[ Started: 2022-11-09 01:05:25 CET ]
[ decoupleR v2.3.2 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

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘decoupleR.Rmd’

--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2022-11-09 01:05:41] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2022-11-09 01:05:41] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-11-09 01:05:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-11-09 01:05:41] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2022-11-09 01:05:41] [TRACE]   [OmnipathR] Contains 1 files.
[2022-11-09 01:05:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2022-11-09 01:05:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2022-11-09 01:05:41] [TRACE]   [OmnipathR] Pandoc version: `2.5`.
[2022-11-09 01:05:41] [TRACE]   [OmnipathR] Cache locked: FALSE
Quitting from lines 101-103 (pw_bk.Rmd) 
Error: processing vignette 'pw_bk.Rmd' failed with diagnostics:
cannot open the connection to 'https://omnipathdb.org/resources'
--- failed re-building ‘pw_bk.Rmd’

--- re-building ‘pw_sc.Rmd’ using rmarkdown
Attaching SeuratObject
Quitting from lines 78-80 (pw_sc.Rmd) 
Error: processing vignette 'pw_sc.Rmd' failed with diagnostics:
cannot open the connection to 'https://omnipathdb.org/resources'
--- failed re-building ‘pw_sc.Rmd’

--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2022-11-09 01:05:44] [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`
[2022-11-09 01:05:44] [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`
[2022-11-09 01:05:44] [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`
[2022-11-09 01:05:44] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2022-11-09 01:05:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2022-11-09 01:05:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2022-11-09 01:05:45] [INFO]    [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2022-11-09 01:05:45] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2022-11-09 01:05:53] [SUCCESS] [OmnipathR] Downloaded 278482 interactions.
Warning: ggrepel: 19 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 19 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘tf_bk.Rmd’

--- re-building ‘tf_sc.Rmd’ using rmarkdown
[2022-11-09 01:06:05] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2022-11-09 01:06:05] [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`
[2022-11-09 01:06:13] [SUCCESS] [OmnipathR] Loaded 278482 interactions from cache.
Centering and scaling data matrix

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Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
`summarise()` has grouped output by 'cluster'. You can override using the `.groups` argument.
--- finished re-building ‘tf_sc.Rmd’

SUMMARY: processing the following files failed:
  ‘pw_bk.Rmd’ ‘pw_sc.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2022-11-09 01:06:39 CET ]