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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vsclust.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vsclust_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/vsclust.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vsclust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vsclust’ version ‘1.4.0’
* 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 ‘vsclust’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
runFuncEnrich: no visible global function definition for
  ‘compareCluster’
runFuncEnrich: no visible global function definition for ‘new’
Undefined global functions or variables:
  compareCluster new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: vsclust-package.Rd:29-31: Dropping empty section \seealso
prepare_Rd: vsclust-package.Rd:32-33: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'estimClustNum':
estimClustNum
  Code: function(dat, maxClust = 25, scaling = "standardize", cores =
                 1)
  Docs: function(dat, maxClust = 25, cores = 1)
  Argument names in code not in docs:
    scaling
  Mismatches in argument names:
    Position: 3 Code: scaling Docs: cores

Codoc mismatches from documentation object 'runClustWrapper':
runClustWrapper
  Code: function(dat, NClust, proteins = NULL, VSClust = TRUE, scaling
                 = "standardize", cores, verbose = FALSE)
  Docs: function(dat, NClust, proteins = NULL, VSClust = TRUE, cores,
                 verbose = FALSE)
  Argument names in code not in docs:
    scaling
  Mismatches in argument names:
    Position: 5 Code: scaling Docs: cores
    Position: 6 Code: cores Docs: verbose

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
calcBHI         11.233  0.598  23.405
estimClust.plot  0.182  0.045  24.550
optimalClustNum  0.165  0.042  23.864
estimClustNum    0.107  0.035  21.361
runClustWrapper  0.078  0.017  18.860
ClustComp        0.021  0.014  17.384
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/vsclust.Rcheck/00check.log’
for details.