[ Started: 2024-11-08 12:32:46 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 [2024-11-08 12:32:53] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-11-08 12:32:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:32:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:32:54] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-08 12:32:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-08 12:32:54] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-08 12:32:54] [TRACE] [OmnipathR] Contains 1 files. [2024-11-08 12:32:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-08 12:32:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:32:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:32:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-08 12:32:54] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-08 12:32:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-08 12:32:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:32:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-08 12:32:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:32:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-08 12:32:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:32:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-08 12:32:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:32:54] [TRACE] [OmnipathR] Cache locked: FALSE [2024-11-08 12:32:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-11-08 12:32:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:32:54] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:32:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:32:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:32:54] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:32:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:32:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:32:54] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-11-08 12:32:54] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-11-08 12:32:54] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:32:54] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:32:54] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:32:54] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:32:59] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:32:59] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:32:59] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:33:04] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:05] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:05] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 [2024-11-08 12:33:05] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:33:05] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:33:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:33:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:33:05] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2. [2024-11-08 12:33:05] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html [2024-11-08 12:33:05] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:05] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:05] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:05] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:33:10] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:10] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:10] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:33:15] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:15] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:15] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 [2024-11-08 12:33:15] [WARN] [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2024-11-08 12:33:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-11-08 12:33:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-11-08 12:33:15] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-11-08 12:33:15] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-11-08 12:33:15] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-11-08 12:33:17] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-11-08 12:33:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:33:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:33:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:33:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:33:17] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`. [2024-11-08 12:33:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-11-08 12:33:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-11-08 12:33:19] [INFO] [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1] [2024-11-08 12:33:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:33:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:33:19] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`. [2024-11-08 12:33:19] [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 [2024-11-08 12:33:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-11-08 12:33:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:33:31] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:33:31] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:33:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:33:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:33:31] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3. [2024-11-08 12:33:31] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html [2024-11-08 12:33:31] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:31] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:31] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:31] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:33:36] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:36] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:36] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:33:41] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:42] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:42] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 [2024-11-08 12:33:42] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:33:42] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:33:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:33:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:33:42] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4. [2024-11-08 12:33:42] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html [2024-11-08 12:33:42] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:42] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:42] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:42] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:33:47] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:47] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:47] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:33:52] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:52] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:52] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 [2024-11-08 12:33:52] [WARN] [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2024-11-08 12:33:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-11-08 12:33:53] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-11-08 12:33:53] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-11-08 12:33:53] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2024-11-08 12:33:58] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:33:58] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:33:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:33:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:33:58] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5. [2024-11-08 12:33:58] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html [2024-11-08 12:33:58] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:58] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:33:58] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:33:58] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:34:03] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:03] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:03] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:34:08] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:09] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:09] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 [2024-11-08 12:34:09] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:34:09] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:34:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:34:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:34:09] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6. [2024-11-08 12:34:09] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html [2024-11-08 12:34:09] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:09] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:09] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:09] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:34:14] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:14] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:14] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:34:19] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:19] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:19] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 [2024-11-08 12:34:19] [WARN] [OmnipathR] Accessing `collectri` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2024-11-08 12:34:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-11-08 12:34:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-11-08 12:34:19] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-11-08 12:34:19] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-11-08 12:34:19] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-11-08 12:34:20] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-11-08 12:34:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:34:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:34:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:34:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:34:20] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`. [2024-11-08 12:34:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-11-08 12:34:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-11-08 12:34:21] [INFO] [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1] [2024-11-08 12:34:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:34:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:34:21] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`. [2024-11-08 12:34:21] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-11-08 12:34:24] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any Quitting from lines 118-120 [collectri] (tf_bk.Rmd) Error: processing vignette 'tf_bk.Rmd' failed with diagnostics: argument is of length zero --- failed re-building ‘tf_bk.Rmd’ --- re-building ‘tf_sc.Rmd’ using rmarkdown [2024-11-08 12:34:28] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:34:28] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:34:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:34:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:34:28] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7. [2024-11-08 12:34:28] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html [2024-11-08 12:34:28] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:28] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:28] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:28] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:34:33] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:33] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:33] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:34:38] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:38] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:38] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 [2024-11-08 12:34:38] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:34:38] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:34:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:34:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:34:38] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 8. [2024-11-08 12:34:38] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-8.html [2024-11-08 12:34:38] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:38] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:39] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:39] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:34:44] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:44] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:44] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:34:49] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:34:49] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:34:49] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 [2024-11-08 12:34:49] [WARN] [OmnipathR] Accessing `collectri` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2024-11-08 12:34:49] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-11-08 12:34:49] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-11-08 12:34:49] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-11-08 12:34:49] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-11-08 12:34:53] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any Quitting from lines 86-88 [collectri] (tf_sc.Rmd) Error: processing vignette 'tf_sc.Rmd' failed with diagnostics: argument is of length zero --- failed re-building ‘tf_sc.Rmd’ SUMMARY: processing the following files failed: ‘decoupleR.Rmd’ ‘tf_bk.Rmd’ ‘tf_sc.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2024-11-08 12:34:55 CET ]