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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings decoupleR_2.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/decoupleR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.8.0’
* 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 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 ... OK
* 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
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Contains 8 files.
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘decoupleR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_dorothea
> ### Title: DoRothEA gene regulatory network.
> ### Aliases: get_dorothea
> 
> ### ** Examples
> 
> dorothea <- get_dorothea(organism='human', levels=c('A', 'B', 'C'))
[2023-11-02 09:54:15] [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`
[2023-11-02 09:54:15] [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`
[2023-11-02 09:54:15] [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`
[2023-11-02 09:54:15] [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`
[2023-11-02 09:54:15] [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`
[2023-11-02 09:54:15] [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`
[2023-11-02 09:54:15] [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`
[2023-11-02 09:54:25] [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`
[2023-11-02 09:54:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:54:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:54:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:54:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:54:25] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2023-11-02 09:54:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-11-02 09:54:28] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-11-02 09:54:28] [INFO]    [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2023-11-02 09:54:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:54:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:54:28] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2023-11-02 09:54:28] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 906959 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [2023-11-02 09:56:30] [TRACE]   [OmnipathR] Cache locked: FALSE
  [2023-11-02 09:56:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
  [2023-11-02 09:56:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
  [2023-11-02 09:56:32] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
  [2023-11-02 09:56:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
  [2023-11-02 09:56:32] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
  [2023-11-02 09:56:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
  [2023-11-02 09:56:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
  [2023-11-02 09:56:32] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
  [2023-11-02 09:56:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
  [2023-11-02 09:56:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
  [2023-11-02 09:56:32] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
  [2023-11-02 09:56:32] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
  [2023-11-02 09:56:32] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
  [2023-11-02 09:56:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/decoupleR.Rcheck/00check.log’
for details.