##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DuoClustering2018.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DuoClustering2018_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/DuoClustering2018.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘DuoClustering2018/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DuoClustering2018’ version ‘1.22.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DuoClustering2018’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* 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 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 whether startup messages can be suppressed ... 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
ari_df: no visible binding for global variable ‘cell’
plot_entropy: no visible binding for global variable ‘dataset’
plot_entropy: no visible binding for global variable ‘method’
plot_entropy: no visible binding for global variable ‘run’
plot_entropy: no visible binding for global variable ‘k’
plot_entropy: no visible binding for global variable ‘cluster’
plot_entropy: no visible binding for global variable ‘trueclass’
plot_entropy: no visible binding for global variable ‘s’
plot_entropy: no visible binding for global variable ‘s.true’
plot_entropy: no visible binding for global variable ‘est_k’
plot_entropy: no visible binding for global variable ‘sce’
plot_entropy: no visible binding for global variable ‘filtering’
plot_entropy: no visible binding for global variable ‘truenclust’
plot_entropy: no visible binding for global variable ‘entropy’
plot_entropy: no visible binding for global variable ‘ARI’
plot_entropy: no visible binding for global variable ‘s.norm’
plot_entropy: no visible binding for global variable ‘s.true.norm’
plot_entropy: no visible binding for global variable ‘ds’
plot_entropy: no visible binding for global variable ‘ds.norm’
plot_k_diff: no visible binding for global variable ‘dataset’
plot_k_diff: no visible binding for global variable ‘method’
plot_k_diff: no visible binding for global variable ‘run’
plot_k_diff: no visible binding for global variable ‘k’
plot_k_diff: no visible binding for global variable ‘cluster’
plot_k_diff: no visible binding for global variable ‘trueclass’
plot_k_diff: no visible binding for global variable ‘est_k’
plot_k_diff: no visible binding for global variable ‘elapsed’
plot_k_diff: no visible binding for global variable ‘sce’
plot_k_diff: no visible binding for global variable ‘filtering’
plot_k_diff: no visible binding for global variable ‘truenclust’
plot_k_diff: no visible binding for global variable ‘ARI’
plot_k_diff: no visible binding for global variable ‘medARI’
plot_k_diff: no visible binding for global variable ‘k_diff’
plot_k_diff: no visible binding for global variable ‘estnclust’
plot_performance: no visible binding for global variable ‘dataset’
plot_performance: no visible binding for global variable ‘method’
plot_performance: no visible binding for global variable ‘run’
plot_performance: no visible binding for global variable ‘k’
plot_performance: no visible binding for global variable ‘cluster’
plot_performance: no visible binding for global variable ‘trueclass’
plot_performance: no visible binding for global variable ‘est_k’
plot_performance: no visible binding for global variable ‘elapsed’
plot_performance: no visible binding for global variable ‘sce’
plot_performance: no visible binding for global variable ‘filtering’
plot_performance: no visible binding for global variable ‘ARI’
plot_performance: no visible binding for global variable ‘truenclust’
plot_performance: no visible binding for global variable ‘medianARI’
plot_performance: no visible binding for global variable ‘estnclust’
plot_stability: no visible binding for global variable ‘dataset’
plot_stability: no visible binding for global variable ‘method’
plot_stability: no visible binding for global variable ‘k’
plot_stability: no visible binding for global variable ‘data.wide’
plot_stability: no visible binding for global variable ‘stability’
plot_stability: no visible binding for global variable ‘truenclust’
plot_stability: no visible binding for global variable ‘sce’
plot_stability: no visible binding for global variable ‘filtering’
plot_stability: no visible binding for global variable ‘ari.stab’
plot_stability: no visible binding for global variable
  ‘median.stability’
plot_timing: no visible binding for global variable ‘dataset’
plot_timing: no visible binding for global variable ‘method’
plot_timing: no visible binding for global variable ‘run’
plot_timing: no visible binding for global variable ‘k’
plot_timing: no visible binding for global variable ‘cluster’
plot_timing: no visible binding for global variable ‘trueclass’
plot_timing: no visible binding for global variable ‘est_k’
plot_timing: no visible binding for global variable ‘elapsed’
plot_timing: no visible binding for global variable ‘sce’
plot_timing: no visible binding for global variable ‘filtering’
plot_timing: no visible binding for global variable ‘truenclust’
plot_timing: no visible binding for global variable ‘median.elapsed’
plot_timing: no visible binding for global variable ‘med.t’
plot_timing: no visible binding for global variable ‘norm.time’
plot_timing: no visible binding for global variable ‘medianelapsed’
Undefined global functions or variables:
  ARI ari.stab cell cluster data.wide dataset ds ds.norm elapsed
  entropy est_k estnclust filtering k k_diff med.t medARI
  median.elapsed median.stability medianARI medianelapsed method
  norm.time run s s.norm s.true s.true.norm sce stability trueclass
  truenclust
* 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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
sce_full_Koh 5.234  0.259   5.571
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/DuoClustering2018.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL DuoClustering2018
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘DuoClustering2018’ ...
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DuoClustering2018)