[ Started: 2024-08-18 23:40:56 CEST ] [ OmnipathR v3.13.15 for BioC-3.20 from https://github.com/saezlab/OmnipathR@master (652f5c7 2024-08-18 00:41:29) ] * 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 [2024-08-18 23:41:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:09] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Contains 1 files. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpYyvHLT/Rinst17880a23577246/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-08-18 23:41:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:09] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpYyvHLT/Rinst17880a23577246/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-08-18 23:41:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:09] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpYyvHLT/Rinst17880a23577246/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-08-18 23:41:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:09] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpYyvHLT/Rinst17880a23577246/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-08-18 23:41:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:09] [TRACE] [OmnipathR] Cache locked: FALSE Quitting from lines 216-218 [network] (bioc_workshop.Rmd) Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics: :1:23: unexpected ')' 1: gri <- transcriptional) ^ --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2024-08-18 23:41:09] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2024-08-18 23:41:09] [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. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2024-08-18 23:41:09] [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. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2024-08-18 23:41:09] [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. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Bypassing call: `translate_ids("MAM00001", "metabolicatlas", "recon3d", chalmers = TRUE)`. [2024-08-18 23:41:09] [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. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_network()`. [2024-08-18 23:41:09] [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. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Bypassing call: `stitch_actions()`. [2024-08-18 23:41:09] [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. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Bypassing call: `stitch_links()`. [2024-08-18 23:41:09] [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. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Bypassing call: `stitch_network()`. [2024-08-18 23:41:09] [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. [2024-08-18 23:41:09] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:09] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:09] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-08-18 23:41:09] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-08-18 23:41:09] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-08-18 23:41:09] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-08-18 23:41:10] [TRACE] [OmnipathR] HTTP 200 [2024-08-18 23:41:10] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-08-18 23:41:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:10] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-08-18 23:41:10] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-08-18 23:41:10] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:10] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-08-18 23:41:10] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-08-18 23:41:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-08-18 23:41:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-08-18 23:41:10] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-08-18 23:41:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:10] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-08-18 23:41:10] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-08-18 23:41:10] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. Quitting from lines 176-179 [omnipath] (cosmos.Rmd) Error: processing vignette 'cosmos.Rmd' failed with diagnostics: subscript out of bounds --- failed re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2024-08-18 23:41:10] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: `(function (to, from = "accession", reviewed = TRUE, organism = 9606) `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: `{`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` .slow_doctest()`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` From <- To <- NULL`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` strip_semicol <- function(v) {`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` sub(";$", "", v)`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` }`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` reviewed <- if ("trembl" %in% ids) `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` FALSE`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` else if ("swissprot" %in% ids) `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` TRUE`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` else reviewed`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` reens <- "ENS[A-Z]+\\d+"`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` to_ens <- to == "xref_ensembl"`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` from_ens <- from == "xref_ensembl"`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` "for organism %d (only reviewed: %s)"), from, to, organism, `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` reviewed)`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` To = strip_semicol(To)) %>% separate_rows(From, sep = "[; ]") %>% `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` separate_rows(To, sep = "[; ]") %>% filter(!is.na(From) & `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` !is.na(To)) %>% {`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` if (from_ens) `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` mutate(., From = str_extract(From, reens))`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` else .`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` } %>% {`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` if (to_ens) `. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` mutate(., To = str_extract(To, reens))`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` else .`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: ` } %>% trim_and_distinct`. [2024-08-18 23:41:10] [TRACE] [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`. [2024-08-18 23:41:10] [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. [2024-08-18 23:41:10] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2024-08-18 23:41:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2024-08-18 23:41:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2024-08-18 23:41:21] [TRACE] [OmnipathR] Organism(s): 9606 [2024-08-18 23:41:21] [TRACE] [OmnipathR] Orthology targets: [2024-08-18 23:41:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-08-18 23:41:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-08-18 23:41:21] [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` [2024-08-18 23:41:21] [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` [2024-08-18 23:41:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-08-18 23:41:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-08-18 23:41:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-08-18 23:41:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-08-18 23:41:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:22] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2024-08-18 23:41:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-08-18 23:41:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-08-18 23:41:22] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2024-08-18 23:41:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:22] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2024-08-18 23:41:24] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown Quitting from lines 56-58 [load-interactions] (extra_attrs.Rmd) Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics: :1:46: unexpected ')' 1: i <- post_translationalfields = 'extra_attrs') ^ --- 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 167-178 [interactions] (omnipath_intro.Rmd) Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics: :11:20: unexpected ')' 10: ## We visualize the first interactions in the data frame. 11: printhead(pathways)) ^ --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2024-08-18 23:41:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2024-08-18 23:41:27] [TRACE] [OmnipathR] Organism(s): 9606 [2024-08-18 23:41:27] [TRACE] [OmnipathR] Orthology targets: [2024-08-18 23:41:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-08-18 23:41:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-08-18 23:41:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-08-18 23:41:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-08-18 23:41:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-08-18 23:41:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-08-18 23:41:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-08-18 23:41:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-08-18 23:41:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-08-18 23:41:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:28] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2024-08-18 23:41:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2024-08-18 23:41:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2024-08-18 23:41:28] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2024-08-18 23:41:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:28] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2024-08-18 23:41:28] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2024-08-18 23:41:28] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2024-08-18 23:41:28] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-08-18 23:41:28] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2024-08-18 23:41:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:28] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2024-08-18 23:41:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2024-08-18 23:41:28] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-08-18 23:41:28] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-08-18 23:41:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2024-08-18 23:41:28] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2024-08-18 23:41:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-08-18 23:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-18 23:41:28] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2024-08-18 23:41:28] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records Quitting from lines 88-97 [tfs-from-network] (paths.Rmd) Error: processing vignette 'paths.Rmd' failed with diagnostics: :5:43: unexpected ',' 4: # we use only the 3 levels with highest confidence 5: dorothea_levels = c('A', 'B', 'C'), ^ --- failed re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘bioc_workshop.Rmd’ ‘cosmos.Rmd’ ‘extra_attrs.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2024-08-18 23:41:28 CEST ]