Package: OmicsMarkeR

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.10.0.tar.gz

StartedAt: 2018-04-12 07:13:25 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:17:57 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 271.5 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 --no-vignettes --timings OmicsMarkeR_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 loading without being on the library search path ... 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       15.983  0.177  17.306
perm.class          13.142  0.284  13.658
fs.stability        12.316  0.310  12.886
performance.metrics 11.833  0.298  12.339
predictNewClasses   11.443  0.292  11.927
perm.features       10.915  0.246  11.383
fit.only.model       4.800  0.242   5.375
* 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

* installing *source* package ‘OmicsMarkeR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OmicsMarkeR)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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")
solo last variable══ testthat results  ═══════════════════════════════════════════════════════════
OK: 100 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 74.825   0.936  77.279 

name	user	system	elapsed
RPT	0.023	0.003	0.028
aggregation	0.006	0.001	0.007
canberra	0.003	0.000	0.003
canberra_stability	0.002	0.001	0.002
create.corr.matrix	0.036	0.006	0.041
create.discr.matrix	0.122	0.004	0.129
create.random.matrix	0.007	0.001	0.009
denovo.grid	0.014	0.002	0.017
feature.table	15.983	0.177	17.306
fit.only.model	4.800	0.242	5.375
fs.ensembl.stability	0.001	0.000	0.001
fs.stability	12.316	0.310	12.886
jaccard	0.002	0.000	0.002
kuncheva	0.002	0.000	0.003
modelList	0.002	0.000	0.002
ochiai	0.002	0.000	0.002
pairwise.model.stability	0.028	0.001	0.031
pairwise.stability	0.007	0.000	0.007
params	0.003	0.001	0.003
performance.metrics	11.833	0.298	12.339
perm.class	13.142	0.284	13.658
perm.features	10.915	0.246	11.383
pof	0.001	0.000	0.001
predictNewClasses	11.443	0.292	11.927
sorensen	0.002	0.000	0.002
spearman	0.002	0.000	0.002
svmrfeFeatureRanking	0.384	0.001	0.391
svmrfeFeatureRankingForMulticlass	0.164	0.000	0.166