Package: OmicsMarkeR

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OmicsMarkeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OmicsMarkeR_1.15.0.tar.gz

StartedAt: 2019-04-09 04:03:50 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:09:36 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 345.9 seconds

RetCode: 0

Status:  OK

CheckDir: OmicsMarkeR.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:OmicsMarkeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OmicsMarkeR_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/OmicsMarkeR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmicsMarkeR/DESCRIPTION’ ... OK
* this is package ‘OmicsMarkeR’ version ‘1.15.0’
* 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 ‘OmicsMarkeR’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
feature.table       17.906  1.656  19.562
perm.class          17.618  1.458  19.078
performance.metrics 16.402  1.472  17.878
perm.features       16.492  1.369  17.862
predictNewClasses   16.441  1.356  17.809
fs.stability        16.083  1.494  17.577
fit.only.model       5.942  0.939   6.882
* 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 OmicsMarkeR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘OmicsMarkeR’ ...
** 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 (OmicsMarkeR)

R Under development (unstable) (2019-03-18 r76245) -- "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(OmicsMarkeR)
> 
> test_check("OmicsMarkeR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 100 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 93.979   5.815 100.131 

name	user	system	elapsed
RPT	0.005	0.003	0.010
aggregation	0.010	0.001	0.011
canberra	0.002	0.000	0.003
canberra_stability	0.001	0.000	0.002
create.corr.matrix	0.011	0.001	0.012
create.discr.matrix	0.008	0.001	0.010
create.random.matrix	0.011	0.004	0.015
denovo.grid	0.021	0.007	0.027
feature.table	17.906	1.656	19.562
fit.only.model	5.942	0.939	6.882
fs.ensembl.stability	0.001	0.001	0.001
fs.stability	16.083	1.494	17.577
jaccard	0.001	0.000	0.001
kuncheva	0.002	0.001	0.002
modelList	0.003	0.000	0.003
ochiai	0.001	0.000	0.001
pairwise.model.stability	0.021	0.001	0.021
pairwise.stability	0.008	0.000	0.009
params	0.005	0.000	0.005
performance.metrics	16.402	1.472	17.878
perm.class	17.618	1.458	19.078
perm.features	16.492	1.369	17.862
pof	0.001	0.000	0.001
predictNewClasses	16.441	1.356	17.809
sorensen	0.002	0.000	0.002
spearman	0.002	0.000	0.002
svmrfeFeatureRanking	0.128	0.002	0.130
svmrfeFeatureRankingForMulticlass	0.213	0.002	0.216