Package: OmicsMarkeR

Version: 1.19.0

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_1.19.0.tar.gz

StartedAt: 2020-01-16 07:05:30 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:11:23 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 352.3 seconds

RetCode: 0

Status:  OK

CheckDir: OmicsMarkeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/OmicsMarkeR.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 ‘OmicsMarkeR/DESCRIPTION’ ... OK
* this is package ‘OmicsMarkeR’ version ‘1.19.0’
* 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 (user + system) or elapsed time > 5s
                      user system elapsed
perm.class          18.316  1.382  19.699
perm.features       16.426  1.343  17.772
feature.table       16.045  1.589  17.640
predictNewClasses   15.468  1.568  17.037
performance.metrics 15.293  1.436  16.730
fs.stability        15.191  1.485  16.677
fit.only.model       6.001  1.074   7.076
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OmicsMarkeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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) (2019-12-14 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(OmicsMarkeR)
> 
> test_check("OmicsMarkeR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 100 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 96.966   5.813 103.067 

name	user	system	elapsed
RPT	0.005	0.001	0.008
aggregation	0.007	0.002	0.008
canberra	0.003	0.001	0.003
canberra_stability	0.002	0.001	0.002
create.corr.matrix	0.011	0.003	0.014
create.discr.matrix	0.010	0.003	0.013
create.random.matrix	0.010	0.004	0.014
denovo.grid	0.020	0.005	0.025
feature.table	16.045	1.589	17.640
fit.only.model	6.001	1.074	7.076
fs.ensembl.stability	0.000	0.000	0.001
fs.stability	15.191	1.485	16.677
jaccard	0.001	0.000	0.001
kuncheva	0.003	0.000	0.003
modelList	0.003	0.000	0.004
ochiai	0.001	0.000	0.002
pairwise.model.stability	0.022	0.000	0.023
pairwise.stability	0.011	0.001	0.011
params	0.005	0.001	0.005
performance.metrics	15.293	1.436	16.730
perm.class	18.316	1.382	19.699
perm.features	16.426	1.343	17.772
pof	0.001	0.000	0.002
predictNewClasses	15.468	1.568	17.037
sorensen	0.002	0.000	0.002
spearman	0.001	0.001	0.002
svmrfeFeatureRanking	0.132	0.002	0.133
svmrfeFeatureRankingForMulticlass	0.187	0.004	0.191