[ Started: 2023-12-07 12:16:41 CET ]
[ dorothea v1.7.3 for BioC-3.17 from https://github.com/saezlab/dorothea@master ]

* 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
[2023-12-07 12:17:16] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:16] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Contains 1 files.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-12-07 12:17:16] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:16] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:16] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2023-12-07 12:17:16] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] HTTP 200
[2023-12-07 12:17:16] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:16] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2023-12-07 12:17:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:17] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2023-12-07 12:17:17] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2023-12-07 12:17:17] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:17] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2023-12-07 12:17:17] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2023-12-07 12:17:17] [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`
[2023-12-07 12:17:17] [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`
[2023-12-07 12:17:17] [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`
[2023-12-07 12:17:17] [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`
[2023-12-07 12:17:17] [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`
[2023-12-07 12:17:17] [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`
[2023-12-07 12:17:17] [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`
[2023-12-07 12:17:21] [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`
[2023-12-07 12:17:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:21] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2023-12-07 12:17:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-12-07 12:17:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-12-07 12:17:22] [INFO]    [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2023-12-07 12:17:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-07 12:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-07 12:17:22] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2023-12-07 12:17:22] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2023-12-07 12:17:35] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2023-12-07 12:17:48] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2023-12-07 12:21:26] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
The magick package is required to crop "/tmp/RtmpTrVdyd/Rbuild32972b15e4dba6/dorothea/vignettes/dorothea_files/figure-html/n_genes-1.png" but not available.
The magick package is required to crop "/tmp/RtmpTrVdyd/Rbuild32972b15e4dba6/dorothea/vignettes/dorothea_files/figure-html/n_edges-1.png" but not available.
The magick package is required to crop "/tmp/RtmpTrVdyd/Rbuild32972b15e4dba6/dorothea/vignettes/dorothea_files/figure-html/prop-1.png" but not available.
[2023-12-07 12:21:34] [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&license=academic`
[2023-12-07 12:21:34] [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&license=academic`
[2023-12-07 12:21:34] [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&license=academic`
[2023-12-07 12:21:34] [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&license=academic`
[2023-12-07 12:21:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-07 12:21:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-07 12:21:34] [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&license=academic`
[2023-12-07 12:21:38] [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&license=academic` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
[2023-12-07 12:21:43] [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&license=academic`
[2023-12-07 12:21:46] [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&license=academic` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
[2023-12-07 12:21:51] [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&license=academic`
[2023-12-07 12:21:55] [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&license=academic` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
[2023-12-07 12:21:55] [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&license=academic`; error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
[2023-12-07 12:21:55] [TRACE]   [OmnipathR] Attempting `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-07 12:21:55] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-07 12:21:55] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
Warning in endian %in% c("big", "little", "swap") :
  closing unused connection 6 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic)
Warning in endian %in% c("big", "little", "swap") :
  closing unused connection 5 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic)
Warning in endian %in% c("big", "little", "swap") :
  closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic)
[2023-12-07 12:21:58] [WARN]    [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 1/3); error: transfer closed with outstanding read data remaining
[2023-12-07 12:22:03] [TRACE]   [OmnipathR] Attempt 2/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-07 12:22:07] [WARN]    [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 2/3); error: transfer closed with outstanding read data remaining
[2023-12-07 12:22:12] [TRACE]   [OmnipathR] Attempt 3/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-07 12:22:16] [ERROR]   [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 3/3); error: transfer closed with outstanding read data remaining
[2023-12-07 12:22:16] [WARN]    [OmnipathR] Failed to download: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`; error: transfer closed with outstanding read data remaining
[2023-12-07 12:22:16] [ERROR]   [OmnipathR] `only_from` can be called only on data frames with `evidences` column.

Quitting from lines 151-153 [collectri] (dorothea.Rmd)
Error: processing vignette 'dorothea.Rmd' failed with diagnostics:
`only_from` can be called only on data frames with `evidences` column.
--- failed re-building ‘dorothea.Rmd’

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

Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-12-07 12:22:16 CET ]