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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EnMCB.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings EnMCB_1.7.3.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/EnMCB.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 'EnMCB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EnMCB' version '1.7.3'
* 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 whether package 'EnMCB' 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
DiffMCB: no visible binding for global variable 'AdjustedPvalues'
Undefined global functions or variables:
  AdjustedPvalues
* checking Rd files ... OK
* 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 'DiffMCB':
DiffMCB
  Code: function(methylation_matrix, class_vector, mcb_matrix = NULL,
                 min.cpgsize = 5, pVals_num = 0.05, base_method =
                 c("Fstat", "Tstat", "eBayes")[1], sec_method =
                 c("ttest", "kstest")[1], ...)
  Docs: function(methylation_matrix, class_vector, mcb_matrix = NULL,
                 min.cpgsize = 5, base_method = c("Fstat", "Tstat",
                 "eBayes")[1], sec_method = c("ttest", "kstest")[1],
                 ...)
  Argument names in code not in docs:
    pVals_num
  Mismatches in argument names:
    Position: 5 Code: pVals_num Docs: base_method
    Position: 6 Code: base_method Docs: sec_method
    Position: 7 Code: sec_method Docs: ...

* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
metricMCB.cv            11.78   2.09   13.88
IdentifyMCB             11.74   0.73   12.47
pre_process_methylation  4.94   2.10    7.03
fast_roc_calculation     4.42   1.99    6.40
ensemble_model           4.93   0.61    5.53
* 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, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/EnMCB.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL EnMCB
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'EnMCB' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'EnMCB'
    finding HTML links ... done
    CompareMCB                              html  
    DiffMCB                                 html  
    IdentifyMCB                             html  
    as.data.frame.ridgemat                  html  
    as.ridgemat                             html  
    create_demo                             html  
    demo_MCBinformation                     html  
    demo_data                               html  
    demo_survival_data                      html  
    draw_survival_curve                     html  
    ensemble_model                          html  
    ensemble_prediction                     html  
    fast_roc_calculation                    html  
    metricMCB                               html  
    metricMCB.cv                            html  
    multi_coxph                             html  
    pre_process_methylation                 html  
    predict.mcb.coxph.penal                 html  
    univ_coxph                              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 (EnMCB)
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.

> library(testthat)
> library(EnMCB)
> 
> test_check("EnMCB")
Start calculating the correlation, this may take a while...
(or you can try to use IdentifyMCB_parallel function instead)

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Now gathering the results, please wait ...
Statistics ( 4  MCBs in total):
chr2 : total MCBs: 1  Mean Length: 167  (Range:  167 167 )
chr6 : total MCBs: 1  Mean Length: 129  (Range:  129 129 )
chr8 : total MCBs: 2  Mean Length: 303.5  (Range:  181 426 )
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  16.87    0.95   17.81