BioC 3.3: CHECK report for OmicsMarkeR on oaxaca

Package: OmicsMarkeR

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.4.2.tar.gz

StartedAt: 2016-10-13 04:18:38 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:25:48 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 430.6 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_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmicsMarkeR/DESCRIPTION’ ... OK
* this is package ‘OmicsMarkeR’ version ‘1.4.2’
* 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 ... 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
CLA: no visible global function definition for ‘head’
EE: no visible global function definition for ‘head’
EM: no visible global function definition for ‘head’
ES: no visible global function definition for ‘head’
MeanSD: no visible binding for global variable ‘sd’
create.discr.matrix: no visible global function definition for ‘runif’
create.random.matrix: no visible global function definition for ‘rnorm’
create.random.matrix: no visible global function definition for ‘runif’
extract.features: no visible binding for global variable ‘head’
extract.features: no visible global function definition for ‘head’
extract.features: no visible global function definition for ‘coef’
extract.features : <anonymous>: no visible global function definition
  for ‘coef’
fit.only.model: no visible binding for global variable ‘sd’
fs.ensembl.stability: no visible binding for global variable ‘sd’
fs.ensembl.stability: no visible binding for global variable ‘setNames’
fs.stability: no visible binding for global variable ‘sd’
fs.stability: no visible binding for global variable ‘setNames’
modelTuner: no visible global function definition for ‘complete.cases’
modelTuner_loo: no visible global function definition for
  ‘complete.cases’
noise.matrix: no visible global function definition for ‘runif’
optimize.model: no visible global function definition for
  ‘flush.console’
pamTune: no visible global function definition for ‘complete.cases’
perm.class: no visible binding for global variable ‘outIndex’
perm.class: no visible global function definition for ‘plot’
perm.class: no visible global function definition for ‘density’
perm.class: no visible global function definition for ‘sd’
perm.class: no visible global function definition for ‘abline’
perm.class: no visible global function definition for ‘legend’
perm.features: no visible global function definition for ‘coef’
plus_minus: no visible global function definition for ‘rbinom’
predictNewClasses: no visible global function definition for ‘predict’
predicting: no visible global function definition for ‘predict’
tune.instructions: no visible global function definition for
  ‘aggregate’
verify: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  abline aggregate coef complete.cases density flush.console head
  legend outIndex plot predict rbinom rnorm runif sd setNames
Consider adding
  importFrom("graphics", "abline", "legend", "plot")
  importFrom("stats", "aggregate", "coef", "complete.cases", "density",
             "predict", "rbinom", "rnorm", "runif", "sd", "setNames")
  importFrom("utils", "flush.console", "head")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
feature.table       11.494  0.126  11.816
perm.class           9.876  0.370  10.245
fs.stability         8.689  0.135   8.823
perm.features        8.537  0.217   9.952
predictNewClasses    8.489  0.245   9.857
performance.metrics  8.281  0.238   8.975
fit.only.model       3.747  0.231   5.665
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/OmicsMarkeR.Rcheck/00check.log’
for details.

* 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	0.004	0.001	0.064
aggregation	0.004	0.000	0.004
canberra	0.007	0.000	0.007
canberra_stability	0.003	0.000	0.003
create.corr.matrix	0.010	0.002	0.012
create.discr.matrix	0.012	0.000	0.013
create.random.matrix	0.011	0.001	0.013
denovo.grid	0.010	0.001	0.010
feature.table	11.494	0.126	11.816
fit.only.model	3.747	0.231	5.665
fs.ensembl.stability	0.000	0.000	0.001
fs.stability	8.689	0.135	8.823
jaccard	0.001	0.000	0.001
kuncheva	0.003	0.001	0.002
modelList	0.003	0.000	0.003
ochiai	0.002	0.001	0.002
pairwise.model.stability	0.012	0.000	0.013
pairwise.stability	0.010	0.000	0.011
params	0.005	0.000	0.005
performance.metrics	8.281	0.238	8.975
perm.class	9.876	0.370	10.245
perm.features	8.537	0.217	9.952
pof	0.002	0.000	0.001
predictNewClasses	8.489	0.245	9.857
sorensen	0.002	0.000	0.001
spearman	0.002	0.004	0.006
svmrfeFeatureRanking	0.064	0.004	1.099
svmrfeFeatureRankingForMulticlass	0.116	0.001	0.117