BioC 3.5: CHECK report for OmicsMarkeR on veracruz2

Package: OmicsMarkeR

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.8.0.tar.gz

StartedAt: 2017-08-16 06:06:36 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:10:50 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 254.5 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.8.0’
* 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       14.590  0.282  15.818
perm.class          13.025  0.275  13.730
fs.stability        12.358  0.285  13.772
perm.features       11.968  0.373  12.742
predictNewClasses   11.708  0.332  12.558
performance.metrics 11.318  0.284  12.526
fit.only.model       4.841  0.155   6.168
* 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)

name	user	system	elapsed
RPT	0.189	0.001	0.198
aggregation	0.006	0.001	0.006
canberra	0.001	0.000	0.002
canberra_stability	0.002	0.001	0.003
create.corr.matrix	0.033	0.001	0.042
create.discr.matrix	0.119	0.014	0.135
create.random.matrix	0.007	0.001	0.008
denovo.grid	0.012	0.002	0.014
feature.table	14.590	0.282	15.818
fit.only.model	4.841	0.155	6.168
fs.ensembl.stability	0.001	0.000	0.001
fs.stability	12.358	0.285	13.772
jaccard	0.001	0.000	0.002
kuncheva	0.002	0.000	0.002
modelList	0.002	0.001	0.002
ochiai	0.001	0.000	0.002
pairwise.model.stability	0.033	0.000	0.035
pairwise.stability	0.007	0.001	0.007
params	0.003	0.000	0.003
performance.metrics	11.318	0.284	12.526
perm.class	13.025	0.275	13.730
perm.features	11.968	0.373	12.742
pof	0.002	0.000	0.001
predictNewClasses	11.708	0.332	12.558
sorensen	0.001	0.000	0.001
spearman	0.001	0.000	0.001
svmrfeFeatureRanking	0.415	0.001	0.423
svmrfeFeatureRankingForMulticlass	0.168	0.001	0.171