BioC 3.4: CHECK report for OmicsMarkeR on morelia

Package: OmicsMarkeR

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.8.1.tar.gz

StartedAt: 2017-04-15 05:49:16 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 05:53:29 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 252.9 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_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmicsMarkeR/DESCRIPTION’ ... OK
* this is package ‘OmicsMarkeR’ version ‘1.8.1’
* 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
perm.class          14.484  0.334  15.009
perm.features       14.184  0.256  15.396
predictNewClasses   13.870  0.272  14.539
performance.metrics 12.856  0.305  13.239
fs.stability        12.209  0.321  12.540
feature.table        9.785  0.304  10.113
* 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	0.004	0.001	0.075
aggregation	0.003	0.000	0.004
canberra	0.002	0.001	0.002
canberra_stability	0.002	0.000	0.002
create.corr.matrix	0.007	0.001	0.009
create.discr.matrix	0.006	0.001	0.008
create.random.matrix	0.012	0.001	0.014
denovo.grid	0.015	0.002	0.018
feature.table	9.785	0.304	10.113
fit.only.model	4.112	0.289	4.401
fs.ensembl.stability	0.001	0.000	0.001
fs.stability	12.209	0.321	12.540
jaccard	0.001	0.000	0.002
kuncheva	0.002	0.001	0.002
modelList	0.002	0.000	0.002
ochiai	0.002	0.000	0.001
pairwise.model.stability	0.014	0.000	0.013
pairwise.stability	0.010	0.001	0.012
params	0.004	0.000	0.004
performance.metrics	12.856	0.305	13.239
perm.class	14.484	0.334	15.009
perm.features	14.184	0.256	15.396
pof	0.002	0.000	0.002
predictNewClasses	13.870	0.272	14.539
sorensen	0.002	0.001	0.002
spearman	0.002	0.000	0.002
svmrfeFeatureRanking	0.105	0.001	0.106
svmrfeFeatureRankingForMulticlass	0.186	0.000	0.186