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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:vsclust.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings vsclust_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/vsclust.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘vsclust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vsclust’ version ‘1.8.0’
* 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++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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         5.172  0.431  14.537
estimClust.plot 0.134  0.040  12.078
optimalClustNum 0.105  0.023  12.334
runClustWrapper 0.041  0.043   7.885
estimClustNum   0.060  0.008  10.763
ClustComp       0.013  0.005   7.547
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/vsclust.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL vsclust
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘vsclust’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c vsclust_algo.cpp -o vsclust_algo.o
vsclust_algo.cpp: In function ‘double c_plusplus_means(const Rcpp::NumericMatrix&, Rcpp::NumericMatrix&, Rcpp::NumericVector&, Rcpp::NumericVector&, int, int, double, int, Rcpp::NumericMatrix&, double, Rcpp::IntegerVector&, double, double)’:
vsclust_algo.cpp:380:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  380 |       if(verbose)
      |       ^~
vsclust_algo.cpp:383:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  383 |         ermin = new_fitness;
      |         ^~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o vsclust.so RcppExports.o vsclust_algo.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-vsclust/00new/vsclust/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (vsclust)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(vsclust)
> 
> test_check("vsclust")
Running cluster number 3
Running cluster number 4
Running cluster number 5
Running cluster number 6
Running cluster number 7
Running cluster number 8
Running cluster number 9
Running cluster number 10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
Warning message:
In for (v in val) { : closing unused connection 5 (<-localhost:11933)
> 
> proc.time()
   user  system elapsed 
  8.342   0.611  42.376