BioC 3.2: CHECK report for OmicsMarkeR on perceval

Package: OmicsMarkeR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.2.0.tar.gz

StartedAt: 2015-10-27 10:37:43 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 10:42:43 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 300.3 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_1.2.0.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 (2015-10-08 r69496)
* 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 ‘1.2.0’
* 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 ... 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 ... [9s/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 ... [107s/107s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.class          17.594  0.140  17.734
perm.features       15.823  0.170  15.993
feature.table       15.436  0.175  15.630
fs.stability        15.322  0.124  15.467
performance.metrics 15.223  0.134  15.368
predictNewClasses   15.189  0.115  15.306
fit.only.model       6.407  0.072   6.484
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [87s/87s]
 [87s/87s] 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	0.005	0.001	0.027
aggregation	0.004	0.000	0.004
canberra	0.003	0.000	0.003
canberra_stability	0.003	0.000	0.002
create.corr.matrix	0.010	0.003	0.012
create.discr.matrix	0.009	0.002	0.012
create.random.matrix	0.013	0.002	0.016
denovo.grid	0.016	0.001	0.017
feature.table	15.436	0.175	15.630
fit.only.model	6.407	0.072	6.484
fs.ensembl.stability	0.000	0.000	0.001
fs.stability	15.322	0.124	15.467
jaccard	0.001	0.000	0.002
kuncheva	0.002	0.000	0.003
modelList	0.003	0.000	0.003
ochiai	0.002	0.000	0.002
pairwise.model.stability	0.019	0.001	0.019
pairwise.stability	0.010	0.000	0.011
params	0.003	0.000	0.003
performance.metrics	15.223	0.134	15.368
perm.class	17.594	0.140	17.734
perm.features	15.823	0.170	15.993
pof	0.002	0.000	0.001
predictNewClasses	15.189	0.115	15.306
sorensen	0.002	0.000	0.002
spearman	0.002	0.000	0.002
svmrfeFeatureRanking	0.098	0.002	0.112
svmrfeFeatureRankingForMulticlass	0.201	0.002	0.203