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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.8.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/decoupleR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.8.2’
* 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 hidden files and directories ... NOTE
Found the following hidden files and directories:
  .bumpversion.cfg
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... WARNING
Output(s) listed in 'build/vignette.rds' but not in package:
  ‘inst/doc/decoupleR.html’
  ‘inst/doc/pw_bk.html’
  ‘inst/doc/pw_sc.html’
  ‘inst/doc/tf_bk.html’
  ‘inst/doc/tf_sc.html’
* 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 dependencies in R code ... WARNING
[2024-03-03 20:05:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:05:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:01] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 20:05:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-03 20:05:01] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 20:05:01] [TRACE]   [OmnipathR] Contains 8 files.
[2024-03-03 20:05:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:02] [TRACE]   [OmnipathR] Cache locked: FALSE
'::' or ':::' import not declared from: ‘reshape2’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.ulm_analysis: no visible global function definition for ‘cor’
.ulm_analysis: no visible global function definition for ‘pt’
Undefined global functions or variables:
  cor pt
Consider adding
  importFrom("stats", "cor", "pt")
to your NAMESPACE file.
* 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘decoupleR.Rmd’ ‘pw_bk.Rmd’ ‘pw_sc.Rmd’ ‘tf_bk.Rmd’ ‘tf_sc.Rmd’
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
get_dorothea  406.026  5.784 423.823
get_collectri 102.901  1.806 111.815
run_fgsea      21.683  0.336  22.195
run_aucell      8.637  1.114   9.906
get_progeny     6.593  0.569  14.439
* 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. ├─dplyr::select(., pathway, genesymbol, weight, p_value)
    5. ├─dplyr::bind_rows(.)
    6. │ └─rlang::list2(...)
    7. ├─purrr::map(...)
    8. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
    9. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
   10. ├─dplyr::group_split(.)
   11. ├─dplyr::group_by(., pathway)
   12. ├─dplyr::select(., genesymbol, p_value, pathway, weight)
   13. ├─dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
   14. └─dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
  ‘decoupleR.Rmd’
  ‘pw_bk.Rmd’
  ‘pw_sc.Rmd’
  ‘tf_bk.Rmd’
  ‘tf_sc.Rmd’
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/decoupleR.Rcheck/00check.log’
for details.