b56f5fdca/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-03 00:09:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:52] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpioWoIh/Rinst29903b56f5fdca/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-03 00:09:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:53] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpioWoIh/Rinst29903b56f5fdca/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-03 00:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:53] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpioWoIh/Rinst29903b56f5fdca/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-03 00:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:53] [TRACE] [OmnipathR] Cache locked: FALSE [2025-03-03 00:09:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2025-03-03 00:09:53] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-03-03 00:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:53] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-03-03 00:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:53] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-03-03 00:09:53] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-03-03 00:09:53] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-03-03 00:09:53] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-03-03 00:09:53] [TRACE] [OmnipathR] HTTP 200 [2025-03-03 00:09:53] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-03-03 00:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:53] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-03-03 00:09:53] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-03-03 00:09:53] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-03-03 00:09:53] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-03-03 00:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:53] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-03-03 00:09:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-03-03 00:09:53] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-03-03 00:09:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-03-03 00:09:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-03-03 00:09:53] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-03-03 00:09:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:09:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:09:53] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-03-03 00:09:53] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-03-03 00:09:53] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-03 00:09:53] [TRACE] [OmnipathR] Orthology targets: [2025-03-03 00:09:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-03-03 00:09:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-03-03 00:09:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-03-03 00:09:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-03-03 00:09:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-03-03 00:09:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-03-03 00:09:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-03-03 00:09:54] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: cannot open the connection [2025-03-03 00:09:59] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-03-03 00:09:59] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: cannot open the connection [2025-03-03 00:10:04] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-03-03 00:10:04] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: cannot open the connection [2025-03-03 00:10:04] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`; error: cannot open the connection [2025-03-03 00:10:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-03-03 00:10:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:04] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2025-03-03 00:10:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-03-03 00:10:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-03-03 00:10:04] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2025-03-03 00:10:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:04] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. Quitting from lines 216-218 [network] (bioc_workshop.Rmd) Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics: no applicable method for 'mutate' applied to an object of class "list" --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2025-03-03 00:10:04] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2025-03-03 00:10:04] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-03-03 00:10:04] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2025-03-03 00:10:04] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-03-03 00:10:04] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2025-03-03 00:10:04] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2025-03-03 00:10:04] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2025-03-03 00:10:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2025-03-03 00:10:04] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-03 00:10:04] [TRACE] [OmnipathR] Orthology targets: [2025-03-03 00:10:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:04] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 1/3); error: cannot open the connection [2025-03-03 00:10:09] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:09] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 2/3); error: cannot open the connection [2025-03-03 00:10:14] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:14] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 3/3); error: cannot open the connection [2025-03-03 00:10:14] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`; error: cannot open the connection [2025-03-03 00:10:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:14] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-03-03 00:10:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-03-03 00:10:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-03-03 00:10:14] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-03-03 00:10:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:14] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. Quitting from lines 176-179 [omnipath] (cosmos.Rmd) Error: processing vignette 'cosmos.Rmd' failed with diagnostics: no applicable method for 'mutate' applied to an object of class "list" --- failed re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2025-03-03 00:10:15] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2025-03-03 00:10:15] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2025-03-03 00:10:15] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2025-03-03 00:10:15] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-03-03 00:10:15] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-03-03 00:10:15] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-03-03 00:10:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:15] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2025-03-03 00:10:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-03-03 00:10:15] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-03-03 00:10:15] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-03-03 00:10:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-03-03 00:10:35] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2025-03-03 00:10:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:36] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2025-03-03 00:10:36] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records [2025-03-03 00:10:36] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2025-03-03 00:10:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-03-03 00:10:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-03-03 00:10:47] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-03 00:10:47] [TRACE] [OmnipathR] Orthology targets: [2025-03-03 00:10:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-03 00:10:47] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-03-03 00:10:47] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` Quitting from lines 46-51 [unnamed-chunk-2] (drug_targets.Rmd) Error: processing vignette 'drug_targets.Rmd' failed with diagnostics: no applicable method for 'mutate' applied to an object of class "list" --- failed re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2025-03-03 00:10:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2025-03-03 00:10:47] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-03 00:10:47] [TRACE] [OmnipathR] Orthology targets: [2025-03-03 00:10:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-03-03 00:10:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-03-03 00:10:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-03-03 00:10:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-03-03 00:10:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-03-03 00:10:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-03-03 00:10:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-03-03 00:10:47] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 1/3); error: cannot open the connection [2025-03-03 00:10:52] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-03-03 00:10:52] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 2/3); error: cannot open the connection [2025-03-03 00:10:57] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-03-03 00:10:57] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 3/3); error: cannot open the connection [2025-03-03 00:10:57] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`; error: cannot open the connection [2025-03-03 00:10:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-03-03 00:10:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:57] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2025-03-03 00:10:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2025-03-03 00:10:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2025-03-03 00:10:57] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2025-03-03 00:10:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:10:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:10:57] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. Quitting from lines 56-58 [load-interactions] (extra_attrs.Rmd) Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics: no applicable method for 'mutate' applied to an object of class "list" --- failed re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown Quitting from lines 167-175 [interactions] (omnipath_intro.Rmd) Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics: cannot open the connection to 'https://omnipathdb.org/resources' --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2025-03-03 00:10:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2025-03-03 00:10:58] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-03 00:10:58] [TRACE] [OmnipathR] Orthology targets: Quitting from lines 56-67 [tfcensus-op] (paths.Rmd) Error: processing vignette 'paths.Rmd' failed with diagnostics: cannot open the connection to 'https://omnipathdb.org/resources' --- failed re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘bioc_workshop.Rmd’ ‘cosmos.Rmd’ ‘drug_targets.Rmd’ ‘extra_attrs.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2025-03-03 00:10:59 CET ]