[ Started: 2023-01-09 01:05:50 CET ]
[ decoupleR v2.3.2 for BioC-3.16 from https://github.com/saezlab/decoupleR@master ]

* using log directory ‘/home/omnipath/testing/bioc/decoupler/bioc-3.16/2023-01-09_0103/decoupleR/decoupleR.Rcheck’
* using R version 4.2.2 Patched (2022-11-10 r83330)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.3.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       5.6Mb
    extdata   1.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2023-01-09 01:06:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:06:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:11] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:06:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-01-09 01:06:11] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:06:11] [TRACE]   [OmnipathR] Contains 3 files.
[2023-01-09 01:06:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-01-09 01:06:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:06:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:06:12] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-01-09 01:06:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-01-09 01:06:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-01-09 01:06:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-01-09 01:06:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-01-09 01:06:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:12] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘decoupleR-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_dorothea
> ### Title: DoRothEA gene regulatory network.
> ### Aliases: get_dorothea
> 
> ### ** Examples
> 
> dorothea <- get_dorothea(organism='human', levels=c('A', 'B', 'C'))
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:30] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Contains 1 files.
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:06:30] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-01-09 01:06:30] [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`
[2023-01-09 01:06:30] [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`
[2023-01-09 01:06:30] [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`
[2023-01-09 01:06:30] [WARN]    [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
[2023-01-09 01:06:35] [TRACE]   [OmnipathR] Attempt 2/3: `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`
[2023-01-09 01:06:36] [WARN]    [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-01-09 01:06:41] [TRACE]   [OmnipathR] Attempt 3/3: `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`
[2023-01-09 01:06:41] [ERROR]   [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.
Error in open.connection(5L, "rb") : HTTP error 500.
Calls: get_dorothea ... import_omnipath -> do.call -> <Anonymous> -> download_base
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    4. │   └─OmnipathR:::import_omnipath(...)
    5. │     ├─base::do.call(omnipath_download, download_args)
    6. │     └─OmnipathR (local) `<fn>`(...)
    7. │       └─OmnipathR:::download_base(url, fun, ...)
    8. ├─dplyr::select(...)
    9. ├─dplyr::mutate(...)
   10. ├─dplyr::mutate(...)
   11. ├─dplyr::mutate(...)
   12. ├─dplyr::distinct(...)
   13. └─dplyr::select(...)
  
  [ FAIL 4 | WARN 323 | SKIP 0 | PASS 31 ]
  Error: Test failures
  In addition: There were 11 warnings (use warnings() to see them)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘decoupleR.Rmd’ using ‘UTF-8’... OK
  ‘pw_bk.Rmd’ using ‘UTF-8’... OK
  ‘pw_sc.Rmd’ using ‘UTF-8’... OK
  ‘tf_bk.Rmd’ using ‘UTF-8’... OK
  ‘tf_sc.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘decoupleR.Rmd’ using rmarkdown
--- finished re-building ‘decoupleR.Rmd’

--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:08:24] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Contains 2 files.
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:08:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:08:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-09 01:08:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-09 01:08:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-09 01:08:25] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-01-09 01:08:30] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-09 01:08:30] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-01-09 01:08:35] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-09 01:08:35] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 3/3); error: HTTP error 500.
Quitting from lines 101-103 (pw_bk.Rmd) 
Error: processing vignette 'pw_bk.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘pw_bk.Rmd’

--- re-building ‘pw_sc.Rmd’ using rmarkdown
Warning in for (i in c("width", "height")) { :
  closing unused connection 5 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic)
Warning in for (i in c("width", "height")) { :
  closing unused connection 4 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic)
[2023-01-09 01:08:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-01-09 01:08:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:08:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-01-09 01:08:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-01-09 01:08:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-09 01:08:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-09 01:08:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-09 01:08:38] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-01-09 01:08:43] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-09 01:08:43] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-01-09 01:08:48] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-01-09 01:08:48] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 3/3); error: HTTP error 500.
Quitting from lines 78-80 (pw_sc.Rmd) 
Error: processing vignette 'pw_sc.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘pw_sc.Rmd’

--- re-building ‘tf_bk.Rmd’ using rmarkdown
Warning in defer(env_bind0(.env, old), envir = .frame) :
  closing unused connection 5 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic)
Warning in defer(env_bind0(.env, old), envir = .frame) :
  closing unused connection 4 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic)
[2023-01-09 01:08:48] [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`
[2023-01-09 01:08:48] [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`
[2023-01-09 01:08:48] [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`
[2023-01-09 01:08:48] [WARN]    [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
[2023-01-09 01:08:53] [TRACE]   [OmnipathR] Attempt 2/3: `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`
[2023-01-09 01:08:53] [WARN]    [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-01-09 01:08:58] [TRACE]   [OmnipathR] Attempt 3/3: `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`
[2023-01-09 01:08:59] [ERROR]   [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.
Quitting from lines 107-109 (tf_bk.Rmd) 
Error: processing vignette 'tf_bk.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘tf_bk.Rmd’

--- re-building ‘tf_sc.Rmd’ using rmarkdown
Warning in .Internal(exists(x, envir, mode, inherits)) :
  closing unused connection 5 (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)
Warning in .Internal(exists(x, envir, mode, inherits)) :
  closing unused connection 4 (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)
[2023-01-09 01:08:59] [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`
[2023-01-09 01:08:59] [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`
[2023-01-09 01:08:59] [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`
[2023-01-09 01:08:59] [WARN]    [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
Warning in .Internal(getRegisteredNamespace(name)) :
  closing unused connection 8 (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)
[2023-01-09 01:09:04] [TRACE]   [OmnipathR] Attempt 2/3: `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`
[2023-01-09 01:09:04] [WARN]    [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-01-09 01:09:09] [TRACE]   [OmnipathR] Attempt 3/3: `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`
[2023-01-09 01:09:10] [ERROR]   [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.
Quitting from lines 84-86 (tf_sc.Rmd) 
Error: processing vignette 'tf_sc.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘tf_sc.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 2 NOTEs
See
  ‘/home/omnipath/testing/bioc/decoupler/bioc-3.16/2023-01-09_0103/decoupleR/decoupleR.Rcheck/00check.log’
for details.

[ Finished: 2023-01-09 01:09:12 CET ]