Multiple platform build/check report for BioC 3.8 - CHECK report for OmicsMarkeR on merida1

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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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.0’
* 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          16.032  0.356  16.515
predictNewClasses   14.751  0.435  15.478
perm.features       14.412  0.406  15.171
feature.table       13.513  0.492  14.136
performance.metrics 13.154  0.407  13.682
fs.stability        12.357  0.439  12.870
fit.only.model       4.886  0.303   5.221
* 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

Installation output

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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/3.5/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)

Tests output


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 
 81.969   1.727  84.713

Example timings

name	user	system	elapsed
RPT	0.004	0.000	0.005
aggregation	0.007	0.001	0.008
canberra	0.002	0.001	0.002
canberra_stability	0.002	0.000	0.002
create.corr.matrix	0.009	0.002	0.011
create.discr.matrix	0.008	0.002	0.011
create.random.matrix	0.007	0.002	0.009
denovo.grid	0.015	0.002	0.018
feature.table	13.513	0.492	14.136
fit.only.model	4.886	0.303	5.221
fs.ensembl.stability	0	0	0
fs.stability	12.357	0.439	12.870
jaccard	0.001	0.000	0.001
kuncheva	0.001	0.001	0.002
modelList	0.002	0.000	0.002
ochiai	0.001	0.000	0.001
pairwise.model.stability	0.014	0.001	0.015
pairwise.stability	0.008	0.000	0.008
params	0.003	0.000	0.003
performance.metrics	13.154	0.407	13.682
perm.class	16.032	0.356	16.515
perm.features	14.412	0.406	15.171
pof	0.001	0.000	0.001
predictNewClasses	14.751	0.435	15.478
sorensen	0.001	0.000	0.002
spearman	0.001	0.000	0.001
svmrfeFeatureRanking	0.081	0.001	0.082
svmrfeFeatureRankingForMulticlass	0.193	0.004	0.200

CHECK report for OmicsMarkeR on merida1

Summary

Command output

Installation output

Tests output

Example timings