BioC 3.5: CHECK report for OmicsMarkeR on malbec2

Package: OmicsMarkeR

Version: 1.8.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.8.0.tar.gz

StartedAt: 2017-08-16 01:04:04 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:07:21 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 197.6 seconds

RetCode: 0

Status:  OK

CheckDir: OmicsMarkeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 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       11.596  0.012  11.901
perm.class          10.328  0.000  10.336
fs.stability         9.036  0.000   9.063
perm.features        8.868  0.012   8.887
predictNewClasses    8.684  0.008   8.698
performance.metrics  8.636  0.008   8.652
* 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	0.024	0.004	0.036
aggregation	0.008	0.000	0.007
canberra	0.004	0.000	0.003
canberra_stability	0.004	0.000	0.002
create.corr.matrix	0.044	0.000	0.042
create.discr.matrix	0.124	0.000	0.130
create.random.matrix	0.004	0.000	0.004
denovo.grid	0.012	0.000	0.009
feature.table	11.596	0.012	11.901
fit.only.model	3.556	0.004	3.558
fs.ensembl.stability	0.004	0.000	0.000
fs.stability	9.036	0.000	9.063
jaccard	0.000	0.000	0.002
kuncheva	0.000	0.000	0.001
modelList	0.000	0.000	0.001
ochiai	0.000	0.000	0.001
pairwise.model.stability	0.020	0.000	0.021
pairwise.stability	0.008	0.000	0.005
params	0.000	0.000	0.002
performance.metrics	8.636	0.008	8.652
perm.class	10.328	0.000	10.336
perm.features	8.868	0.012	8.887
pof	0.004	0.000	0.001
predictNewClasses	8.684	0.008	8.698
sorensen	0.000	0.000	0.001
spearman	0.004	0.000	0.000
svmrfeFeatureRanking	0.288	0.000	0.290
svmrfeFeatureRankingForMulticlass	0.136	0.000	0.134