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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_2.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    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 ‘2.9.1’
* 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
[2024-03-02 02:47:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 02:47:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 02:47:02] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 02:47:02] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-02 02:47:02] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 02:47:02] [TRACE]   [OmnipathR] Contains 8 files.
[2024-03-02 02:47:02] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-02 02:47:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 02:47:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 02:47:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 02:47:03] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-02 02:47:03] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-02 02:47:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 02:47:03] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-02 02:47:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 02:47:03] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-02 02:47:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 02:47:03] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-02 02:47:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 02:47:03] [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 ... ERROR
Running examples in ‘decoupleR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run_gsva
> ### Title: Gene Set Variation Analysis (GSVA)
> ### Aliases: run_gsva
> 
> ### ** Examples
> 
> inputs_dir <- system.file("testdata", "inputs", package = "decoupleR")
> 
> mat <- readRDS(file.path(inputs_dir, "mat.rds"))
> net <- readRDS(file.path(inputs_dir, "net.rds"))
> 
> run_gsva(mat, net, minsize=0, verbose = FALSE)
Error in as.vector(x, "character") : 
  cannot coerce type 'closure' to vector of type 'character'
Calls: run_gsva ... <Anonymous> -> .Defunct -> as.character -> as.character.default
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’