[ Started: 2024-03-27 12:41:34 CET ]
[ dorothea v1.7.4 for BioC-3.18 from https://github.com/saezlab/dorothea@master (1461fb7 2024-02-24 12:55:48) ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘dorothea’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘dorothea.Rmd’ using rmarkdown
[2024-03-27 12:42:08] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:08] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-03-27 12:42:08] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:08] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:08] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-03-27 12:42:08] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] HTTP 200
[2024-03-27 12:42:08] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:08] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-03-27 12:42:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:09] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-03-27 12:42:09] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-03-27 12:42:09] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:09] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-03-27 12:42:09] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 12:42:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 12:42:09] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 12:42:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 12:42:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 12:42:09] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: Failed to connect to omnipathdb.org port 443 after 21 ms: Connection refused
[2024-03-27 12:42:14] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 12:42:14] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: Failed to connect to omnipathdb.org port 443 after 33 ms: Connection refused
[2024-03-27 12:42:19] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 12:42:19] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: Failed to connect to omnipathdb.org port 443 after 25 ms: Connection refused
[2024-03-27 12:42:19] [WARN]    [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`; error: Failed to connect to omnipathdb.org port 443 after 25 ms: Connection refused
[2024-03-27 12:42:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 12:42:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:19] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2024-03-27 12:42:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-03-27 12:42:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-03-27 12:42:19] [INFO]    [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2024-03-27 12:42:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 12:42:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-27 12:42:19] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2024-03-27 12:42:19] [ERROR]   [OmnipathR] `only_from` can be called only on data frames with `evidences` column.
[2024-03-27 12:42:19] [WARN]    [OmnipathR] Accessing `dorothea` 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 67-69 [model] (dorothea.Rmd)
Error: processing vignette 'dorothea.Rmd' failed with diagnostics:
Failed to connect to no-tls.static.omnipathdb.org port 80 after 21 ms: Connection refused
--- failed re-building ‘dorothea.Rmd’

SUMMARY: processing the following file failed:
  ‘dorothea.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2024-03-27 12:42:19 CET ]