[ Started: 2023-06-17 22:34:02 CEST ] [ decoupleR v2.5.2 for BioC-3.16 from https://github.com/saezlab/decoupleR@master ] * 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 --- finished re-building ‘decoupleR.Rmd’ --- re-building ‘pw_bk.Rmd’ using rmarkdown [2023-06-17 22:34:17] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:17] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Contains 1 files. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-06-17 22:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-06-17 22:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-06-17 22:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-06-17 22:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:17] [TRACE] [OmnipathR] Cache locked: FALSE [2023-06-17 22:34:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2023-06-17 22:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:17] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:17] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:17] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2023-06-17 22:34:17] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2023-06-17 22:34:17] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2023-06-17 22:34:17] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2023-06-17 22:34:18] [TRACE] [OmnipathR] HTTP 200 [2023-06-17 22:34:18] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2023-06-17 22:34:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:18] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2023-06-17 22:34:18] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2023-06-17 22:34:18] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2023-06-17 22:34:18] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2023-06-17 22:34:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:18] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2023-06-17 22:34:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2023-06-17 22:34:18] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2023-06-17 22:34:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2023-06-17 22:34:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2023-06-17 22:34:18] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2023-06-17 22:34:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:18] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2023-06-17 22:34:18] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2023-06-17 22:34:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2023-06-17 22:34:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-06-17 22:34:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-06-17 22:34:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-06-17 22:34:19] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: HTTP error 500. [2023-06-17 22:34:24] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-06-17 22:34:24] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 2/3); error: HTTP error 500. [2023-06-17 22:34:29] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-06-17 22:34:29] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 3/3); error: HTTP error 500. Quitting from lines 116-118 [progeny] (pw_bk.Rmd) Error: processing vignette 'pw_bk.Rmd' failed with diagnostics: HTTP error 500. --- failed re-building ‘pw_bk.Rmd’ --- re-building ‘pw_sc.Rmd’ using rmarkdown Warning in for (i in seq_len(n)) { : closing unused connection 5 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic) Warning in for (i in seq_len(n)) { : closing unused connection 4 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic) [2023-06-17 22:34:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2023-06-17 22:34:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2023-06-17 22:34:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-06-17 22:34:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-06-17 22:34:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-06-17 22:34:32] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: HTTP error 500. [2023-06-17 22:34:37] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-06-17 22:34:37] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 2/3); error: HTTP error 500. [2023-06-17 22:34:42] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-06-17 22:34:43] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 3/3); error: HTTP error 500. Quitting from lines 93-95 [progeny] (pw_sc.Rmd) Error: processing vignette 'pw_sc.Rmd' failed with diagnostics: HTTP error 500. --- failed re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2023-06-17 22:34:43] [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` [2023-06-17 22:34:43] [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` [2023-06-17 22:34:43] [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` Warning: closing unused connection 5 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic) Warning: closing unused connection 4 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic) Warning in x : closing unused connection 6 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic) [2023-06-17 22:34:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:49] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`. [2023-06-17 22:34:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2023-06-17 22:34:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2023-06-17 22:34:49] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1] [2023-06-17 22:34:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:34:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:34:49] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`. [2023-06-17 22:34:49] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2023-06-17 22:34:53] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2023-06-17 22:34:56] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any [2023-06-17 22:36:26] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2023-06-17 22:36:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2023-06-17 22:36:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:36:26] [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` [2023-06-17 22:36:26] [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` [2023-06-17 22:36:26] [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` [2023-06-17 22:36:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:36:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:36:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:36:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:36:27] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`. [2023-06-17 22:36:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2023-06-17 22:36:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2023-06-17 22:36:27] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1] [2023-06-17 22:36:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-17 22:36:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:36:27] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`. [2023-06-17 22:36:27] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2023-06-17 22:36:27] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2023-06-17 22:36:27] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI [2023-06-17 22:36:27] [SUCCESS] [OmnipathR] Downloaded 232 interactions. Warning: ggrepel: 37 unlabeled data points (too many overlaps). Consider increasing max.overlaps --- finished re-building ‘tf_bk.Rmd’ --- re-building ‘tf_sc.Rmd’ using rmarkdown [2023-06-17 22:36:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2023-06-17 22:36:40] [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` [2023-06-17 22:36:40] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2023-06-17 22:36:43] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2023-06-17 22:36:46] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any [2023-06-17 22:38:14] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2023-06-17 22:38:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2023-06-17 22:38:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-17 22:38:15] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2023-06-17 22:38:15] [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` [2023-06-17 22:38:15] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2023-06-17 22:38:15] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2023-06-17 22:38:15] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI [2023-06-17 22:38:15] [SUCCESS] [OmnipathR] Downloaded 232 interactions. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘tf_sc.Rmd’ SUMMARY: processing the following files failed: ‘pw_bk.Rmd’ ‘pw_sc.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2023-06-17 22:38:23 CEST ]