##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CancerSubtypes.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CancerSubtypes_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CancerSubtypes.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CancerSubtypes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CancerSubtypes' version '1.21.0'
* 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 whether package 'CancerSubtypes' 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 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
displayClusters: no visible global function definition for 'grey'
Undefined global functions or variables:
  grey
Consider adding
  importFrom("grDevices", "grey")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
sigclustTest  23.73   0.33   24.07
ExecuteSNF.CC 12.09   0.37   12.78
survAnalysis   9.43   0.04    9.52
FSbyCox        9.03   0.02    9.05
ExecuteCC      6.42   1.44    7.87
drawHeatmap    4.97   0.14    5.11
ExecuteCNMF    2.19   0.36   14.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/CancerSubtypes.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CancerSubtypes
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CancerSubtypes' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CancerSubtypes'
    finding HTML links ... done
    DiffExp.limma                           html  
    ExecuteCC                               html  
    ExecuteCNMF                             html  
    finding level-2 HTML links ... done

    ExecuteSNF.CC                           html  
    ExecuteSNF                              html  
    ExecuteWSNF                             html  
    ExecuteiCluster                         html  
    FSbyCox                                 html  
    FSbyMAD                                 html  
    FSbyPCA                                 html  
    FSbyVar                                 html  
    GeneExp                                 html  
    Ranking                                 html  
    affinityMatrix                          html  
    data.checkDistribution                  html  
    data.imputation                         html  
    data.normalization                      html  
    dist2                                   html  
    drawHeatmap                             html  
    miRNAExp                                html  
    saveFigure                              html  
    sigclustTest                            html  
    silhouette_SimilarityMatrix             html  
    spectralAlg                             html  
    status                                  html  
    survAnalysis                            html  
    time                                    html  
** 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 (CancerSubtypes)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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.

> BiocGenerics:::testPackage("CancerSubtypes")
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 79/80


RUNIT TEST PROTOCOL -- Thu Mar 17 18:41:10 2022 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CancerSubtypes RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.50    0.18    2.65