BioC 3.6: CHECK report for OmicsMarkeR on veracruz1

Package: OmicsMarkeR

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.9.0.tar.gz

StartedAt: 2017-08-16 06:23:34 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:27:46 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 251.2 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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.9.0’
* 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       14.151  0.238  14.751
perm.class          12.843  0.277  13.822
perm.features       12.429  0.209  14.674
predictNewClasses   11.626  0.265  12.841
performance.metrics 11.222  0.253  11.728
fs.stability        11.063  0.278  11.844
fit.only.model       4.911  0.157   5.788
* 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	0.191	0.001	0.206
aggregation	0.004	0.001	0.005
canberra	0.002	0.000	0.003
canberra_stability	0.003	0.000	0.002
create.corr.matrix	0.029	0.001	0.031
create.discr.matrix	0.118	0.013	0.138
create.random.matrix	0.004	0.000	0.005
denovo.grid	0.012	0.002	0.015
feature.table	14.151	0.238	14.751
fit.only.model	4.911	0.157	5.788
fs.ensembl.stability	0.000	0.001	0.001
fs.stability	11.063	0.278	11.844
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	0.032	0.000	0.033
pairwise.stability	0.007	0.001	0.008
params	0.003	0.000	0.003
performance.metrics	11.222	0.253	11.728
perm.class	12.843	0.277	13.822
perm.features	12.429	0.209	14.674
pof	0.001	0.000	0.002
predictNewClasses	11.626	0.265	12.841
sorensen	0.002	0.000	0.002
spearman	0.001	0.000	0.002
svmrfeFeatureRanking	0.412	0.001	0.667
svmrfeFeatureRankingForMulticlass	0.175	0.002	0.184