[ Started: 2024-03-27 12:39:12 CET ] [ decoupleR v2.9.6 for BioC-3.18 from https://github.com/saezlab/decoupleR@master (68bf5f6 2024-03-24 13:38:34) ] * 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 [2024-03-27 12:39:28] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:28] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Contains 1 files. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-27 12:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-27 12:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-27 12:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-27 12:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:28] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-27 12:39:28] [WARN] [OmnipathR] [decoupleR] Failed to check the list of available resources in OmniPath. Proceeding anyways. [2024-03-27 12:39:28] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:28] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:28] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-27 12:39:28] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-27 12:39:28] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-27 12:39:28] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-27 12:39:28] [TRACE] [OmnipathR] HTTP 200 [2024-03-27 12:39:28] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-27 12:39:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:28] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-27 12:39:29] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-27 12:39:29] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-27 12:39:29] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-27 12:39:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:29] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-27 12:39:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-27 12:39:29] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-27 12:39:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-27 12:39:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-27 12:39:29] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-27 12:39:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:29] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-27 12:39:29] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-27 12:39:29] [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. [2024-03-27 12:39:29] [ERROR] [OmnipathR] [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log. Quitting from lines 125-127 [progeny] (pw_bk.Rmd) Error: processing vignette 'pw_bk.Rmd' failed with diagnostics: [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log. --- failed re-building ‘pw_bk.Rmd’ --- re-building ‘pw_sc.Rmd’ using rmarkdown [2024-03-27 12:39:32] [WARN] [OmnipathR] [decoupleR] Failed to check the list of available resources in OmniPath. Proceeding anyways. [2024-03-27 12:39:32] [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. [2024-03-27 12:39:32] [ERROR] [OmnipathR] [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log. Quitting from lines 93-95 [progeny] (pw_sc.Rmd) Error: processing vignette 'pw_sc.Rmd' failed with diagnostics: [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log. --- failed re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2024-03-27 12:39:32] [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` [2024-03-27 12:39:32] [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` [2024-03-27 12:39:32] [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` [2024-03-27 12:39:32] [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` [2024-03-27 12:39:32] [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` [2024-03-27 12:39:33] [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` [2024-03-27 12:39:33] [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` [2024-03-27 12:39:33] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` (attempt 1/3); error: Failed to connect to omnipathdb.org port 443 after 25 ms: Connection refused [2024-03-27 12:39:38] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-03-27 12:39:38] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` (attempt 2/3); error: Failed to connect to omnipathdb.org port 443 after 21 ms: Connection refused [2024-03-27 12:39:43] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` [2024-03-27 12:39:43] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic` (attempt 3/3); error: Failed to connect to omnipathdb.org port 443 after 23 ms: Connection refused [2024-03-27 12:39:43] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`; error: Failed to connect to omnipathdb.org port 443 after 23 ms: Connection refused [2024-03-27 12:39:43] [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` [2024-03-27 12:39:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:43] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`. [2024-03-27 12:39:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-03-27 12:39:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-03-27 12:39:43] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1] [2024-03-27 12:39:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 12:39:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 12:39:43] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`. [2024-03-27 12:39:43] [ERROR] [OmnipathR] `only_from` can be called only on data frames with `evidences` column. [2024-03-27 12:39:43] [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. Quitting from lines 118-120 [collectri] (tf_bk.Rmd) Error: processing vignette 'tf_bk.Rmd' failed with diagnostics: Failed to connect to no-tls.static.omnipathdb.org port 80 after 23 ms: Connection refused --- failed re-building ‘tf_bk.Rmd’ --- re-building ‘tf_sc.Rmd’ using rmarkdown [2024-03-27 12:39:43] [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` [2024-03-27 12:39:43] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-03-27 12:39:43] [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` [2024-03-27 12:39:43] [ERROR] [OmnipathR] `only_from` can be called only on data frames with `evidences` column. [2024-03-27 12:39:43] [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. Quitting from lines 86-88 [collectri] (tf_sc.Rmd) Error: processing vignette 'tf_sc.Rmd' failed with diagnostics: Failed to connect to no-tls.static.omnipathdb.org port 80 after 22 ms: Connection refused --- failed re-building ‘tf_sc.Rmd’ SUMMARY: processing the following files failed: ‘pw_bk.Rmd’ ‘pw_sc.Rmd’ ‘tf_bk.Rmd’ ‘tf_sc.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2024-03-27 12:39:43 CET ]