BioC 3.1: CHECK report for OmicsMarkeR on petty

Package: OmicsMarkeR

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.0.1.tar.gz

StartedAt: 2015-10-06 00:49:45 -0700 (Tue, 06 Oct 2015)

EndedAt: 2015-10-06 00:54:21 -0700 (Tue, 06 Oct 2015)

EllapsedTime: 276.6 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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmicsMarkeR/DESCRIPTION’ ... OK
* this is package ‘OmicsMarkeR’ version ‘1.0.1’
* 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 ... [13s/13s] 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 ... NOTE
perm.class: no visible binding for global variable ‘outIndex’
* 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 ... [135s/135s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.class          21.027  0.150  21.182
fs.stability        20.228  0.152  20.432
performance.metrics 19.961  0.163  20.168
feature.table       19.785  0.202  20.095
predictNewClasses   19.109  0.148  19.265
perm.features       19.106  0.142  19.256
fit.only.model       8.321  0.084   8.427
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [5s/5s]
 [6s/6s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/OmicsMarkeR.Rcheck/00check.log’
for details.

* installing *source* package ‘OmicsMarkeR’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (OmicsMarkeR)

name	user	system	elapsed
RPT	0.005	0.000	0.005
aggregation	0.005	0.000	0.006
canberra	0.002	0.000	0.002
create.corr.matrix	0.049	0.004	0.052
create.discr.matrix	0.042	0.005	0.046
create.random.matrix	0.043	0.002	0.045
denovo.grid	0.048	0.001	0.048
feature.table	19.785	0.202	20.095
fit.only.model	8.321	0.084	8.427
fs.ensembl.stability	0.002	0.001	0.002
fs.stability	20.228	0.152	20.432
jaccard	0.001	0.000	0.001
kuncheva	0.002	0.000	0.002
ochiai	0.002	0.001	0.002
pairwise.model.stability	0.011	0.000	0.012
pairwise.stability	0.002	0.000	0.002
params	0.005	0.000	0.005
performance.metrics	19.961	0.163	20.168
perm.class	21.027	0.150	21.182
perm.features	19.106	0.142	19.256
pof	0.001	0.000	0.001
predictNewClasses	19.109	0.148	19.265
sorensen	0.001	0.000	0.002
spearman	0.001	0.000	0.001
svmrfeFeatureRanking	0.167	0.001	0.184
svmrfeFeatureRankingForMulticlass	0.278	0.002	0.279