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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings decoupleR_2.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.5.0’
* 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
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Contains 6 files.
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 19:45:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 19:45:30] [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 ... WARNING
Found the following significant warnings:

  Warning: 'OmnipathR::import_dorothea_interactions' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
run_fgsea    21.321  0.226  21.547
get_dorothea 20.485  0.573  23.667
run_aucell    7.060  0.199   7.260
get_progeny   5.917  0.338  13.869
* 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:
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 1 | WARN 342 | SKIP 0 | PASS 34 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-utils-dataset-converters.R:84:5'): missing quos ──────────────
  `convert_to_foo()` did not throw the expected error.
  
  [ FAIL 1 | WARN 342 | SKIP 0 | PASS 34 ]
  Error: Test failures
  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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck/00check.log’
for details.