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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:vsclust.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings vsclust_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/vsclust.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vsclust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vsclust’ version ‘1.6.0’
* 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: ‘g++ (GCC) 10.3.1’
* 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 code 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 ... 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 Rd file 'estimClustNum.Rd':
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 Rd file 'runClustWrapper.Rd':
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         7.699  0.908  12.614
estimClust.plot 0.107  0.007  15.027
optimalClustNum 0.089  0.020  14.723
estimClustNum   0.066  0.004  13.821
runClustWrapper 0.042  0.010  10.299
ClustComp       0.016  0.004  10.101
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/vsclust.Rcheck/00check.log’
for details.