[ Started: 2023-05-18 01:04:05 CEST ]
[ dorothea v1.7.3 for BioC-3.16 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
[2023-05-18 01:04:41] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-18 01:04:41] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-18 01:04:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-18 01:04:41] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-05-18 01:04:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-18 01:04:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-18 01:04:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-18 01:04:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-18 01:04:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-18 01:04:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-18 01:04:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-18 01:04:43] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2023-05-18 01:04:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-05-18 01:04:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-05-18 01:04:43] [INFO]    [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2023-05-18 01:04:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-18 01:04:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-18 01:04:44] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2023-05-18 01:04:50] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
Quitting from lines 151-153 (dorothea.Rmd) 
Error: processing vignette 'dorothea.Rmd' failed with diagnostics:
'get_collectri' is not an exported object from 'namespace:decoupleR'
--- failed re-building ‘dorothea.Rmd’

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

Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-05-18 01:05:00 CEST ]