Package: EnMCB

Version: 0.99.15

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EnMCB_0.99.15.tar.gz

StartedAt: 2020-01-16 04:06:53 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:17:56 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 662.4 seconds

RetCode: 0

Status:  OK

CheckDir: EnMCB.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EnMCB_0.99.15.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/EnMCB.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnMCB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnMCB’ version ‘0.99.15’
* 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 ‘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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
IdentifyMCB             28.994  1.793  30.817
pre_process_methylation 21.667  5.072  26.741
fast_roc_calculation    22.650  3.825  26.478
metricMCB               20.675  3.908  24.625
ensemble_model          16.099  2.142  18.244
ensemble_prediction     15.978  2.108  18.088
draw_survival_curve      4.668  0.827   5.757
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EnMCB
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘EnMCB’ ...
** using staged installation
** R
** data
** 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 (EnMCB)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> 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 )
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 50.663   3.608  54.222 

name	user	system	elapsed
IdentifyMCB	28.994	1.793	30.817
create_demo	0.556	0.043	0.598
draw_survival_curve	4.668	0.827	5.757
ensemble_model	16.099	2.142	18.244
ensemble_prediction	15.978	2.108	18.088
fast_roc_calculation	22.650	3.825	26.478
metricMCB	20.675	3.908	24.625
pre_process_methylation	21.667	5.072	26.741
univ_coxph	0.290	0.019	0.308