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: 2017-10-18 06:54:35 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:59:11 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 275.9 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 --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 3.4.2 (2017-09-28)
* 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       15.592  0.230  16.477
perm.class          13.896  0.279  14.597
perm.features       12.198  0.193  12.747
predictNewClasses   11.943  0.146  12.414
performance.metrics 11.546  0.262  12.260
fs.stability        11.327  0.267  12.044
fit.only.model       4.814  0.190   5.203
* 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	0.021	0.001	0.030
aggregation	0.006	0.001	0.006
canberra	0.002	0.000	0.003
canberra_stability	0.002	0.000	0.003
create.corr.matrix	0.033	0.001	0.037
create.discr.matrix	0.378	0.003	0.392
create.random.matrix	0.007	0.001	0.008
denovo.grid	0.013	0.002	0.014
feature.table	15.592	0.230	16.477
fit.only.model	4.814	0.190	5.203
fs.ensembl.stability	0.000	0.001	0.000
fs.stability	11.327	0.267	12.044
jaccard	0.001	0.000	0.001
kuncheva	0.002	0.001	0.002
modelList	0.002	0.000	0.003
ochiai	0.002	0.000	0.002
pairwise.model.stability	0.029	0.000	0.029
pairwise.stability	0.006	0.001	0.007
params	0.003	0.000	0.003
performance.metrics	11.546	0.262	12.260
perm.class	13.896	0.279	14.597
perm.features	12.198	0.193	12.747
pof	0.001	0.000	0.002
predictNewClasses	11.943	0.146	12.414
sorensen	0.001	0.000	0.001
spearman	0.002	0.000	0.001
svmrfeFeatureRanking	0.436	0.005	0.446
svmrfeFeatureRankingForMulticlass	0.167	0.001	0.174