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 02:36:41 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:41:13 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 272.3 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) (2018-11-27 r75683)
* 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       14.618  0.537  15.319
perm.class          14.648  0.450  15.208
perm.features       13.877  0.399  14.387
predictNewClasses   13.775  0.434  14.421
fs.stability        13.489  0.375  13.986
performance.metrics 13.051  0.408  13.550
fit.only.model       5.262  0.327   5.623
* 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’ ...
** 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
* DONE (OmicsMarkeR)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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 
 80.483   1.980  83.272 

name	user	system	elapsed
RPT	0.004	0.001	0.005
aggregation	0.006	0.001	0.008
canberra	0.002	0.001	0.002
canberra_stability	0.001	0.000	0.002
create.corr.matrix	0.006	0.002	0.007
create.discr.matrix	0.007	0.002	0.009
create.random.matrix	0.006	0.001	0.009
denovo.grid	0.014	0.003	0.016
feature.table	14.618	0.537	15.319
fit.only.model	5.262	0.327	5.623
fs.ensembl.stability	0.000	0.000	0.001
fs.stability	13.489	0.375	13.986
jaccard	0.001	0.001	0.001
kuncheva	0.002	0.000	0.002
modelList	0.002	0.000	0.001
ochiai	0.001	0.001	0.001
pairwise.model.stability	0.015	0.000	0.015
pairwise.stability	0.005	0.001	0.005
params	0.003	0.000	0.004
performance.metrics	13.051	0.408	13.550
perm.class	14.648	0.450	15.208
perm.features	13.877	0.399	14.387
pof	0.001	0.000	0.001
predictNewClasses	13.775	0.434	14.421
sorensen	0.001	0.000	0.001
spearman	0.001	0.000	0.001
svmrfeFeatureRanking	0.105	0.001	0.107
svmrfeFeatureRankingForMulticlass	0.175	0.002	0.193