Package: OmicsMarkeR

Version: 1.16.0

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_1.16.0.tar.gz

StartedAt: 2019-10-16 05:12:25 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:18:21 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 355.9 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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.16.0’
* 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
perm.class          18.867  1.260  20.136
feature.table       18.360  1.695  20.055
performance.metrics 17.037  1.342  18.412
perm.features       16.836  1.322  18.159
predictNewClasses   16.835  1.313  18.148
fs.stability        16.636  1.391  18.068
fit.only.model       6.103  0.900   7.009
* 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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 99.441   5.813 105.833 

name	user	system	elapsed
RPT	0.005	0.001	0.006
aggregation	0.009	0.002	0.010
canberra	0.002	0.000	0.003
canberra_stability	0.002	0.000	0.002
create.corr.matrix	0.012	0.004	0.017
create.discr.matrix	0.010	0.004	0.013
create.random.matrix	0.012	0.005	0.017
denovo.grid	0.022	0.007	0.029
feature.table	18.360	1.695	20.055
fit.only.model	6.103	0.900	7.009
fs.ensembl.stability	0.000	0.000	0.001
fs.stability	16.636	1.391	18.068
jaccard	0.002	0.000	0.001
kuncheva	0.002	0.000	0.003
modelList	0.003	0.000	0.003
ochiai	0.001	0.001	0.001
pairwise.model.stability	0.023	0.001	0.024
pairwise.stability	0.008	0.001	0.009
params	0.004	0.000	0.005
performance.metrics	17.037	1.342	18.412
perm.class	18.867	1.260	20.136
perm.features	16.836	1.322	18.159
pof	0.001	0.001	0.002
predictNewClasses	16.835	1.313	18.148
sorensen	0.001	0.001	0.002
spearman	0.002	0.000	0.001
svmrfeFeatureRanking	0.130	0.009	0.139
svmrfeFeatureRankingForMulticlass	0.180	0.002	0.181