[ Started: 2024-12-02 13:10:05 CET ] [ decoupleR v2.10.0 for BioC-3.19 from https://git.bioconductor.org/packages/decoupleR@RELEASE_3_19 (7e6c106 2024-04-30 11:34:47) ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘decoupleR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘decoupleR.Rmd’ using rmarkdown Quitting from lines 32-46 [vignette_setup] (decoupleR.Rmd) Error: processing vignette 'decoupleR.Rmd' failed with diagnostics: there is no package called 'AUCell' --- failed re-building ‘decoupleR.Rmd’ --- re-building ‘pw_bk.Rmd’ using rmarkdown [2024-12-02 13:10:13] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:13] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Contains 1 files. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-02 13:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-02 13:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-02 13:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-02 13:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:13] [TRACE] [OmnipathR] Cache locked: FALSE [2024-12-02 13:10:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-02 13:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:13] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:13] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:13] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-12-02 13:10:13] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-12-02 13:10:13] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-12-02 13:10:13] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-12-02 13:10:14] [TRACE] [OmnipathR] HTTP 200 [2024-12-02 13:10:14] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-12-02 13:10:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:14] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-12-02 13:10:14] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-12-02 13:10:14] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-12-02 13:10:14] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-12-02 13:10:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:14] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-12-02 13:10:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-12-02 13:10:14] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-12-02 13:10:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-12-02 13:10:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-12-02 13:10:14] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-12-02 13:10:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:14] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-12-02 13:10:14] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-12-02 13:10:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-02 13:10:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-02 13:10:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-02 13:10:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-02 13:10:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-02 13:10:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-02 13:10:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-02 13:10:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-02 13:10:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-02 13:10:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:16] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2024-12-02 13:10:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-12-02 13:10:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-12-02 13:10:18] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2024-12-02 13:10:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:18] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2024-12-02 13:10:18] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records. Warning: ggrepel: 445 unlabeled data points (too many overlaps). Consider increasing max.overlaps --- finished re-building ‘pw_bk.Rmd’ --- re-building ‘pw_sc.Rmd’ using rmarkdown [2024-12-02 13:10:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-02 13:10:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-02 13:10:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-02 13:10:31] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-12-02 13:10:31] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-12-02 13:10:31] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2024-12-02 13:10:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-12-02 13:10:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-12-02 13:10:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-12-02 13:10:36] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-12-02 13:10:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-12-02 13:10:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-12-02 13:10:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-12-02 13:10:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-12-02 13:10:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:42] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`. [2024-12-02 13:10:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-12-02 13:10:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-12-02 13:10:43] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1] [2024-12-02 13:10:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:10:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:10:43] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`. [2024-12-02 13:10:43] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-12-02 13:10:46] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-12-02 13:10:49] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none [2024-12-02 13:12:03] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2024-12-02 13:12:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-02 13:12:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:12:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-12-02 13:12:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-12-02 13:12:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-12-02 13:12:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-12-02 13:12:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-12-02 13:12:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-12-02 13:12:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-12-02 13:12:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-12-02 13:12:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:12:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:12:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:12:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:12:04] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`. [2024-12-02 13:12:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-12-02 13:12:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-12-02 13:12:04] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1] [2024-12-02 13:12:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-02 13:12:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:12:04] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`. [2024-12-02 13:12:04] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-12-02 13:12:04] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2024-12-02 13:12:04] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2024-12-02 13:12:04] [SUCCESS] [OmnipathR] Downloaded 232 interactions. Warning: ggrepel: 754 unlabeled data points (too many overlaps). Consider increasing max.overlaps --- finished re-building ‘tf_bk.Rmd’ --- re-building ‘tf_sc.Rmd’ using rmarkdown [2024-12-02 13:12:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-12-02 13:12:21] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-12-02 13:12:21] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-12-02 13:12:21] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-12-02 13:12:24] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-12-02 13:12:27] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none [2024-12-02 13:13:44] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2024-12-02 13:13:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-12-02 13:13:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-02 13:13:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-12-02 13:13:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-12-02 13:13:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-12-02 13:13:44] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-12-02 13:13:44] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2024-12-02 13:13:44] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2024-12-02 13:13:44] [SUCCESS] [OmnipathR] Downloaded 232 interactions. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘tf_sc.Rmd’ SUMMARY: processing the following file failed: ‘decoupleR.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2024-12-02 13:13:51 CET ]