BioC 3.4: CHECK report for OmicsMarkeR on malbec1

Package: OmicsMarkeR

Version: 1.8.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.8.1.tar.gz

StartedAt: 2017-04-15 00:14:18 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:17:33 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 194.5 seconds

RetCode: 0

Status:  OK

CheckDir: OmicsMarkeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.1’
* 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 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          11.064  0.004  11.078
perm.features       10.164  0.004  10.173
predictNewClasses   10.060  0.008  10.076
feature.table        9.984  0.032  10.034
fs.stability         9.648  0.004   9.662
performance.metrics  9.472  0.004   9.485
* 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	0.008	0.000	0.038
aggregation	0.004	0.000	0.004
canberra	0.004	0.000	0.004
canberra_stability	0.004	0.000	0.003
create.corr.matrix	0.012	0.000	0.011
create.discr.matrix	0.008	0.000	0.006
create.random.matrix	0.008	0.000	0.009
denovo.grid	0.008	0.000	0.011
feature.table	9.984	0.032	10.034
fit.only.model	3.816	0.000	3.822
fs.ensembl.stability	0.000	0.000	0.001
fs.stability	9.648	0.004	9.662
jaccard	0.000	0.000	0.001
kuncheva	0.000	0.000	0.001
modelList	0.000	0.000	0.001
ochiai	0.000	0.000	0.001
pairwise.model.stability	0.008	0.000	0.008
pairwise.stability	0.004	0.000	0.004
params	0.004	0.000	0.002
performance.metrics	9.472	0.004	9.485
perm.class	11.064	0.004	11.078
perm.features	10.164	0.004	10.173
pof	0.000	0.000	0.001
predictNewClasses	10.060	0.008	10.076
sorensen	0.000	0.000	0.001
spearman	0.000	0.000	0.001
svmrfeFeatureRanking	0.068	0.004	0.071
svmrfeFeatureRankingForMulticlass	0.14	0.00	0.14