BioC 3.2: CHECK report for OmicsMarkeR on perceval

Package: OmicsMarkeR

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.1.2.tar.gz

StartedAt: 2015-08-24 03:29:28 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:34:46 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 317.9 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_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-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 ‘1.1.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmicsMarkeR’ can be installed ... [10s/10s] 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 ... [117s/117s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.class          18.653  0.157  18.811
perm.features       17.239  0.179  17.420
predictNewClasses   17.077  0.205  17.282
feature.table       16.965  0.228  17.305
performance.metrics 16.708  0.163  16.873
fs.stability        16.673  0.179  16.872
fit.only.model       7.625  0.098   7.851
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [90s/90s]
 [91s/91s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.003	0.000	0.004
aggregation	0.003	0.000	0.004
canberra	0.002	0.000	0.002
canberra_stability	0.002	0.000	0.001
create.corr.matrix	0.008	0.002	0.011
create.discr.matrix	0.008	0.003	0.011
create.random.matrix	0.014	0.003	0.016
denovo.grid	0.015	0.001	0.016
feature.table	16.965	0.228	17.305
fit.only.model	7.625	0.098	7.851
fs.ensembl.stability	0.001	0.001	0.001
fs.stability	16.673	0.179	16.872
jaccard	0.001	0.000	0.001
kuncheva	0.002	0.001	0.002
modelList	0.002	0.000	0.002
ochiai	0.001	0.000	0.002
pairwise.model.stability	0.009	0.000	0.009
pairwise.stability	0.005	0.000	0.005
params	0.003	0.000	0.003
performance.metrics	16.708	0.163	16.873
perm.class	18.653	0.157	18.811
perm.features	17.239	0.179	17.420
pof	0.002	0.000	0.002
predictNewClasses	17.077	0.205	17.282
sorensen	0.002	0.000	0.002
spearman	0.001	0.000	0.002
svmrfeFeatureRanking	0.080	0.001	0.081
svmrfeFeatureRankingForMulticlass	0.179	0.002	0.181