[ Started: 2023-01-31 01:04:51 CET ]
[ decoupleR v2.3.3 for BioC-3.16 from https://github.com/saezlab/decoupleR@master ]

* 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
[2023-01-31 01:05:08] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:08] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Contains 1 files.
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-01-31 01:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-01-31 01:05:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-31 01:05:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-31 01:05:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-31 01:05:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-31 01:05:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-31 01:05:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:11] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2023-01-31 01:05:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-01-31 01:05:13] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-01-31 01:05:13] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2023-01-31 01:05:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-31 01:05:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:13] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2023-01-31 01:05:13] [SUCCESS] [OmnipathR] Downloaded 700257 annotation records.
Warning: ggrepel: 66 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘pw_bk.Rmd’

--- re-building ‘pw_sc.Rmd’ using rmarkdown
[2023-01-31 01:05:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-01-31 01:05:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-01-31 01:05:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:23] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-01-31 01:05:23] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-31 01:05:23] [SUCCESS] [OmnipathR] Loaded 700257 annotation records from cache.

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--- finished re-building ‘pw_sc.Rmd’

--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2023-01-31 01:05:29] [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`
[2023-01-31 01:05:29] [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`
[2023-01-31 01:05:29] [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`
[2023-01-31 01:05:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-31 01:05:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-31 01:05:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:30] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2023-01-31 01:05:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-01-31 01:05:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-01-31 01:05:30] [INFO]    [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2023-01-31 01:05:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-31 01:05:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-31 01:05:30] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
Quitting from lines 107-109 (tf_bk.Rmd) 
Error: processing vignette 'tf_bk.Rmd' failed with diagnostics:
ℹ In argument: `n_references = ifelse(...)`.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `.f()`:
! Arguments in `...` must be passed by position, not name.
✖ Problematic argument:
• outsep = outsep
--- failed re-building ‘tf_bk.Rmd’

--- re-building ‘tf_sc.Rmd’ using rmarkdown
[2023-01-31 01:05:31] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-01-31 01:05:31] [INFO]    [OmnipathR] Loaded from cache: `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`
Quitting from lines 84-86 (tf_sc.Rmd) 
Error: processing vignette 'tf_sc.Rmd' failed with diagnostics:
ℹ In argument: `n_references = ifelse(...)`.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `.f()`:
! Arguments in `...` must be passed by position, not name.
✖ Problematic argument:
• outsep = outsep
--- failed re-building ‘tf_sc.Rmd’

SUMMARY: processing the following files failed:
  ‘tf_bk.Rmd’ ‘tf_sc.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-01-31 01:05:32 CET ]