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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-mac-arm64/meat/decoupleR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* 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
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-17 11:14:55] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] Contains 8 files.
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-17 11:14:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-17 11:14:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-17 11:14:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-17 11:14:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-17 11:14:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-17 11:14:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-17 11:14:56] [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  340.136  2.037 344.120
get_collectri  84.795  0.859 166.339
run_fgsea      26.629  0.132  26.787
run_aucell     10.401  1.081  11.507
get_progeny     8.087  0.365   9.395
* 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:
  [97] 0.29           - 0.49             [97]          
   ... ...              ...              and 4 more ...
  
    `actual$p_value[104:113]`: 0.98 0.20 0.20 0.22 0.22 0.87 0.87 0.19 0.19 0.18
  `expected$p_value[104:113]`: 0.98 0.20 0.20 0.21 0.21 0.94 0.94 0.19 0.19 0.18
  
    `actual$p_value[118:127]`: 0.13 0.11 0.11 0.99 0.99 0.12 0.12 0.16 0.16 0.59
  `expected$p_value[118:127]`: 0.13 0.11 0.11 1.00 1.00 0.13 0.13 0.16 0.16 0.59
  
    `actual$p_value[132:139]`: 0.12 0.59 0.59 0.17 0.17 0.20 0.20 0.59
  `expected$p_value[132:139]`: 0.12 0.59 0.59 0.18 0.18 0.20 0.20 0.59
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 33 ]
  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-mac-arm64/meat/decoupleR.Rcheck/00check.log’
for details.